492 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY

For many years, the post-transcriptional regulation (PTR) of immuno-

logical mRNAs was studied in isolated, transcript-restricted settings
and thus it was assumed to be a process lacking the coordinative
ability of immunological transcription. The identification of non-
coding RNAs such as microRNAs (miRNAs) and long noncoding
RNAs as specific entities able to concurrently regulate several mRNAs
proved to some extent that such viewpoints were unwarranted.
We propose here that immunologists should additionally consider
three fundamental features of PTR that are often neglected. First,
most PTR events involve the interaction of RNA with RNA-binding
proteins (RBPs) that are abundant in mammalian cells
1
. Second,
RBPs bear many structural modules (beyond their RNA-recognition
domains) that facilitate protein-protein interactions and catalytic
events; thus, they are integrated into many intracellular events
2
. Third,
RBPs, mRNAs and, in specific cases, noncoding RNAs assemble in
ribonucleoprotein (RNP) complexes, the actual functional units of
PTR. The composition of such complexes is in constant flux, with
some RBPs gaining or losing access during the subcellular journey of
an RNA and others remaining bound to their RNA target through-
out its life
3
. The potential importance of changes in RNP complexes
emerged through data obtained with technological platforms used
to assess RBP-RNA interactions at the nucleotide level
4
. Analysis
of such data suggests that the composition of RNP complexes can
depend on the ability of constituent RBPs to read regulatory RNA
sequences or structures (generally called elements; Box 1) present
in the untranslated termini or body of each RNA. The concomitant
presence of such elements in mRNAs that encode functionally
related factors seems to allow their coordinated regulation and use
5
.
Moreover, the ever-expanding list of mutant mouse lines with modifi-
cations in RBP-encoding genes (Table 1) demonstrates the importance
of RBPs in immunological homeostasis and connects the functions
of RBPs to signal-induced immunological expression programs. Such
connections suggest that PTR has not evolved solely as a proofing
extension of immunological transcription but instead has evolved as
an additional determinant of immunological reactions able to alter
the original transcriptomic definition of types of cells of the immune
system. Here we discuss key examples of post-transcriptional events
in such cells and highlight the importance of changes in RNP com-
plexes during immunological physiology and pathology.
Mechanics of PTR
Genomic studies have provided evidence of the execution of nuclear
and cytoplasmic PTR events in cells of the immune system that alter
the maturation, destruction and protein synthesis of mRNA
611
. Such
events are executed by core post-transcriptional machinery that can
be engaged differently by regulatory RNP complexes. The sum of
PTR events that occur in cells of the immune system is very broad;
here we focus on four core post-transcriptional processes to exem-
plify the regulatory functions of RBPs: splicing, editing, decay and
translation (Fig. 1a).
The first such process involves the excision of intronic sequences
from pre-mRNA; in eukaryotes this can occur concurrently with
transcription
6,9
and after the addition of a 5 7-methylguanosine cap
that renders mRNA competent for cap-dependent translation. In its
canonical form, splicing requires recognition of intronic boundaries
on the pre-mRNA by the spliceosome, a macromolecular RNP nucle-
ated by small nuclear RNP complexes of the U class. The assembly
of such complexes on individual introns results in their removal and
exon joining. In eukaryotes, protein production and function is diver-
sified further via alternative splicing; i.e., the selective inclusion or
Division of Immunology, Biomedical Sciences Research Center Alexander
Fleming, Vari, Greece. Correspondence should be addressed to D.L.K.
(kontoyiannis@fleming.gr).
Received 18 February; accepted 1 April; published online 19 May 2014;
doi:10.1038/ni.2884
Post-transcriptional coordination of
immunological responses by RNA-binding
proteins
Panagiota Kafasla, Antonis Skliris & Dimitris L Kontoyiannis
Immunological reactions are propelled by ever-changing signals that alter the translational ability of the RNA in the cells involved.
Such alterations are considered to be consequential modifications in the transcriptomic decoding of the genetic blueprint.
The identification of RNA-binding protein (RBP) assemblies engaged in the coordinative regulation of state-specific RNAs
indicates alternative and exclusive means for determining the activation, plasticity and tolerance of cells of the immune system.
Here we review current knowledge about RBP-regulated post-transcriptional events involved in the reactivity of cells of the
immune system and the importance of their alteration during chronic inflammatory pathology and autoimmunity.
POST- TRANSCRI PTI ONAL AND POST- TRANSLATI ONAL CONTROL OF I MMUNI TY REVI EW
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NATURE IMMUNOLOGY VOLUME 15 NUMBER 6 JUNE 2014 493
exclusion of introns, exons and regulatory regions in the final mRNA
product
12
. This can occur in response to peripheral signals and is
usually orchestrated by auxiliary and regulatory RBPs. Examples
include the many heterogeneous nuclear RNPs (hnRNPs; hnRNPA
hnRNPU), which usually bind splicing silencers (Box 1), and the
serine-argininerich (SR) RBPs, which usually recognize splicing-
enhancer motifs
12,13
(Fig. 1c).
A second nuclear process that can diversify immunological mRNAs
is RNA editing; this acts to enforce nucleotide conversions that alter
protein coding or affect RNA structure. In mammals, the most com-
mon form of editing is the deamination of adenine to produce inosine;
this is facilitated by members of the ADAR (adenosine deaminases
acting on RNA) family of double-stranded RNA (dsRNA)-binding
enzymes
10
(Fig. 1b).
As eukaryotic mRNA matures and becomes stable with the addition
of the poly(A) tail, nuclear RBPs with access to additional RNA ele-
ments remain bound for further use
5,12
. Those multifunctional RBPs
have individual functions but also act as scaffolds (Fig. 1a) and nucle-
ate the assembly of novel regulatory RNP entities; thus, they allow
interactions with cytoskeletal and signal-transduction machinery to
control the export of mRNA from the nucleus and prime mRNA for
subsequent use in the cytoplasm. Prominent examples include vari-
ous hnRNPs
14
as well as the so-called ARE-BPs (AU-rich element
(ARE)-binding proteins) that recognize AREs (Box 1) located in the
3 untranslated regions (UTRs) of many immunological mRNAs.
In the cytoplasm, regulatory RNPs can be remodeled further with the
inclusion of RBPs that define the balance between two major PTR
events: decay of mRNA and translation of mRNA.
Three pathways of mRNA decay
15
seem to predominate in cells
of the immune system (Fig. 1a,d). The first, exonucleolytic decay,
occurs through the progressive removal of the poly(A) tail (dead-
enylation) from exonuclease complexes such as PARN or the large
CCR4-NOT complex (Fig. 1a). Subsequently, mRNA bodies can
either be degraded from the 3 end by the large exonucleolytic exo-
some complex or lose their 5 cap through the action of decapping
enzymes such as Dcp1 and Dcp2 and then become degraded by the
5-to-3 exonuclease Xrn1 (Fig. 1a). Regulatory RNPs bound to ele-
ments in untranslated termini (such as AREs or constitutive decay
elements (CDEs); Box 1) and miRNA-loaded RNA-induced silencing
complexes (RISCs)
16
containing the translation-initiation factor Ago1
can recruit deadenylation and exonucleolytic machinery for induc-
ible degradation. In the second mechanism, endonucleolytic cleav-
age, site-specific RNases induce internal cleavages that yield RNA
fragments that are then susceptible to exonucleolytic degradation. In
cells of the immune system, this form of degradation is engaged either
by inducible endonucleases or by RISCs containing the slicer Ago2.
The third mechanism, nonsense-mediated decay, is a surveillance
mechanism that eliminates aberrant mRNAs with premature termina-
tion codons and thus prohibits the generation of abnormal proteins.
During the first round of translation, premature termination codons
are detected by a protein complex that contains upstream frameshift
proteins, which orchestrate the stalling of subsequent rounds of trans-
lation and recruit degradation machinery
15
.
The translation of immunological mRNAs is controlled via restric-
tions in the assembly of the 80S ribosome on mRNA from its constitu-
ent 40S and 60S subunits (initiation) (Fig. 1e) or the construction of
the protein sequence from the RNA template (elongation). The former
seems to involve several regulatory RNP configurations, whereas the
latter is directly affected by signal transducers
17
. Initiation control
occurs mainly during the interaction of eIF4F (a complex consisting
of the RNA helicase eIF4A, the cap-binding protein eIF4E and the
scaffold eIF4G) with the 5 cap of mRNA. That interaction is inhibited
by the eIF4E-binding proteins 4E-BP1 and 4E-BP2, which are in turn
deactivated by the metabolic checkpoint kinase complex mTORC1
(ref. 18). Deprivation of nutrients, infection and inflammation can block
the translation regulator mTOR by activating its negative regulators (TSC
proteins) and can thus inhibit protein synthesis. Alternatively, inflam-
matory signals may block the recruitment of eIF2GTPmethionyl
initiator tRNA ternary complex onto the 40S ribosomal subunit.
This stalls the formation of the 43S complex and its interactions with
Box 1 The nature and recognition of regulatory RNA elements
A wide collection of regulatory RNA cis elements can be specically recognized by trans-acting factors, such as RBPs or
noncoding RNA. They are believed to operate as primary structures (sequences), secondary conformations (for example, stem
loops and internal bulges) and/or tertiary multidomain architectures. Rigid structures such as internal ribosome entry sites
can be recognized tightly by factors that bring with them essential components such as ribosomal subunits. Alternatively,
structures may exist in less-rigid conformations, in close or distal proximity with each other within the RNA body. Paradigms
of elements targeted by RBPs include the following: elements on the pre-mRNA that, upon recognition by relevant RBPs
enhance or silence the denition of introns and exons by the spliceosome (and thus act as either exonic splicing enhancers
or exonic splicing silencers that reside in an exon and regulate its inclusion or skipping, respectively) or intronic splicing
