Beruflich Dokumente
Kultur Dokumente
Introduction
MicroRNAs (miRNA) comprise a class of short non- diseases [12] and carcinogenesis [13]. The biogenesis
coding RNAs with 1825 nucleotides in length that are and RNAi functions of miRNA (i.e. how miRNAs are
found in animal and plant cells. In 1993, the rst miR- generated and processed into a mature form, and how
NAs were recognized in Caenorhabditis elegans by Lee they regulate gene expression) have been intensively
et al. [1]. In 2001, various small regulatory RNAs were investigated and well-described [10]. Furthermore,
discovered in plants and mammals [24] and desig- developments in miRNA-related technologies, such as
nated microRNA [5]. Currently, 1100 human miR- miRNA expression proling and synthetic oligoRNA,
NAs are registered in the miRBase database (release have contributed to the identication of miRNAs
16, September 2010) [69]. miRNAs are involved in involved in a number of physiological and pathological
RNA interference (RNAi) machinery to regulate gene phenotypes. However, some questions remain largely
expression post-transcriptionally, and they contribute unanswered, such as how miRNA expression is con-
to diverse physiological and pathophysiological func- trolled and which genes are regulated by each miRNA.
tions, including the regulation of developmental timing Recently, accumulating studies have shown that a sub-
and pattern formation [2], restriction of differentiation group of miRNAs is regulated epigenetically. Although
potential [10], cell signaling [11], cardiovascular epigenetics and miRNAs have been frequently
Abbreviations
DGCR8, DiGeorge syndrome critical region gene 8; DNMT, DNA methyltransferase; EMT, epithelialmesenchymal transition; HDAC, histone
deacetylase; miRNA, microRNA; NF-jB, nuclear factor kappa B; PRC, polycomb repressor complex; RISC, RNA-induced silencer complex;
RLC, RISC-loading complex; RNAi, RNA interference; SNP, single nucleotide polymorphism; TGIF2, TGFb-inducing factor 2; VNTR, variable
nucleotide tandem repeat; YY1, Yin Yang 1.
1598 FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS
F. Sato et al. MicroRNAs and epigenetics
reviewed [1418], few reviews have focused upon the X mental retardation-related protein 1 [23]. Thus,
relationship between epigenetics and miRNA. In the molecular mechanisms of the RISC in translational
present minireview, we illustrate the current knowledge regulation remain to be claried. At the same time,
regarding the epigeneticsmiRNA regulatory networks turnover of miRNAs is mediated by the XRN2 gene
aiming to provide biological insights for a wide range in C. elegans [24]. However, the mechanisms underly-
of biomedical researchers. ing miRNA turnover in human cells also remain
unclear.
Biogenesis and RNAi functions of
miRNAs Epigenetically-regulated miRNAs
As illustrated in Fig. 1, in the nucleus, mainly RNA As described above, the biogenesis of miRNA has been
polymerase II initially transcribes miRNAs into long intensively studied and is well-described. However, the
segments of coding or noncoding RNA, known as regulation of miRNA expression remains largely
pri-miRNAs, which are usually capped and polyaden- unclear. In early studies, promoter regions had been
ylated. Portions in the pri-miRNAs measuring determined for only a small portion of miRNAs.
approximately 70100 nucleotides in length and con- Although several in silico studies attempted to predict
taining a stem-loop, are captured and extracted from the promoter regions of miRNAs [2527], most of
pri-miRNAs by a complex containing RNase type III, these predicted miRNA promoters were not conrmed
Drosha and the dsRNA binding protein DiGeorge in wet-laboratory experiments.
syndrome critical region gene 8 (DGCR8) (also called miRNAs can be classied as either intragenic and
Pasha) [19]. These short stem-loop-shaped RNAs are intergenic, according to whether the miRNA is local-
called pre-miRNAs, and the protein complex of ized in a genome region transcribed by a gene, or not.