enhancers or splicing silencers that reside in an intron and affect the use of proximal splice sites or exons; variable tandems
of loosely dened AU- (and U-rich) motifs (AREs) located in the UTRs of unstable mRNAs
110,111
; spatially restricted
secondary structures that control degradation and cap-mediated translation, such as CDEs, GAIT elements and the
recognition domain of regnase-1 (refs. 34,45,67); and domains bound by miRNA. Regulatory RBPs contain multiple
RNA-binding domains arranged also in tandem or distantly (RRMs, zinc ngers, KH motifs and dsRNA-binding domains)
(Table 1). The various domains in an RBP combine individual weak interactions with specic protein-RNA complexes of
high afnity
2
. When bound to RNA, an RBP can stabilize weak secondary structures and force the formation of secondary
RNA structures by bringing distantly located motifs in closer proximity. In addition, homo- or heteropolymerization of RBPs
on their RNA targets can take place and thus expose or hide regulatory RNA elements, prevent or allow the binding of
other RBPs and connect to essential machinery and signaling modules. In this context, differences in the engagement of
RBPs on selective combinations of RNA elements in RNPs provides specicity and coordination in PTR
5
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494 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY
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eIF4F, other eIF complexes and poly(A)-binding protein, which are all
required for assembly of the 48S initiation complex
19
.
In conditions of infectious stress
20
or inflammatory stress, auxiliary
ribosomal factors, transcript-restricted RNPs and Ago1-containing
RISCs
21
may hinder initiation and divert stalled preinitiation
complexes to subcellular foci known as stress granules, where they
await signal-induced decisions
19
. In the presence of permissive
signals, preinitiation complexes are released; conversely, restrictive
signals drive RNPs to sites enriched for degrading factors such as
processing bodies
19
.
The engagement or inhibition of core post-transcriptional machin-
ery by regulatory RNPs can fine tune complex reactions and diver-
sify cellular phenotypes. Below we discuss prominent examples of
RBP-mediated regulation and highlight the extensive degree of post-
transcriptional networking that underlies immunological reactivity.
RBP-mediated controls in innate immunity
Cells of the innate immune system (for example, monocytes-
macrophages, myeloid dendritic cells and polymorphonuclear cells)
evolved to recognize damaging agents and noxious substances; clear
dying cells and infectious organisms; provide support to the adaptive
arm of immunity; and aid tissue regeneration
20
. To accommodate
such functions, cells of the innate immune system undergo a con-
tinuum of changes in RNP configurations and post-transcriptional
programs induced by the inflammatory microenvironment (Fig. 2).
RBPs in the recognition and clearance of pathogens
Pathogens, infected cells and damaged or transformed tissues are
detected by germline-encoded pattern-recognition receptors (PRRs)
such as Toll-like receptors (TLRs) and RIG-I-like receptors
22,23
, which
are expressed either on cell surfaces or intracellularly. PRRs use a
variety of adaptor complexes to activate intracellular signaling cas-
cades that drive proinflammatory biosynthesis (for example, the tran-
scription factor NF-B, mitogen-activated protein kinases (MAPKs)
or interferon-regulatory factors (IRFs)) and/or cellular execution.
RBPs can alter the signaling thresholds of PRRs in many ways. For
example, prolonged TLR signaling via the adaptor MyD88 activates
nuclear SR proteins to promote the skipping of an exon in Myd88
pre-mRNA
24,25
. The resulting variant MyD88 protein lacks a region
required for assembly of the IRAK proinflammatory signaling com-
plex and prohibits signal transmission. Transcript-specific controls
can also enforce signaling via the NF-B inhibitor IKK and MAPKs;
for example, through changes in the translation of mRNA encod-
ing the kinase Tak1 facilitated by ARE-BPs
26
. Interestingly, RBPs can
also act as protein components of innate receptors. CIRP is an RBP
that aids the translation of mRNA during cold shock and hypoxia.
In hypoxic macrophages and brain microglia, CIRP is transported
to the cell surface and interacts with MD2 (the coreceptor of TLR4)
and enhances its proinflammatory activity
27,28
. The regulatory effect
of surface CIRP is suggested by the effect of its depletion mediated by
antibodies or genetic means, which counteracts acute inflammatory
assaults in rodents
27
.
RNA viruses are detected via endoplasmic or cytoplasmic PRRs
that bind to bacterial single-stranded RNA (ssRNA) (TLR7 and TLR8)
or viral dsRNA (TLR3, TLR9 and the DExDH-box helicases RIG-I,
Mda5 and DHX33)
22,23,29
to promote the production of type I interfer-
ons. Interferons also alert the hosts degradation machinery to attack
viral RNA and mask its translation machinery from exploitation by
Table 1 Recognition of RNA by RBPs, and features of mouse RBP mutants
RBP RBD Other domains RNA element PTR Immunological relevance of mutant Refs.
Upf1 (Rent1) ZnF ST-[Q] NMD Defective thymopoiesis
a
80
Upf2 (Rent2) ZnF MIF4G NMD Defective thymopoiesis
b
81
Zfp36 (TIS11, TTP) ZnF ARE EXD, TR Acute or chronic inammation
a,b
4144
Zfp36L1 (TIS11b, BRF1) ZnF ARE EXD Defective thymopoiesis, T-ALL
b
77
Zfp36L2 (TIS11d, BRF2) ZnF ARE EXD Defective thymopoiesis, T-ALL
b
77
Elavl1 (HuR) RRMs ARE (U-rich) SPL, pA, EXD,
TR, miRNA
Acute or chronic inammation; cancer; defective
thymopoiesis; inhibition of autoreactivity
a,b
61,6466,
85,101
TIA-1 RRMs ARE (U-rich) SPL, TR Sensitivity to acute or chronic inammation
a
5153
hnRNPD (AUF1) RRMs G-rich ARE (U-rich) EXD, TR Acute or chronic inammation
a
54,56,57
Khsrp (KSRP, FUBP2) KH G-rich ARE, miRNA EXD, TR, miRNA Enhanced antiviral responses
b
58
hnRNPL RRM G-, P- rich CA-rich SPL Defective thymopoiesis
b
90
hnRNPLL RRM CA-rich SPL Defective peripheral T cell responses
b
95
Rc3h1 (roquin, roquin-1) ROQ, ZnF RING, P-rich CDE EXD Systemic autoimmunity
a,b
49,97
Rc3h2 (roquin-2) ROQ, ZnF RING, P-rich CDE EXD Systemic autoimmunity
a,b
49,97
Dicer DsRBDs Helicase, PAZ,
RNaseIII
dsRNA miRNA Defective thymopoiesis
b
92,93
NF-90 DsRBDs dsRNA TR Defective peripheral T cell responses
a
100
PKR DsRBDs dsRNA RC Defective viral clearance
a
30
ADAR1 DsRBDs dsRNA RC, ED Defective viral clearance
a
31
L13a Ribosomal GAIT TR Acute or chronic inammation
b
69
ASF (SF2, SRSF1) RRM RS, G-rich AG-rich SPL Systemic autoimmunity
c
88
Zc3h12a (MCPIP1, regnase-1) ZnF PIN Stem-loop END Systemic autoimmunity
a,b
34,96
Arid5a ARID Stem-loop END Resistance to acute inammation and autoimmunity
a
35
CIRBP (Cirp, hnRNPA18) RRM G-rich Unknown TR Resistance to acute inammation
a
27
SRSF2 (SC35) RRM RS, G-rich Unknown SPL Defective thymopoiesis
b
89
S6 (S6R) Ribosomal TR Defective thymopoiesis
a
82
Rpl22 Ribosomal TR Defective thymopoiesis
a
83
eIF4E Ribosomal TR Resistance to infection and inammation; T cell anergy
d
71,73
eEF2 Ribosomal TR Resistance to acute inammation
d
17
Mode for the recognition of RNA by RBPs (synonyms in parentheses) with a proven function in immunological responses, as well as characteristics and phenotypes of mice with
mutant RBPs. ARID, AT-richinteraction domain; ED, editing; END, endonucleolytic decay; EXD, exonucleolytic decay; KH, K-homology domain; MIF4G, middle domain of EIF4G;
NMD, nonsense-mediated decay; PAZ, Piwi, Argonaute and Zwille domain; PIN, ssRNA-cleavage domain of upstream frameshift protein Upfs; RC, receptor function; RING, RING-
nger domain; ROQ, RNA-binding domain of roquin proteins; RRM, RNA-recognition motif; RS, arginine-serinerich domain; SPL, splicing; pA, polyadenylation; TR, translation;
ZnF, CCCH or other zinc nger; ribosomal, connections via the ribosome; T-ALL, T cell acute lymphoblastic leukemia.
a
Germline-encoded mutations.
b
Myeloid cell or T cellrestricted mutations via Cre-loxPmediated somatic recombination.
c
Human permutation.
d
Inferred by deletion of regulators.
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NATURE IMMUNOLOGY VOLUME 15 NUMBER 6 JUNE 2014 495
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e
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F
4
A
Cytoplasm Nucleus Cytoplasm Nucleus
40S subunit
elF2-GTP and met-tRNAi
43S
complex
Cytoplasm Nucleus
3
1
3
4
1
1
2
3
1
4
3
4
2
1
4
1
P
P
P P
P P
P
P
PSF TLR
MyD88
TCR
dsRNA
virus
I
Localization
A
A
A
A
AAAA
AAAA
AAAA
AAAA
AAAA
Editing and splicing
Stress
granules
Exosome
complex
RBP1
RBP2
Introns Exons
RBP3 (MF)
RBP4 (MF)
RNA elements
a
b c
NMD
p38
Erk
PKC- IKK
and IKK
ARE
ARE GAIT
TTP
Adaptor
Regnase-1
AMD or CDE
TNFR
TLR4
Endonucleolytic d e
Cap
A
AAAA
AAAA
AAAA
AAAA
AAAA
AAAA
Translation
Decay
AAAA
AAAA
AAAA
CCR4-NOT DCP1 and DCP2 Xrn1
A
A
A
A
A
ADAR
IFNAR
GSK3
hnRNP LL hnRNP L
SF3b
Cytoplasm
LPS
SF3a
M
y
D
8
8
Ub
AAAA
CDE AAAA
AAAA
CBP
elF3
AUG PTC EJ
EJC
60S
Upf2
SMG1
Upf1
Roquin
Roquin
IFN-R
4E-BPs
4E-BPs
mTORC1
TSCs eEF2K
K
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u
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G
r
o
u
p
Stress, nutrient deprivation, infection
eIF4E
e
IF
4
E
P
P
P
P
P
elF4G
PABP
AAAAAAAAAAA
elF3
60S
eEF2
EPRS
L13 GAPDH
TIA-1
and
TIAR
Stress
granules
Figure 1 Immune systemrelated PTR events. (a) RBPs accompany RNA from the very early steps of its life, via the recognition of relevant RNA
elements, and form RNP complexes. Nuclear RNPs orchestrate early post-transcriptional events, such as pre-mRNA splicing, editing and the
nucleocytoplasmic trafficking of mRNA. Multifunctional (MF) RBPs remain bound on regulatory elements and selectively coordinate regulatory RNP
configurations in the cytoplasm. Cytoplasmic RNPs drive mRNA through translation by the ribosome. In contrast, RNPs remodeled because of external
signals guide their target mRNA to destructive machinery that acts to promote deadenylation (for example, CCR4-NOT), decapping (for example,
DCP1 and DCP22), 3-to-5 exonucleolytic degradation (for example, the exosome complex) or 5-to-3 exonucleolytic degradation (for example, Xrn1).
(bd) Paradigms of the involvement of RNPs in immunological reactions include the following: the type I interferoninduced editing of viral dsRNA by
ADAR1, which converts adenine to inosine and compromises viral integrity (b); the TLR- or TCR-induced activation of alternative splicing mediated
by hnRNPL, hnRNP LL and PSF or the SR proteins SF3a and SF3b, all of which affect the inclusion or skipping of exons (c); and basal and inducible
mRNA-degradation mechanisms that occur in cells of the immune system (d). These exonucleolytic events are promoted by TTP and roquin after they
bind onto the relevant elements (AREs or CDEs) of target mRNA and recruit degradation machinery. The inducible functions of TTP can be inhibited
during inflammatory activation via phosphorylation by MAPKs or SAPKs. Alternatively, the endonucleolytic cleavage of target mRNA is promoted by
regnase-1, which is in turn inhibited by signaling via IKK and IKK and protein kinase C- (PKC-) and proteosomal degradation. Finally, aberrant
transcripts containing premature termination codons are sensed by Upf-containing complexes and are selectively degraded by nonsense-mediated decay
(NMD). IFNAR, receptor for IFN-; GSK3, glycogen synthase kinase 3; LPS, lipopolysaccharide; TNFR, receptor for TNF; Erk, MAPK; CBP, cap-binding
complex; SMG1, phosphatidylinositol 3-kinase-related kinase; PTC, premature termination codon; EJ, exon junction; EJC, exon-junction complex.
(e) Impediments to the translation of specific mRNAs can be imposed via inducible blockade of mTORC by TSC proteins and mTORs inability to
deactivate 4E-BP1 and 4E-BP2 by phosphorylation, which otherwise prevent eIF4E from reaching capped mRNAs. Alternatively, stress signals can stall
the formation of eIF2-containing preinitiation complexes via inhibitory phosphorylation of eIF2 and sequestration of these complexes in cytoplasmic
stress granules by ARE-BPs like TIA-1. Moreover, IFN- can lead to the phosphorylation of L13a and can be diverted from ribosomal subunits to mRNA
containing GAIT elements and block the translation of that mRNA. Finally, translation elongation can be controlled by the stress-induced inhibitory
phosphorylation of eEF2 kinase, which releases eEF2 to allow its recruitment to ribosomes. Such processes may also involve the generation and
function of noncoding RNA populations; these have been intentionally omitted here to emphasize the functions of RBPs. IFN-R, receptor for IFN-;
PABP, poly(A)-binding protein; EPRS, glutamyl-prolyl-tRNA synthetase; Met-tRNAi, methionyl initiator tRNA.
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496 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY
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viruses. A prominent example involves PKR (protein kinase, RNA
activated), a modular RBP that blocks eIF2 activity and the initiation
of translation upon binding viral dsRNA
30
. Interferons also prime
ADAR enzymes for binding to dsRNA viruses and promote debili-
tating adenine-to-inosine conversions; their antiviral effect has been
partially confirmed in cells from ADAR1-deficient mice
31
. ADAR
enzymes can also tether classic ssRNA-binding RBPs, such as ARE-
BPs, to affect the translation or decay of mRNA
10
; this may add to
their antiviral abilities. Conversely, viruses can use PTR machinery
to evade the host response
32
. For example, ssRNA alphaviruses bind
ARE-BPs and thus subvert the functions of the ARE-BPs for their own
benefit and at the same time deplete the host cell of the ARE-BPs
33
.
RNPs in the control of innate plasticity
During inflammatory progression, PRR signals instruct bactericidal
and antiviral activities, phagocytic clearance, the synthesis of inflam-
matory mediators and support of responses by the T
H
1 and T
H
17
subsets of helper T cells that further augment the proinflammatory
loop. As inciting agents are being cleared, proinflammatory activity
is deactivated and converts to an alternatively polarized response that
promotes homeostasis, supports T
H
2 responses and aids tissue regen-
eration
20
. Deactivation and polarization occur via intracellular signal-
ing inhibitors or via immunomodulatory cytokines such as autocrine
or regulatory T cellderived interleukin 10 (IL-10) and transforming
growth factor- (TGF-) or T
H
2 cellderived IL-4.
The degradation of mRNA seems to be the most efficient deter-
minant of innate deactivation, since it restricts the accumulation of
proinflammatory mediators whose prolonged release can destroy or
transform tissues. Regulatory endonucleases can be directly engaged
to restrict the basal transcription of genes encoding inflammatory
molecules. In macrophages, such a role has been assigned to the endo-
nuclease regnase-1, which targets a loosely defined stem-loop struc-
ture in the 3 UTR of Il6 mRNA. In resting macrophages, regnase-1
is active; TLR signaling leads to the phosphorylation of regnase-1 by
kinases of the NF-B pathway (IKKs) and its subsequent proteasomal
degradation. The loss of primary signals restores regnase-1 activity
and inhibits proinflammatory IL-6 (ref. 34). The anti-inflammatory
effects of regnase-1 have been demonstrated in mice lacking the gene
encoding regnase-1, which develop a complex autoimmune syndrome.
Alternatively, access of regnase-1 to its target site can be outcompeted
by inducible RBPs. One such example is Arid5a, which protects Il6
mRNA from regnase-1-mediated degradation; Arid5a deficiency in
mice attenuates acute inflammation and autoimmunity
35
.
The degradation of ARE-containing mRNAs, known as ARE-
mediated decay (AMD), is a prominent example of how changes
in the composition of regulatory RNPs impose anti-inflammatory
control. Central to AMD are the functions of members of the tris-
tetraprolin (TTP; also known as TIS11 or Zfp36) family
36
. The
prototype, TTP, binds to the AREs of various mRNAs encoding
inflammatory molecules and acts to recruit deadenylation and decap-
ping complexes, thus promoting exonucleolytic degradation. In innate
cells, TTP expression is induced by activating signals transmitted
from TLRs, receptors for tumor-necrosis factor (TNF) and receptors
for interferons
36
; downstream signals include those from MAPKs
or stress-activated protein kinases (SAPKs) that also phosphorylate
TTP to interact with intracellular protein adaptors or chaperones.
Such interactions prohibit the sequestration of TTP at mRNA but also
protect it from proteasomal degradation (Fig. 1d). That allows macro-
phages to secrete proinflammatory mediators such as TNF, GM-CSF
and related chemokines and allows dendritic cells to produce IL-23
Figure 2 Paradigms of RNPs that underlie
changes in innate immune systemactivation
programs. (a) During the progression of
inflammation, innate cells convert their
phenotype from a proinflammatory one to
one of alternative activation and thus
balance pathogen clearance, homeostasis
and tissue restoration. DC, dendritic cell;
M, macrophage; NO, nitric oxide; IR-M,
immunoregulatory alternative macrophage;
Reg-M, regenerative alternative macrophage;
Gr, granulocyte; PGEs, prostaglandins; GCs,
glucocorticoids; Igs, immune complexes;
MMPs, matrix metalloproteinases.
(b) Underlying the conversions in a are PTR
events incurred through RNPs that target
proinflammatory mRNAs (red) or alternative
mRNAs (blue) that prime and impose
state-specific confinements on overlapping
transcription programs. Prior to activation,
stochastic mRNA expression can be silenced
by basal endonucleolytic and exonucleolytic
RNPs (for example, regnase-1 and roquin
proteins). The initial recognition of danger
signals (pathogen-associated or danger-
associated molecular patterns) via PRRs
activates mainly proinflammatory transcription programs and, to a lesser extent, alternative transcription programs; subsequent to the maturation
of the transcripts in the nucleus, multifunctional RBPs may prime state-specific mRNAs for their cytoplasmic fate by means of their cis elements.
In the cytoplasm, these RBPs can nucleate signal-induced regulatory RNP configurations. At first, such RNPs act to suppress alternative programs
through translational impediments (for example, TSC-mediated blockade of mTOR, or GAIT activation) and/or prohibit basal and inducible degradation
machinery that targets mRNAs encoding proinflammatory molecules (e.g., regnase-1 and TTP). As the proinflammatory response reaches its maximum
by autocrine or feedback loops instructed by T
H
1 or T
H
17 cells and the initial signals subside, anti-inflammatory RNPs are released or enhanced to
promote the degradation of mRNAs encoding inflammatory molecules; they also stall the translation of mRNAs encoding proinflammatory molecules
(e.g., TIA-1). Underlying immunoregulatory networks can then build up to enhance alternative transcription and alleviate blocks in mTOR-mediated
translation. Autocrine and paracrine feedback loops further enforce alternative identities and complete polarization.
IFN-
IFN-
NO
TNF, IL-6
CCL2, CCL3
IL-12
IL-23
IR-M
Reg-M
Wound
healing
Homeostatic
suppression
Proinflammatory programming
Bacteria
Virus
PRRs
Monocyte
or DC
Priming
Recruit
DC
M
Pathogen
clearance
Restriction on proinflammatory
permission for alternative programming
IL-4, IL-10, IL-13,
PGEs, GCs, Igs, TGFs
T
H
0
B
Gr T
H
2
T
reg
T
H
17
T
H
1
TTP
Exonucleolytic decay
Regnase-1 Endonucleolytic decay
TIA-1, TIAR
Roquin proteins
TSCs, GAIT Transcript restricted inhibition
of mRNA translation
Proinflammatory translation Alternative translation
Maturation
and
priming
Fate
decision
Outcome
a
b
IFN-
VEGF, MMPs
Cellular conversions
RNP conversions
Transcription (proinflammatory or alternative)
Splicing (snRNPs, hnRNPs, SRs)
Multifunctional regulatory RNPs (e.g., hnRNPs, HuR, TIA-1, AUF1)
K
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NATURE IMMUNOLOGY VOLUME 15 NUMBER 6 JUNE 2014 497
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to support T
H
17 responses. When counteracting signals are enforced,
the reservoir of TTP is dephosphorylated and gains access to its target
mRNAs and promotes their destruction. Deactivating or polarizing
cytokines, such as IL-4, IL-10 and TGF- (refs. 3739), further enforce
TTP expression and thus provide a failsafe mechanism against chronic
inflammation. This is compatible with the phenotypes of mutant mice
that lack TTP; these mice are sensitive to acute inflammatory assaults
and develop cachexia, arthritis, dermatitis and myeloid hyperplasia
reversed by blockade of the proinflammatory mediators TNF, CCL3,
IL-23 and IL-17 (refs. 4044).
Multiple RNA elements may be engaged to ensure the deactiva-
tion of innate immune responses via the degradation of mRNA. This
can be inferred from the coexistence of AREs and CDEs in mRNAs
encoding inflammatory molecules, such as Tnf mRNA
45
. The modular
RPBs roquin-1 and roquin-2 contain E3 ubiquitin-ligase domains
that can promote the degradation of stress-induced protein signal-
ers
45,46
. They also have domains for recognizing RNA, one of which
(ROQ) is a unique domain that binds to CDEs; in doing so, it recruits
exonucleolytic machinery in a way similar to TTP but in a nonin-
ducible manner
47
. The synergy between ARE-mediated control and
CDE-mediated control can also be inferred from the colocalization
of ARE-BPs and roquins to stress granules
19,48
. In agreement with
that, roquin-null mice that lack T cells and B cells seem to be sensitive