RNase, Drosha and DGCR8 is known as the micro- Our in silico analysis (see Materials and methods)
processor complex. Pre-miRNAs form a complex with revealed that, among 939 miRNAs, 293 (31.2%) of
exportin-5 and RAN-GTP, and are then exported miRNAs were intergenic, whereas 317 (44.4%), 119
from the nucleus to the cytoplasm. The pre-miRNAs (12.7%) and 110 (11.7%) were overlapped by RNA
are further processed to a double-stranded miRNA transcripts in the same, opposite and both directions,
duplex by a dsRNase type III, Dicer. This double- respectively. Localization of promoters for intergenic
stranded miRNA duplex is incorporated into a RNA- and inversely-directed intragenic miRNAs is largely
induced silencer complex (RISC)-loading complex unknown, whereas promoters for overlapping primary
(RLC) in an ATP-dependent manner [20]. Next, one genes are considered to be promoters for the intragenic
strand (the passenger strand) of the miRNA is miRNAs that are localized in the same direction as the
removed from the RLC, whereas the other strand (the primary gene. However, some studies have identied
guide strand) remains in the complex to form a that an independent promoter within the intron in
mature RNA-induced silencer complex (mature RISC) which a miRNA is embedded can also regulate miR-
and serves as a template for capturing target mRNAs. NA expression [28]. Additionally, as shown in one
Under most conditions, the mature RISC represses study [29], a single member of a miRNA cluster,
gene expression post-transcriptionally. For highly although ordinarily expressed from the same pri-miR-
complementary target mRNAs, the mature RISC NA, can alternatively be regulated independently by its
complex cleaves target mRNAs via a catalytic domain own promoter in certain scenarios. Furthermore, the
(RNase III domain) of Argonaute proteins, a core total amount of miRNAs contained within a given
component of the RISC complex, and degrades them quantity of total RNA can be reduced in cancer cells
by the SKI complex and XRN1 [21]. For partially and rapidly proliferating cells [13,30], a nding for
complementary targets, the RISC complex decaps and which the underlying mechanism is still unknown.
deadenylates target mRNAs via the DCP1-DCP2 and Thus, the means by which miRNA expression is regu-
CAF1-CCR4-NOT complexes, respectively, to reduce lated appears somewhat complicated.
the stability of the target mRNAs [22]. In addition, Recently, Saito et al. [29] established that the expres-
the RISC complex also represses the translation of sion of miR-127 is regulated epigenetically. In their
target genes under most conditions. However, not all study, pharmacological unmasking of epigenetically
miRNAs work in translational repression. Under silenced miRNAs activated 17 of 313 miRNAs investi-
serum-starved conditions, miR-369-3 activates transla- gated in the bladder cancer cell line T24 and the nor-
tion of tumor necrosis factor-a by binding to AU-rich mal broblast cell line LD419. The gene for miR-127
elements in the 3 UTR of the transcript with fragile was upregulated the most in epigenetically unmasked
FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS 1599
MicroRNAs and epigenetics F. Sato et al.
Fig. 1. EpigeneticsmiRNA regulatory circuit. Epigenetics and miRNAs regulate whole gene expression pattern transcriptionally and post-
transcriptionally, respectively. At the same time, epigenetics and miRNAs controll each other to form a regulatory circuit and to maintain nor-
mal physiological functions. A disruption of this regulatory circuit may cause various diseases, such as cardiovascular diseases and cancers.
PABP, poly(A) binding protein; TF, transcriptional factors; TRBP, Tar RNA binding protein.
cancer cells. DNA methylation level and histone modi- acute lymphoblastic leukemia [3134]. In breast cancer,
cation status at identied promoter regions of the miR-9-1 locus is highly methylated not only in
miR-127 correlated signicantly with mature miR-127 invasive ductal carcinoma, but also in ductal carci-
expression. Subsequent to this initial report, the num- noma in situ and the intraductal component of invasive
ber of studies documenting the epigenetic regulation of ductal carcinoma [34]. In addition, an in vitro experi-
miRNAs has increased dramatically (Table 1). We mental study showed that xenoestrogen exposure may
summarize the ndings regarding some of the more induce aberrant epigenetic patterns at various miRNA
intensively studied miRNAs for which expression is gene loci, including miR-9-3 [35]. These ndings sug-
regulated by epigenetic mechanisms. gest that epigenetic silencing of miR-9 loci constitutes
an early event in breast carcinogenesis. Furthermore,
the miR-9 DNA methylation signature is correlated
miR-9
with cancer metastasis [33]. Target genes of mature
miR-9 is expressed from three genomic loci, miR-9-1, miR-9 responsible for carcinogenesis and cancer metas-
miR-9-2 and miR-9-3, all of which are associated with tasis remain largely unknown. However, a recent study
CpG islands. Hypermethylation of miR-9 loci is demonstrated that mature miR-9 targets nuclear factor
observed in various malignant tissues, including breast, kappa B (NF-jB), which is overexpressed in a number
lung, colon, head and neck cancers, melanoma and of different cancers [36].