to acute, TNF-driven inflammation and arthritis in a way similar to
TTP-deficient mice
49
.
The translation of mRNAs encoding proinflammatory molecules
is also a major determinant of the activation of innate cells. Some
controls seem to be more general; for example, translation elongation
is promoted by inflammatory signaling via MAPKs or SAPKs that
activates the elongation factor eEF2 (ref. 17). In most cases, however,
translational controls are imposed on specific transcripts that carry
regulatory RNPs, some of which are originally assigned in the nucleus.
Examples of this include the RBPs TIA-1 and TIAR, which were iden-
tified as nuclear splicing factors in cytotoxic T lymphocytes
50
. In the
cytoplasm of macrophages, these RBPs can stall preinitiation com-
plexes of ARE-containing mRNAs and facilitate their sequestration
in stress granules
19
. In mice, deletion of TIA-1 confers sensitivity to
acute inflammatory challenge, lung pathology and a propensity for
chronic arthritis
5153
; it also exacerbates the chronic inflammation
of TTP-deficient mice
52
, which suggests that inhibitory RNPs acting
against the stability and translation of mRNA act in concert toward
proinflammatory control.
An additional set of multifunctional RBPs bound to mRNAs
encoding proinflammatory molecules in the nucleus may facilitate
the sequestration of cytoplasmic RBPs that execute changes in degra-
dation or translation. A prominent example of this involves the four
spliced isoforms of the RBP AUF1 (hnRNPD). In the nucleus, AUF1
facilitates the maintenance of telomeres
54
, but it also forms dimers on
the U-rich portions of AREs and engages in cytoplasmic regulation
of AREs
55
. The recruitment of monocytes to inflammatory sites and
activation of macrophages via TLRs can alter the presence of AUF1 in
the cytoplasm, whereas the transient phosphorylation of AUF1 may
relax its binding to AREs and thus render them more accessible to
decay and translation regulators. Mice with germline mutations in the
gene encoding AUF1 develop chronic inflammation reminiscent of
the phenotype that results from TTP deficiency, including sensitivity
to acute inflammation and chronic dermatitis
56,57
. A similar mode
of function has been proposed for the RBP KSRP, which is involved
in the nuclear and cytoplasmic maturation of selective miRNAs but
can also induce cytoplasmic AMD via an undefined mechanism.
In plasmacytoid dendritic cells, the activation of mRNAs encoding
interferon- (IFN-) and IFN- is controlled by KSRP, and KSRP
dysfunction in the mouse leads to overexpression of these interferons
and rapid clearance of virus
58
.
For many years, the effects of inhibitory RNPs were assumed to
be counteracted by protective RNPs. For ARE-containing mRNA,
protection was proposed to occur by RNPs containing the RBP HuR
(Elavl1). HuR is involved in various events mediated by nuclear,
cytoplasmic and noncoding RNA
5962
; it also forms multimers on
ambiguous U-rich stretches
60,63
. Thus, HuR was assumed to mask
AREs and miRNA-binding sites from inhibitory RNPs to dictate the
balance between suppression of mRNA and activation of mRNA.
Genetic evidence has disproven that supposition. Mice that lack HuR
in macrophages become hypersensitive to endotoxemia, chronic
intestinal inflammation, inflammatory carcinogenesis and hind-
limb ischemic necrosis
61,64
; conversely, overexpression of HuR in
macrophages attenuates such pathological manifestations
61,65
. The
anti-inflammatory effects of HuR are related to its ability to bind to
its targets during the time frame of deactivation
61
, as are those of
negative regulators. During that time frame, HuR can silence the
translation of mRNAs encoding inflammatory molecules and chemo-
kine circuits that facilitate the recruitment of monocytes and macro-
phages
61,65
. However, HuR can both promote the decay of mRNAs
encoding inflammatory molecules and inhibit such decay
61,65
.
Mechanistic studies have demonstrated that HuR can engage in
complex interactions with regulatory entities. For example, it can
prohibit the binding of miRNAs but can also facilitate the maturation
and function of miRNAs that inhibit mRNA translation
62
. Similarly,
HuR has been proposed to oppose the functions of AUF1 and TTP
in AMD but can also act together with TIA-1 to effect translational
silencing
65
. Interestingly, the spectrum of HuR-targeted mRNAs
includes not only those encoding proinflammatory factors but also
those encoding immunoregulatory factors (for example, IL-10, TGF-
and VEGF) required for progression toward alternatively activated
states
61,64,66
. The same seems to apply to TIA-1, since loss of TIA-1
exacerbates T
H
1, T
H
17 and T
H
2 responses
53
. Such findings indicate
that HuR can act together with other RBPs to mark inflammatory
moleculeencoding mRNAs that bear loosely defined RNA elements
and allow the gradual assembly of discriminatory RNP configura-
tions that promote one activation state over another.
Alternative polarization may also involve additional RNP con-
figurations. One such example involves the GAIT (IFN--activated
inhibitor of translation) complex
67,68
. The main component of
this complex is the ribosomal protein L13a, which normally scaf-
folds the initiation complex. Proinflammatory IFN- diverts L13a to
an RNA element (GAIT) found in some mRNAs and thus stalls
their translation. At present, this is considered an additional anti-
inflammatory mechanism, as mice that lack L13a in macrophages
develop enhanced susceptibility to endotoxemia and increased
infiltration of macrophages into inflamed tissues
69
. However, GAIT-
containing mRNAs (for example, those encoding the chemokines
CCL22, CXCL13 and CCL8 and the proangiogenic cytokine VEGF)
mark alternative macrophages, which suggests that PTR by GAIT
may block polarization
69
.
In the context of the observations noted above, alternative polari-
zation may proceed via both the post-transcriptional limitation
of proinflammatory programs and the enforcement of alternative
transcriptional programs (for example, via the transcription factors
STAT6 and PPAR-) (Fig. 2). The balance between those states
seems to be dictated by changes in cellular metabolism that affect
mTOR. This is most elegantly demonstrated in macrophages that
lack mTOR activity
70
or are infected by Legionella pneumophila
71
, the
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498 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY
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intracellular pathogen of Legionnaires disease. Infection with virulent
L. pneumophila leads to degradation of the mTOR-activating kinase
Akt, release of TSC proteins and blockade of mTORC1-mediated
translation; at the same time, however, it enhances the translation
of mRNAs encoding proinflammatory molecules, as do inhibitors
of mTORC1. Conversely, infection with avirulent L. pneumophila or
loss of TSC proteins activates mTORC1 to promote the expression of
immunoregulatory factors but deactivates the translation of mRNAs
encoding proinflammatory molecules. Akt is a key signaling molecule
in the polarization of alternative macrophages
72
, and mTOR is both
controlled by Akt and feeds back (via mTORC2) to modulate alterna-
tive polarization
73
. In this context, cross-regulation of Akt and mTOR
acts as a rheostat to balance proinflammatory and alternative states.
A prominent question is how inhibition of mTOR alleviates the block-
ades imposed on mRNAs encoding proinflammatory molecules. This
may involve interactive effects with ARE-BPs. For example, metabolic
changes that activate AMP-activated protein kinase can block both
Akt-mTORC1mediated translation and inhibitory ARE-BP func-
tion
74,75
. Moreover, the translational inhibition of mRNA containing
a 5 terminal oligopyrimidine tract, which is mediated exclusively by
mTOR, involves cross-recognition of the mRNA by TIAR
76
, which
may then become limiting for binding to AREs.
Collectively, the functions of RBPs in cells of the innate immune
system provide fine examples of how remodeling of RNPs can alter the
activation states of cells of the immune system by PTR; in this setting,
emphasis has been placed on processes that change the quantity of
state-specific transcriptomes. However, the interplay between nuclear
RNPs and cytoplasmic RNPs can also alter the quality (e.g., via alter-
native splicing) and the quantity (via degradation and or translation)
of lineage- and state-specific programs, as demonstrated in cells that
confer adaptive immunity.
PTR in adaptive immunity: the case of T cells
PTR is involved in several processes that affect the maturation, activa-
tion and control of tolerance of lymphocytes or specialized functions
such as immunoglobulin editing, affinity maturation and secretion
in B cells. Data that integrate the configurations of regulatory RNPs
with B cell biology are limited. In contrast, analysis of PTR in T cells
has revealed an extensive degree of overlapping RNP-mediated events,
which we focus on below (Fig. 3).
RBPs that control T cell maturation
The conversion of lymphocytic progenitor cells into signaling-competent
T cells in the thymus is instructed in part by sequential signaling
by receptors of the Notch family and the precursor to the T cell anti-
gen receptor (TCR) - and -chains (pre-TCR). Two homologs of
TTP, ZFP36L1 and L2, control Notch signaling by imposing AMD on
Notch1 mRNA
77
. Before the pre-TCR is expressed, Notch signal-
ing may limit the activity of ZFP36L1 and L2 through phosphoryla-
tion
78
and allow lineage commitment and proliferation; subsequently,
AMD allows substitution of the Notch signal by the pre-TCR. If
this system failsfor example, in mice that lack both ZFP36L1 and
L2thymic progenitor cells bypass the requirement for a pre-TCR
and transform into T cell acute lymphoblastic leukemia due to excess
Notch-1 protein
77
. Relevant to the same process is the competition
between the transcriptional ability of Notch and that of the transcrip-
tion factor Ikaros that aims to shut down alternative commitment
programs and allow transcription of the gene encoding pre-TCR.
Notch3 induces alternative splicing of Ikaros pre-mRNA potentiated
by members of the Elavl family; the resulting variant of Ikaros cannot
compete for access to the locus encoding pre-TCR, which allows
instruction of T cells by Notch
79
.
A stringent set of post-transcriptional events aids the elimination of
unproductive rearrangements in the gene encoding TCR. Aberrant
Figure 3 Various RNPs control the maturation, egress, activation and
tolerance of T cells. The states of immunodeficiency, autoimmunity or
leukemia induced by RBP dysfunction connect regulatory RNPs (white
boxes) to several T cell programs. In the thymic cortex, RNPs instruct
progenitor cells (CD4

CD8

stages DN1DN4) toward the T cell lineage

by controlling the extent of the interactions of Notch with Delta ligands
presented by thymic stroma. The DN2-to-DN3a transition indicates
rearrangements of genes encoding TCR, TCR () or TCR. At the
DN3b stage, RNPs clear transcripts bearing frameshifts or premature
termination codons and facilitate the apoptotic elimination of cells lacking
TCR. RNPs also facilitate the instructive effects of the pre-TCR (p)
toward transition to the CD8
+
immature single-positive (ISP) stage and the
CD4
+
CD8
+
DP stage. CD4
+
CD8
+
DP cells rearrange their TCR-encoding
loci to express mature TCR () for interaction with antigens presented
by the thymic epithelium. The quality of these interactions is also
controlled by RNPs to guide the positive selection of non-self lymphocytes
and eliminate self-reactive and anergic thymocytes. In parallel, an array
of RNP-regulated chemokine signals facilitate the movement of CD4
+
or
CD8
+
SP cells from the cortex to the medulla toward the peripheral blood
for the establishment of the naive T cell pool. Antigens, costimulatory
molecules and cytokine feedback loops in peripheral lymphoid organs
instruct RNPs to modify the activation, helper and regulatory profiles
of CD4
+
T cells or support their deactivation by anergy and death.
Peripheral CD8
+
responses may also be affected by other RNPs whose
functions remain to be determined and thus have been omitted here.
NK, natural killer cell; tT
reg
, thymic T
reg
cell; T
FH
, follicular helper T cell;
Tr1, T regulatory type 1 cell.
p
N
o
t
c
h
P
r
e
-
T
C
R
T
C
R
DN3b

DP
Zfp36L1,
Zfp36L2
HuD
Upf1, Upf2
Dicer
HuR
hnRNPL
HuR
T
FH
eIF4E
Roquins
hnRNPLL
PSF
Naive
CD4
+
Anergy
eIF4E
ARE-BPs
Elimination
CD8
+
pool
Thymus
Periphery
eIF4E
ARE-BPs
hnRNPA1
tT
reg
Tr1
iT
reg
tT
reg
NK
CD8
SP
CD4
SP
Activated
CD4
+
T
H
2
T
H
1
T
H
17
T
H
9
DN1
DN2
DN3a

DN4
ISP
K
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g

G
r
o
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p
RPL22
Celf2
ASF (SF2)
SC35
hnRNPL
HuR
hnRNPC1
hnRNPI
HuR
TIA-1
Regnase-1
hnRNPI
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NATURE IMMUNOLOGY VOLUME 15 NUMBER 6 JUNE 2014 499
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TCR-encoding transcripts with premature termination codons
need to be selectively degraded, because they are otherwise consid-
ered productive and shut down beneficial recombination events by
allelic exclusion. Studies of mutant mice that lack functional upstream
frameshift proteins (Upf1 and Upf2), which are effectors of nonsense-
mediated decay, have revealed that the clearance of unproductive
rearrangements proceeds via nonsense-mediated decay
80,81
. In the
absence of upstream frameshift proteins, thymopoiesis is blocked
because of the accumulation of stabilized out-of-frame transcripts.
Active translation is also required for the abortive death of cells unable
to express a pre-TCR on their surface, a finding revealed by stud-
ies of mutant mice that lack factors regulating ribosomal biogenesis
and function. The ribosomal protein S6, a major substrate of mTOR,
is also involved in the biogenesis of the 40S ribosomal subunit in
eukaryotes. Deletion of S6 in the mouse blocks transition from the
CD4

CD8

double-negative (DN) state to the CD4

+
CD8
+
double-
positive (DP) state
82
due to genotoxic stress mediated by the tumor
suppressor p53 that cannot be counteracted because of the lack of
functional ribosomes. Mice that lack auxiliary ribosomal factors that
aid translation initiation, such as the ribosomal protein L22, display
a phenocopy of that same effect
83
. The genetic instability induced by
TCR rearrangements can also promote the binding of ARE-BPs to
mRNAs encoding factors involved in the p53 and ATM-ATR path-
ways
84
. This is suggested in part by the increased proliferation of
HuR-deficient cells at the DN3 stage that are passing -selection
85
. A
final step of PTR involves the activation of transcription of the gene
encoding TCR during the DN-to-DP transition and is guided by
the splicing abilities of CUGBP family of RBPs. The CUGBP Celf2 is
induced by the pre-TCR to promote the inclusion of a domain in
the mRNA encoding the transcription factor LEF1; this domain thus
allows LEF1 to bind to the enhancer of the gene encoding TCR in
DP cells and finalize maturation of the TCR complex
86
.
RNPs controlling central T cell tolerance
T cells expressing mature TCR chains along with coreceptor com-
plexes (CD3, CD4 and CD8) engage antigens presented by the major
histocompatibility complex of the thymic stroma. The thresholds of
these interactions guide the selection of the nonself-reacting CD4
+
or
CD8
+
single-positive (SP) repertoire (positive selection) and the elimi-
nation of self-reacting cells (negative selection). These processes are
subject to PTR that affects the signaling ability of the TCR complex.
The proper splicing of coding regions or 3 UTRs of CD3 (CD247)
pre-mRNA confers signal competence onto TCR, as the CD3 chain
is its main intracellular adaptor. In T cells from patients with systemic
lupus erythematosus, CD3 expression is diminished and is replaced
with expression of the Fc receptor, which leads to nonspecific acti-
vation by excessive calcium influx. This is due to the generation of
alternatively spliced CD3 mRNAs that lack either coding regions or
a portion of the AREs from their 3 UTR, which renders them unstable
due to loss of HuR binding
87
. Such effects have been partially attrib-
uted to a decrease in the SR protein ASF (SF2), which leads to inap-
propriate retention of introns in the CD3 mRNA
88
. Interaction of
CD3 with the signaling kinase Zap70 is subject to complex PTR that
affects phosphorylation of Zap70 by the receptor-proximal Src kinase
Lck. Under resting conditions, Lck is phosphorylated at two tyrosine
residues: one that characterizes its on status, and one that inhibits
its activity. Release from inhibition and enforcement of activation
involves the transmembrane tyrosine phosphatase CD45. Multiple
isoforms of Cd45 mRNA can be generated by the alternative splicing of
three of its exons, which results in CD45 proteins with variable extra-
cellular domains and activities. Immature DP cells express mainly
the short, less-active CD45RO isoform, whereas CD4
+
or CD8
+
SP
cells express the longer CD45RB isoform. In thymic T cells, inclu-
sion of exons in Cd45 pre-mRNA is controlled by the SR proteins
ASF (SF2) and SRSF2 (SC35), whereas exon skipping is aided by the
heterogenous nuclear RNP hnRNPL. Deletion of SRSF2 (SC35)
89
or
hnRNPL
90
in thymocytes induces a blockade in the DN4-to-DP tran-
sition due to changes in CD45 activity that inhibit or hyperactivate
Lck. Connections between the activity of Lck and other RBPs, such
as HuR, have also been demonstrated and correlate with alterations
in positive and negative selection
85
. Several ARE-containing mRNAs
are predicted to be targeted by HuR in T cells at the level of their deg-
radation or translation
85,91
. However, HuR is also involved in nuclear
splicing reactions
60
, which suggests that it may control TCR signaling
in a manner similar to that used by hnRNPL. This is suggested partly
by the involvement of those RBPs in the migration of mature thymo-
cytes. Both hnRNPL-null SP T cells and HuR-null SP T cells seem to be
refractory to movement toward medullar endothelial cells and egress
from the thymus toward the bloodstream induced by the chemokine
CCL21 and its receptor CCR7 and by the chemokine CXCL12 and its
receptor CXCR4 (refs. 85,90).
Remarkably, the maturation of conventional T cells does not seem
to require miRNA function; however, miRNAs are involved in the
maturation of alternative T cell subsets. For example, Dicer is needed
for the generation of invariant natural killer T cells by lipids pre-
sented by the antigen-presenting molecule CD1 (ref. 92) and for the
transcription factor Foxp3driven generation of thymic regulatory
T cells (T
reg
cells)
93
. The latter may connect to translational events
that control the identity of thymic T
reg
cells. Holistic comparison of
polysomal RNAs from thymic T
reg
cells and conventional T cells has
demonstrated that the identity of thymic T
reg
cells, as well as synthe-
sis of the deterministic transcription factor Foxp3, can be dictated
through the subset-restricted engagement of eIF4E during the initia-
tion of translation
7
.
RNPs that control peripheral T cell tolerance
Conceivably, post-transcriptional events that occur in thymocytes may
also occur in peripheral T cell subsets. For example, longer spliced
isoforms of CD45 distinguish naive T cells from activated or memory
T cells that express shorter CD45 variants. This stage-restricted splic-
ing event is promoted by hnRNPLL (a paralog of hnRNPL) and PSF
(polypyrimidine tractbinding protein (PTB)associated splicing
factor)
94
. Expression of hnRNPLL is induced by TCR signaling; PSF
is always present but is subjected to phosphorylation by the TCR-
transduced signals. As a phosphorylated protein, PSF interacts
with intracellular chaperones that prevent its sequestration at exonic
silencers. Genetic evidence for this type of regulation has been provided
by a mouse mutation that results in compromised binding of hnRNPLL
to RNA and smaller peripheral memory cell populations
95
.
A set of decay mechanisms controls peripheral T cell activation,
helper T cell function and tolerance via the regulation of costimula-
tory or coinhibitory mRNAs. Costimulatory signaling molecules, such
as members of the CD28 superfamily, act to confirm that the antigenic
signal is genuine and that the cell must be activated by proliferation
or the execution of helper T cell programs. The involvement of PTR
in costimulation is demonstrated during the development of CD4
+