1600 FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS
F. Sato et al. MicroRNAs and epigenetics
Table 1. Epigenetically-regulated miRNAs. The numbers in the binding sites column represent the distance (bp) between the stop codon
and binding sites of seed sequences in the miRNAs. The letters c and p with respect to miRNA binding site numbers indicate that the
miRNA binding sites are the conserved region and poorly conserved region among vertebrates, according to the TargetScan database
(http://www.targetscan.org ).
miRNA genes Inter- intra genic Locus Host gene Target genes Binding sites References
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MicroRNAs and epigenetics F. Sato et al.
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F. Sato et al. MicroRNAs and epigenetics
activation. In addition, several isoforms of DNA methy- as a result of polycomb-mediated modication in epi-
transferase (DNMT)3b are targeted by miR-148 within genetic patterns.
their coding region (described in detail below). There-
fore, although being targeted epigenetically, miR-148
let-7a-3
may itself exert effects on DNA methylation in cells.
Epigenetic control of let-7a-3 expression was discovered
by a comparison between parent and DNMT1-3B dou-
The miR-200 family
ble-knockout HCT116 colon cancer cells [55]. The let-
The miR-200 family consists of miR-141, 200a b c and 7a-3 locus is generally methylated in normal tissues but
429, which share similar seed sequences. miRs- hypomethylated in some types of cancers, such as colon
141 200c and miRs-200a b 429 comprise multicistronic and lung cancer [55]. Methylation levels of let-7a-3
miRs whose genomic loci are located in close proximity correlate inversely with let-7a-3 pri-miRNA expression
to each other. Several studies have established that the levels [55]. However, the effect of let-7a-3 methylation
miR-200 family is involved in epithelialmesenchymal status on mature let-7a expression level is unclear
transition (EMT). EMT occurrence in cancer cells com- because levels of mature let-7a reect the expression of
prises a phenomenon in which these cells obtain pheno- three let-7a genes, let-7a-1, let-7a-2 and let-7a-3.
types characteristic of mesenchymal cells, such as Indeed, let-7a-3 methylation levels in ovarian cancer
spindle-shaped morphology, activated cell motility and correlate with mature let-7a levels. In the context of
invasiveness. Therefore, EMT research is important for miRNA function, let-7a-3 has oncogenic potential. The
understanding the molecular mechanisms underlying introduction of let-7a-3 enhanced the colony-forming
the malignant potential of cancer cells. Recently, Well- ability of A549 lung adenocarcinoma cells. In addition,
ner et al. [51] demonstrated that an EMT activator, let-7a may regulate IGF-II via targeting of IGF2-bind-
ZEB1, suppresses miR-200c, whereas miR-200c targets ing proteins (IMP-1 and 2). Methylation levels at the
ZEB1. This nding suggests that miR200c and ZEB1 let-7a-3 locus correlate inversely with IGF-II levels,
form a feedback loop regulatory mechanism that main- and are also linked to the survival of ovarian cancer
tains EMT [51]. Additional studies showed that both patients. In general, the let-7 family is considered to
the miR-141 200c [52,53] and miR-200a b 429 [53] comprise tumor suppressor miRNAs [5658]. Diversity
clusters are epigenetically regulated. Thus, EMT could in functions among let-7 family members may cause
conceivably be regulated by epigenetic events targeting apparently contradictory observations.
the miR-200 family. Table 1 shows that miR-
200a b 429 binding sites in the 3 UTR of ZEB2 have
Imprinting and miRNAs
several single nucleotide polymorphism (SNP) sites.