follicular helper T cells that aid the maturation of B cells in germinal
centers. The correct expression of mRNAs encoding the inducible
costimulator ICOS and the receptor OX40 that dictates this proc-
ess is subject to decay control by roquin-1, roquin-2 and regnase-1.
Expression of roquin-1 is repressed upon activation of CD4
+
T cells
via a miRNA-mediated silencing mechanism, which allows the
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500 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY
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regulated activation of costimulatory transcripts bearing CDEs
48
. On
the other hand, regnase-1 is under direct control of the TCRprotein
kinase C- axis, which induces the proteolytic degradation of the
endonuclease and controls the cleavage of its targets
96
. Combinatorial
deletion of roquin proteins in mice enforces the overexpression of
ICOS and OX40, the population expansion of follicular helper T cells
and lupus-like B cell autoimmunity
49,97
. Similarly, loss of regnase-1 in
T cells augments the synthesis of ICOS and OX40 and systemic autoim-
munity
96
. T cell activation can also be altered by regulation of CD154
(CD40L), the ligand for the costimulatory receptor CD40. CD154
and cytokine signaling can inhibit the decay of CD154-encoding
mRNA through two 3 UTRassociated RNPs that bind to CU-rich
cis elements
98
. Interestingly, the main components of both of those
RNPs include PTB (hnRNPI), hnRNPL and nucleolin. These factors
are involved mainly in nuclear splicing; their stabilizing effects in the
cytoplasm provide an additional example of nuclear RNP composi-
tions that are maintained to facilitate cytoplasmic PTR events.
The combination of TCR and costimulatory signaling activates
mRNAs encoding cytokines involved in proliferative expansion,
effector T cell function, immunological memory and anergy. A pro-
totypical example is IL-2, which stimulates both T cell activation and
tolerance. The 3 UTR of the mRNA encoding IL-2 is targeted not only
by TTP and regnase-1 (ref. 99) but also by the nuclear factor NF90
(ILF3), which also targets transcription of the gene encoding IL-2. In
the absence of NF90, T cells lose the expression of mRNA encoding
IL-2 due to a partial block in its transcription and the enhancement of
its degradation; thus, cells became incapable of homeostatic popula-
tion expansion
100
. The case of mRNA encoding IL-2 exemplifies the
complex network of RNP interactions that guide the cytokine-induced
determination of helper T cell subsets. The functions of ARE-BPs in
these settings have mostly been inferred from their functions in innate
cells. Limited evidence has been provided for the involvement of HuR
in the specification of T
H
17 celldriven autoreactivity
101
; however,
that effect cannot be easily discriminated from its functions in the
regulation of general TCR signaling.
The elimination of autoreactive T cells in both the thymus and the
periphery is key for all states of tolerance and is achieved to a large
extent through apoptotic cell death. The regulation of pre-mRNA
encoding the cell surface receptor Fas (CD95) is a fascinating example
of PTR involved in this type of death; alternative splicing of its sixth
exon leads to the production of either a membrane-bound form of
Fas that promotes apoptosis or a soluble form of Fas that inhibits
the process. Mutations that disrupt that conversion correlate with
autoimmune lymphoproliferative syndrome
102
. In vitro, inclusion of
that exon in Fas-encoding mRNA is facilitated by hnRNPA1, TIA-1
and TIAR, whereas it is antagonized by PTB, HuR and hnRNP C1
(refs. 50,103). Genetic evidence of the functional effects of this proc-
ess is lacking at present, as is evidence of the concerted action of these
RBPs; however, two points of evidence indicate the involvement of
these molecular interactions in Fas-induced apoptosis. First, HuR can
be cleaved by effector caspases to release its apoptosome-activating
partner PP32, and HuR-deficient thymocytes seem to be resistant
to Fas-induced apoptosis
85,104
. Second, U2 small nuclear RNPs are
cleaved by effector caspases during T cell apoptosis, and Fas splicing
is arrested
105
.
Finally, the absence of costimulation leads T cells to become hypo-
responsive (i.e., anergic) and accumulate mRNAs that are prohibited
from proceeding to translation by means of mTORC1 inhibition
106
.
In a manner similar to that in macrophages, inhibition of mTOR
may also affect the translation of ARE-bearing mRNAs; however, in
this case, blockade of mTOR acts synergistically with ARE-mediated
silencing
107
. It remains to be determined whether this stalling effect
relates to the engagement of subsequent death programs or to other
PTR controls.
Conclusions and future perspectives
The examples on RBP-mediated events mentioned above constitute a
small fraction of regulatory PTR events in cells of the immune system.
The complete map of such events is envisaged to integrate the specific
effects of noncoding RNA populations as well as additional layers of
PTR, such as alternative polyadenylation, surveillance and alterna-
tive mechanisms of decay. One thing is certain, however: maintain-
ing control over the life of mRNA by RBPs is a key strategic step by
which cells of the immune system determine their phenotypes and
functions. The compelling data provided by genetic studies certainly
suggest this is the case. However, definitive proof of the coordina-
tion of immunological programs by PTR is lacking at present, mainly
because of the divergent directions of the disciplines involved in their
analyses. Alignment of molecular and immunological perspectives is
clearly needed to tackle a series of important issues in this field. First,
many aspects of the recognition of RNA by RBPs under cell- and
signal-restricted conditions remain unknown. Second, verifying the
hypothesis of coordination will require the identification of retained
and alternating RNP interactions from the nucleus to the sites of
translation and decay. Third, the post-transcriptional governance of
the definition of cells of the immune system requires full description
of subset-specific RNPs. System-level and advanced imaging plat-
forms assessing RNP interactions in vivo could address these issues,
provided they are applied in specific immunocellular contexts. The
most challenging aspect is the confirmation of tissue-restricted
protein-protein and protein-RNA interactions. So far, this has entailed
the deletion or overexpression of RNP components. Although these
approaches provide a wealth of information on a cells requirement
for individual RBPs, they have a substantial limitation: the end effect
of such experimental interventions may rely not only on the specific
RBP but also on the remodeling of RNPs associating with this RBP.
Such remodeling may allow or prohibit access to alternative RNP
constituents with unaccountable side effects. Additional disturbances
may come from approaches, such as knockdown mediated by small
interfering RNA or hormone-induced transgenes, which may induce
substantial cellular stress and therefore alter multiple PTR programs.
Alternatives include the generation of transgenic mutants bearing
point or domain mutations that preserve proper RBP expression and
RNP integrity, or the simultaneous mutation of genes encoding sev-
eral RNP constituents that result in collapse of the total RNP archi-
tecture. The same applies for the in vivo analysis of RNA elements,
whose permutations at present involve large deletions or substitutions
because of the limited descriptions of them.
The caveats described above are substantial bottlenecks in the
quest to exploit RNPs for biomedical discoveries. It is true that novel
platforms assessing the recognition of RNA by RBPs
4
and genetic
systems of RBP dysfunction provide means for the clinical monitor-
ing and description of divergent immunological conditions. However,
translating such knowledge into clinical therapy is still at a very
early stage. Efforts to identify the lead compounds that consitute
RBP binding
108
are in progress, as are methods for achieving the
extracellular uptake of modified RBPs with cleavage or activation
domains
109
. However, these approaches may suffer from the same
limitations as targeting genes encoding RBPs. Perhaps a solution
could be provided by the tethering of PTR machinery to RNA viruses;
the engineering of decoy RNAs with a specific composition of RNA
elements could be of interest, once the structures of these elements
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NATURE IMMUNOLOGY VOLUME 15 NUMBER 6 JUNE 2014 501
REVI EW
have been fully delineated. Despite the many limitations described
above, all the evidence suggests that PTR and RNPs are worthy of
serious consideration in therapeutic schemes to combat inflamma-
tory and autoimmune syndromes.
ACKNOWLEDGMENTS
We thank G. Panayotou, E. Remboutsika, L. Kioussi and N. Lourou for comments.
Supported by the Hellenic General Secretariat for Research and Technology
ARISTEIA I program (1096-PRECISE) and the Seventh Framework Programme
of the European Union (PEOPLE-2010-IEF 274837, HEALTH-F2-2008-223404-
MASTERSWITCH).
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
Reprints and permissions information is available online at http://www.nature.com/
reprints/index.html.
1. Castello, A. et al. Insights into RNA biology from an atlas of mammalian
mRNA-binding proteins. Cell 149, 13931406 (2012).
2. Lunde, B.M., Moore, C. & Varani, G. RNA-binding proteins: modular design for
efcient function. Nat. Rev. Mol. Cell Biol. 8, 479490 (2007).
3. Glisovic, T., Bachorik, J.L., Yong, J. & Dreyfuss, G. RNA-binding proteins and
post-transcriptional gene regulation. FEBS Lett. 582, 19771986 (2008).
4. Knig, J., Zarnack, K., Luscombe, N.M. & Ule, J. Protein-RNA interactions: new
genomic technologies and perspectives. Nat. Rev. Genet. 13, 7783 (2012).
5. Keene, J.D. RNA regulons: coordination of post-transcriptional events. Nat. Rev.
Genet. 8, 533543 (2007).
6. Bhatt, D.M. et al. Transcript dynamics of proinammatory genes revealed by
sequence analysis of subcellular RNA fractions. Cell 20, 279290 (2012).
This article and ref. 9 indicate that the expression of inammatory molecules is
conveyed similarly by transcriptomic machinery and splicing machinery.
7. Bjur, E. et al. Distinct translational control in CD4
+
T cell subsets. PLoS Genet.
9, e1003494 (2013).
This study demonstrates differences in the engagement of translation in various
T cell subsets.
8. Hao, S. & Baltimore, D. The stability of mRNA inuences the temporal order of
the induction of genes encoding inammatory molecules. Nat. Immunol. 10,
281288 (2009).
This systems-biology approach conrms the involvement of ARE-mediated events
in the control of inammation.
9. Hao, S. & Baltimore, D. RNA splicing regulates the temporal order of TNF-induced
gene expression. Proc. Natl. Acad. Sci. USA 110, 1193411939 (2013).
10. Wang, I.X. et al. ADAR regulates RNA editing, transcript stability, and gene
expression. Cell Rep. 5, 849860 (2013).
11. Yoon, O.K., Hsu, T.Y., Im, J.H. & Brem, R.B. Genetics and regulatory impact of
alternative polyadenylation in human B-lymphoblastoid cells. PLoS Genet. 8,
e1002882 (2012).
12. Kornblihtt, A.R. et al. Alternative splicing: a pivotal step between eukaryotic
transcription and translation. Nat. Rev. Mol. Cell Biol. 14, 153165 (2013).
13. Cooper, T.A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 20, 777793
(2009).
14. Han, S.P., Tang, Y.H. & Smith, R. Functional diversity of the hnRNPs: past,
present and perspectives. Biochem. J. 430, 379392 (2010).
15. Schoenberg, D.R. & Maquat, L.E. Regulation of cytoplasmic mRNA decay. Nat.
Rev. Genet. 13, 246259 (2012).
16. Fukaya, T. & Tomari, Y. MicroRNAs mediate gene silencing via multiple different
pathways in Drosophila. Mol. Cell 48, 825836 (2012).
17. Gonzlez-Tern, B. et al. Eukaryotic elongation factor 2 controls TNF- translation
in LPS-induced hepatitis. J. Clin. Invest. 123, 164178 (2013).
18. Hay, N. & Sonenberg, N. Upstream and downstream of mTOR. Genes Dev. 18,
19261945 (2004).
19. Anderson, P. & Kedersha, N. RNA granules: post-transcriptional and epigenetic
modulators of gene expression. Nat. Rev. Mol. Cell Biol. 10, 430436
(2009).
20. Mosser, D.M. & Edwards, J.P. Exploring the full spectrum of macrophage activation.
Nat. Rev. Immunol. 8, 958969 (2008).
21. Fukaya, T. & Tomari, Y. MicroRNAs mediate gene silencing via multiple different
pathways in Drosophila. Mol. Cell 48, 825836 (2012).
22. Schroder, K. & Tschopp, J. The inammasomes. Cell 19, 821832 (2010).
23. Takeuchi, O. & Akira, S. Pattern recognition receptors and inammation. Cell 19,
805820 (2010).
24. Burns, K. et al. Inhibition of interleukin 1 receptor/Toll-like receptor signaling
through the alternatively spliced, short form of MyD88 is due to its failure to
recruit IRAK-4. J. Exp. Med. 197, 263268 (2003).
25. De Arras, L. & Alper, S. Limiting of the innate immune response by SF3A-
dependent control of MyD88 alternative mRNA splicing. PLoS Genet. 9, e1003855
(2013).
26. Sarkar, S. et al. RNA-binding protein AUF1 regulates lipopolysaccharide-induced
IL10 expression by activating IB kinase complex in monocytes. Mol. Cell. Biol.
31, 602615 (2011).
27. Qiang, X. et al. Cold-inducible RNA-binding protein (CIRP) triggers inammatory
responses in hemorrhagic shock and sepsis. Nat. Med. 19, 14891495
(2013).
28. Rajayer, S.R. et al. Cold-inducible RNA-binding protein is an important mediator
of alcohol-induced brain inammation. PLoS ONE 8, e79430 (2013).
29. Mitoma, H. et al. The DHX33 RNA helicase senses cytosolic RNA and activates
the NLRP3 inammasome. Immunity 39, 123135 (2013).
30. Nakayama, Y. et al. Role of PKR and Type I IFNs in viral control during primary
and secondary infection. PLoS Pathog. 6, e1000966 (2010).
31. George, C.X. & Samuel, C.E. Host response to polyomavirus infection is modulated
by RNA adenosine deaminase ADAR1 but not by ADAR2. J. Virol. 85, 83388347
(2011).
32. Lloyd, R.E. Regulation of stress granules and P-bodies during RNA virus infection.
Wiley. Interdiscip. Rev. RNA. 4, 317331 (2013).
33. Barnhart, M.D., Moon, S.L., Emch, A.W., Wilusz, C.J. & Wilusz, J. Changes in
cellular mRNA stability, splicing, and polyadenylation through HuR protein
sequestration by a cytoplasmic RNA virus. Cell Rep. 5, 909917 (2013).
34. Iwasaki, H. et al. The IB kinase complex regulates the stability of cytokine-
encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1.
Nat. Immunol. 12, 11671175 (2011).
This study presents the rst distinct connection of the NF-kB pathway to mRNA
decay by regnase-1.
35. Masuda, K. et al. Arid5a controls IL-6 mRNA stability, which contributes to elevation
of IL-6 level in vivo. Proc. Natl. Acad. Sci. USA 110, 94099414 (2013).
36. Brooks, S.A. & Blackshear, P.J. Tristetraprolin (TTP): interactions with mRNA and
proteins, and current thoughts on mechanisms of action. Biochim. Biophys. Acta
1829, 666679 (2013).
37. Suzuki, K. et al. IL-4-Stat6 signaling induces tristetraprolin expression and inhibits
TNF-alpha production in mast cells. J. Exp. Med. 198, 17171727 (2003).
38. Schaljo, B. et al. Tristetraprolin is required for full anti-inammatory response of
murine macrophages to IL-10. J. Immunol. 183, 11971206 (2009).
39. Blanco, F.F., Sanduja, S., Deane, N.G., Blackshear, P.J. & Dixon, D.A. Transforming
growth factor regulates P-body formation through induction of the mRNA decay
factor tristetraprolin. Mol. Cell. Biol. 34, 180195 (2014).
40. Kang, J.G. et al. Zinc nger protein tristetraprolin interacts with CCL3 mRNA and
regulates tissue inammation. J. Immunol. 187, 26962701 (2011).
41. Kratochvill, F. et al. Tristetraprolin-driven regulatory circuit controls quality and
timing of mRNA decay in inammation. Mol. Syst. Biol. 7, 560 (2011).
42. Molle, C. et al. Tristetraprolin regulation of interleukin 23 mRNA stability prevents
a spontaneous inammatory disease. J. Exp. Med. 210, 16751684 (2013).
43. Qiu, L.Q., Stumpo, D.J. & Blackshear, P.J. Myeloid-specic tristetraprolin
deciency in mice results in extreme lipopolysaccharide sensitivity in an otherwise
minimal phenotype. J. Immunol. 188, 51505159 (2012).
44. Taylor, G.A. et al. A pathogenetic role for TNF in the syndrome of cachexia,
arthritis, and autoimmunity resulting from tristetraprolin (TTP) deciency.
Immunity 4, 445454 (1996).
This report is the rst demonstration of an ARE-BP acting as a controller of
inammatory processes.
45. Leppek, K. et al. Roquin promotes constitutive mRNA decay via a conserved class
of stem-loop recognition motifs. Cell Identication of CDEs as the RNA element
of Roquins. 153, 869881 (2013).
46. Maruyama, T. et al. Roquin-2 promotes ubiquitin-mediated degradation of ASK1
to regulate stress responses. Sci. Signal. 7, ra8 (2014).
47. Vinuesa, C.G. et al. A RING-type ubiquitin ligase family member required to repress
follicular helper T cells and autoimmunity. Nature 435, 452458 (2005).
This article identies roquin as a controller of costimulatory programs that act
against systemic autoimmunity.
48. Glasmacher, E. et al. Roquin binds inducible costimulator mRNA and effectors
of mRNA decay to induce microRNA-independent post-transcriptional repression.
Nat. Immunol. 11, 725733 (2010).
49. Pratama, A. et al. Roquin-2 shares functions with its paralog Roquin-1 in the
repression of mRNAs controlling T follicular helper cells and systemic inammation.
Immunity 38, 669680 (2013).
50. Izquierdo, J.M. Heterogeneous ribonucleoprotein C displays a repressor activity
mediated by T-cell intracellular antigen-1-related/like protein to modulate Fas
exon 6 splicing through a mechanism involving Hu antigen R. Nucleic Acids Res.
38, 80018014 (2010).
51. Piecyk, M. et al. TIA-1 is a translational silencer that selectively regulates the
expression of TNF-alpha. EMBO J. 19, 41544163 (2000).
52. Phillips, K., Kedersha, N., Shen, L., Blackshear, P.J. & Anderson, P. Arthritis
suppressor genes TIA-1 and TTP dampen the expression of tumor necrosis factor
, cyclooxygenase 2, and inammatory arthritis. Proc. Natl. Acad. Sci. USA 101,
20112016 (2004).
53. Simarro, M. et al. The translational repressor T-cell intracellular antigen-1 (TIA-1)
is a key modulator of Th2 and Th17 responses driving pulmonary inammation
induced by exposure to house dust mite. Immunol. Lett. 146, 814 (2012).
54. Pont, A.R., Sadri, N., Hsiao, S.J., Smith, S. & Schneider, R.J. mRNA decay factor
AUF1 maintains normal aging, telomere maintenance, and suppression of senescence
by activation of telomerase transcription. Mol. Cell 47, 515 (2012).
n
p
g

2
0
1
4

N
a
t
u
r
e

A
m
e
r
i
c
a
,

I
n
c
.

A
l
l

r
i
g
h
t
s

r
e
s
e
r
v
e
d
.
502 VOLUME 15 NUMBER 6 JUNE 2014 NATURE IMMUNOLOGY
55. White, E.J., Brewer, G. & Wilson, G.M. Post-transcriptional control of gene
expression by AUF1: mechanisms, physiological targets, and regulation. Biochim.
Biophys. Acta 1829, 680688 (2013).
56. Lu, J.Y., Sadri, N. & Schneider, R.J. Endotoxic shock in AUF1 knockout mice
mediated by failure to degrade proinammatory cytokine mRNAs. Genes Dev. 20,
31743184 (2006).
57. Sadri, N. & Schneider, R.J. Auf1/Hnrnpd-decient mice develop pruritic
inammatory skin disease. J. Invest. Dermatol. 129, 657670 (2009).
58. Lin, W.J. et al. Posttranscriptional control of type I interferon genes by KSRP in
the innate immune response against viral infection. Mol. Cell. Biol. 31,
31963207 (2011).
59. Brennan, C.M. & Steitz, J.A. HuR and mRNA stability. Cell. Mol. Life Sci. 58,
266277 (2001).
60. Mukherjee, N. et al. Integrative regulatory mapping indicates that the RNA-binding
protein HuR couples pre-mRNA processing and mRNA stability. Mol. Cell 43,
327339 (2011).
This article exemplies the concomitant functions of an ARE-BP in splicing, decay
and translation.
61. Yiakouvaki, A. et al. Myeloid cell expression of the RNA-binding protein HuR
protects mice from pathologic inammation and colorectal carcinogenesis. J. Clin.
Invest. 122, 4861 (2012).
This study connects the functions of the ARE-BP HuR to the control of macrophage
activation.
62. Srikantan, S., Tominaga, K. & Gorospe, M. Functional interplay between RNA-binding
protein HuR and microRNAs. Curr. Protein Pept. Sci. 13, 372379 (2012).
63. Barker, A. et al. Sequence requirements for RNA binding by HuR and AUF1.
J. Biochem. 151, 423437 (2012).
64. Zhang, J. et al. Macrophage
2
integrin-mediated, HuR-dependent stabilization
of angiogenic factor-encoding mRNAs in inammatory angiogenesis. Am. J. Pathol.
180, 17511760 (2012).
65. Katsanou, V. et al. HuR as a negative posttranscriptional modulator in inammation.
Mol. Cell 19, 777789 (2005).
This article demonstrates the interplay between presumed mRNA activators and mRNA
suppressors toward inammation control during modeled inammatory reactions.
66. Chang, S.H. et al. Antagonistic function of the RNA-binding protein HuR and
miR-200b in post-transcriptional regulation of vascular endothelial growth factor-
A expression and angiogenesis. J. Biol. Chem. 288, 49084921 (2013).
67. Mukhopadhyay, R., Jia, J., Arif, A., Ray, P.S. & Fox, P.L. The GAIT system: a
gatekeeper of inammatory gene expression. Trends Biochem. Sci. 34, 324331
(2009).
68. Arif, A., Chatterjee, P., Moodt, R.A. & Fox, P.L. Heterotrimeric GAIT complex
drives transcript-selective translation inhibition in murine macrophages. Mol. Cell.
Biol. 32, 50465055 (2012).
69. Poddar, D. et al. An extraribosomal function of ribosomal protein L13a in
macrophages resolves inammation. J. Immunol. 190, 36003612 (2013).
70. Weichhart, T. et al. The TSC-mTOR signaling pathway regulates the innate
inammatory response. Immunity 29, 565577 (2008).
This article and ref. 71 demonstrate the rheostatic functions of mTOR in
inammation and infection.
71. Ivanov, S.S. & Roy, C.R. Pathogen signatures activate a ubiquitination pathway
that modulates the function of the metabolic checkpoint kinase mTOR. Nat.
Immunol. 14, 12191228 (2013).
72. Arranz, A. et al. Akt1 and Akt2 protein kinases differentially contribute to
macrophage polarization. Proc. Natl. Acad. Sci. USA 109, 95179522 (2012).
73. Byles, V. et al. The TSC-mTOR pathway regulates macrophage polarization.
Nat. Commun. 4, 2834 (2013).
74. Wang, W. et al. AMP-activated kinase regulates cytoplasmic HuR. Mol. Cell. Biol.
22, 34253436 (2002).
75. Hahn-Windgassen, A. et al. Akt activates the mammalian target of rapamycin
by regulating cellular ATP level and AMPK activity. J. Biol. Chem. 280,
3208132089 (2005).
76. Damgaard, C.K. & Lykke-Andersen, J. Translational coregulation of 5TOP mRNAs
by TIA-1 and TIAR. Genes Dev. 25, 20572068 (2011).
77. Hodson, D.J. et al. Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2
leads to perturbed thymic development and T lymphoblastic leukemia. Nat.
Immunol. 11, 717724 (2010).
This study demonstrates that AMD is active during T cell maturation and is a
determinant of T cell acute lymphoblastic leukemia.
78. Benjamin, D., Schmidlin, M., Min, L., Gross, B. & Moroni, C. BRF1 protein
turnover and mRNA decay activity are regulated by protein kinase B at the same
phosphorylation sites. Mol. Cell. Biol. 26, 94979507 (2006).
79. Bellavia, D. et al. Notch3 and the Notch3-upregulated RNA-binding protein HuD
regulate Ikaros alternative splicing. EMBO J. 26, 16701680 (2007).
80. Frischmeyer-Guerrerio, P.A. et al. Perturbation of thymocyte development in
nonsense-mediated decay (NMD)-decient mice. Proc. Natl. Acad. Sci. USA 108,
1063810643 (2011).
81. Weischenfeldt, J. et al. NMD is essential for hematopoietic stem and progenitor
cells and for eliminating by-products of programmed DNA rearrangements.
Genes Dev. 22, 13811396 (2008).
82. Sulic, S. et al. Inactivation of S6 ribosomal protein gene in T lymphocytes activates
a p53-dependent checkpoint response. Genes Dev. 19, 30703082 (2005).
83. Anderson, S.J. et al. Ablation of ribosomal protein L22 selectively impairs
alphabeta T cell development by activation of a p53-dependent checkpoint.
Immunity 26, 759772 (2007).
84. Mazan-Mamczarz, K. et al. ATM regulates a DNA damage response post-
transcriptional RNA operon in lymphocytes. Blood 117, 24412450 (2011).
85. Papadaki, O. et al. Control of thymic T cell maturation, deletion and egress by
the RNA-binding protein HuR. J. Immunol. 182, 67796788 (2009).
86. Mallory, M.J. et al. Signal- and development-dependent alternative splicing of
LEF1 in T cells is controlled by CELF2. Mol. Cell. Biol. 31, 21842195
(2011).
87. Moulton, V.R., Kyttaris, V.C., Juang, Y.T., Chowdhury, B. & Tsokos, G.C. The RNA-
stabilizing protein HuR regulates the expression of chain of the human T cell
receptor-associated CD3 complex. J. Biol. Chem. 283, 2003720044 (2008).
88. Moulton, V.R., Grammatikos, A.P., Fitzgerald, L.M. & Tsokos, G.C. Splicing factor
SF2/ASF rescues IL-2 production in T cells from systemic lupus erythematosus
patients by activating IL-2 transcription. Proc. Natl. Acad. Sci. USA 110,
18451850 (2013).
89. Wang, H.Y., Xu, X., Ding, J.H., Bermingham, J.R. Jr. & Fu, X.D. SC35 plays a
role in T cell development and alternative splicing of CD45. Mol. Cell 7, 331342
(2001).
90. Gaudreau, M.C., Heyd, F., Bastien, R., Wilhelm, B. & Moroy, T. Alternative splicing
controlled by heterogeneous nuclear ribonucleoprotein L regulates development,
proliferation, and migration of thymic pre-T cells. J. Immunol. 188, 53775388
(2012).
91. Mukherjee, N., Lager, P.J., Friedersdorf, M.B., Thompson, M.A. & Keene, J.D.
Coordinated posttranscriptional mRNA population dynamics during T-cell
activation. Mol. Syst. Biol. 5, 288 (2009).
92. Fedeli, M. et al. Dicer-dependent microRNA pathway controls invariant NKT cell
development. J. Immunol. 183, 25062512 (2009).
93. Liston, A., Lu, L.F., OCarroll, D., Tarakhovsky, A. & Rudensky, A.Y. Dicer-
dependent microRNA pathway safeguards regulatory T cell function. J. Exp. Med.
205, 19932004 (2008).
94. Heyd, F. & Lynch, K.W. Phosphorylation-dependent regulation of PSF by GSK3
controls CD45 alternative splicing. Mol. Cell 40, 126137 (2010).
This study provides a mechanistic model of how alternative splicing occurs in
T cells to instruct activation and memory responses.
95. Wu, Z. et al. Memory T cell RNA rearrangement programmed by heterogeneous
nuclear ribonucleoprotein hnRNPLL. Immunity 19, 863875 (2008).
This study provides an example of subset discrimination by PTR.
96. Uehata, T. et al. Malt1-induced cleavage of regnase-1 in CD4
+
helper T cells
regulates immune activation. Cell 153, 10361049 (2013).
97. Vogel, K.U. et al. Roquin paralogs 1 and 2 redundantly repress the Icos and Ox40
costimulator mRNAs and control follicular helper T cell differentiation. Immunity
38, 655668 (2013).
98. Vavassori, S. & Covey, L.R. Post-transcriptional regulation in lymphocytes: the
case of CD154. RNA Biol. 6, 259265 (2009).
99. Li, M. et al. MCPIP1 down-regulates IL-2 expression through an ARE-independent
pathway. PLoS ONE 7, e49841 (2012).
100. Shi, L., Godfrey, W.R., Lin, J., Zhao, G. & Kao, P.N. NF90 regulates inducible
IL-2 gene expression in T cells. J. Exp. Med. 204, 971977 (2007).
101. Chen, J. et al. Posttranscriptional gene regulation of IL-17 by the RNA-binding
protein HuR is required for initiation of experimental autoimmune encephalomyelitis.
J. Immunol. 191, 54415450 (2013).
102. Corrionero, A., Raker, V.A., Izquierdo, J.M. & Valcarcel, J. Strict 3 splice site
sequence requirements for U2 snRNP recruitment after U2AF binding underlie
a genetic defect leading to autoimmune disease. RNA 17, 401411 (2011).
103. Oh, H. et al. hnRNP A1 contacts exon 5 to promote exon 6 inclusion of apoptotic
Fas gene. Apoptosis 18, 825835 (2013).
104. von Roretz, C. et al. Apoptotic-induced cleavage shifts HuR from being a promoter
of survival to an activator of caspase-mediated apoptosis. Cell Death Differ. 20,
154168 (2013).
105. Izquierdo, J.M. Fas splicing regulation during early apoptosis is linked to caspase-
mediated cleavage of U2AF65. Mol. Biol. Cell 19, 32993307 (2008).
106. Zheng, Y., Delgoffe, G.M., Meyer, C.F., Chan, W. & Powell, J.D. Anergic T cells
are metabolically anergic. J. Immunol. 183, 60956101 (2009).
107. Villarino, A.V. et al. Posttranscriptional silencing of effector cytokine mRNA
underlies the anergic phenotype of self-reactive T cells. Immunity 34, 5060
(2011).
108. Meisner, N.C. et al. Identication and mechanistic characterization of
low-molecular-weight inhibitors for HuR. Nat. Chem. Biol. 3, 508515 (2007).
109. Filipovska, A. & Rackham, O. Designer RNA-binding proteins: New tools for
manipulating the transcriptome. RNA Biol. 8, 978983 (2011).
110. Gruber, A.R., Fallmann, J., Kratochvill, F., Kovarik, P. & Hofacker, I.L. AREsite:
a database for the comprehensive investigation of AU-rich elements. Nucleic Acids
Res. 39, D66D69 (2011).
111. Bakheet, T., Williams, B.R. & Khabar, K.S. ARED 3.0: the large and diverse
AU-rich transcriptome. Nucleic Acids Res. 34, D111D114 (2006).
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