However, to date, no study is available demonstrating Genomic imprinting is an epigenetic process by which
the clinical signicance of these SNPs. a small proportion of genes (< 1% of all genes in
mammals) are expressed in a parent-of-origin-specic
manner [59]. In genomic imprinting, DNA methylation
miR-203
and histone modication regulate monoallelic expres-
In hematopoietic malignancies, 12% of miRNAs are sion. These epigenetic patterns are established in germ-
located in fragile genomic regions that encompass only line cells, and are inherited through somatic cells. For
seven megabases (0.2% of whole genome). miR-203 is example, at the well-investigated IGF2 H19 locus, the
one of these regions, and it targets ABL1 and BCR- IGF2 gene is expressed from the paternal allele,
ABL1, an oncogenic fusion gene generated by the Phil- whereas the H19 gene is expressed from the maternal
adelphia translocation [54]. Epigenetic silencing of allele. Abnormal genomic imprinting is associated with
miR-203 enhances activation of the BCR-ABL1 fusion several diseases. Some inheritable disorders, such as
gene, resulting in an elevation of tumor cell growth PraderWilli syndrome and Angelman syndrome, are
rate. Epigenetic inactivation of miR-203 is frequently caused by aberrant imprinting. Furthermore, the phe-
observed in other types of malignancies, including oral nomenon known as loss of imprinting, in which the
cancer, hepatocellular carcinoma, etc. [40,48]. Another normally inactivated allele becomes reactivated as a
candidate target gene of miR-203 is Bmi-1, a member result of hypomethylation or histone abnormalities, is
of the polycomb repressor complex 1 [51], which is a frequently observed in cancers [60].
histone modier complex regulating gene expression. Several miRNAs are located within imprinting-asso-
Introduction of ectopic miR-203 into cancer cells ciated regions, including miR-296 and miR-298 at the
induces apoptosis and represses cell growth [48], possibly GNAS NESP locus, miR-483 and miR-675 at the
FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS 1603
MicroRNAs and epigenetics F. Sato et al.
IGF2 H19 locus, and miR-335, miR-29a and miR-29b corresponding normal tissues, with the highest EZH2
at the MEST KLF14 locus [61]. However, the imprint- levels correlating with advanced disease stages and
ing and expression status of such miRNAs remains lar- poor prognosis. In some cases, EZH2 overabundance
gely unknown. is paralleled by DNA amplication of the gene [63]. A
second mechanism of EZH2 overexpression is post-
transcriptional regulation by miRNAs. EZH2 expres-
miRNAs regulating epigenetic pathway-
sion is controlled by miR-26a, miR-101, miR-205 and
related genes
miR-214 [6468]. Cancer-specic downregulation of
miRNAs themselves are capable of targeting genes that these miRNAs results in overexpression of EZH2.
control epigenetic pathways. As shown in Table 2, var-
ious miRNAs may control chromatin structure by reg-
Bmi-1
ulating histone modier molecules, such as polycomb
group-related genes and histone deacetylase (HDAC). In a subsequent step, PRC2 and the H3K27 methyla-
The polycomb group proteins are transcriptional tion recruit PRC1 binding to chromatin to maintain
repressors that regulate lineage choices occurring dur- stable gene silencing. PRC1 catalyzes ubiquitinylation
ing development and differentiation. There are two of histone H2A and remains anchored to chromatin
polycomb repressor complexes (PRCs), PRC1 and after its modication by the cooperation between
PRC2. The PRC1 core complex contains Cbx, Mph, PRC2 and PRC1. Bmi-1, a component of PRC1, plays
Ring, Bmi-1 and Me118, whereas the PCR2 core com- an important role in gene silencing and is overexpres-
plex consists of Ezh2, Suz12 and Eed [62]. In an initial sed in several cancers, including nonsmall cell lung
step, PRC2 initiates silencing by catalyzing histone H3 cancer and colorectal cancer. Bmi-1 overexpression
Lysine-27 (H3K27) methylation. Recent studies have contributes to self-renewal in some types of cancer
advanced our understanding of the means by which stem cells, including those of the pancreas [69], breast
epigenomic dysregulation potentially contributes to [70], brain [71] and white blood cell lineage [72].
various diseases. Downregulation of miR-128 in glioma tissue causes
elevated expression of Bmi-1, which consequently
enhances self-renewal of the cancer stem cell popula-
EZH2
tion via chromatin remodeling [71]. In addition,
Expression levels of EZH2, a conserved catalytic sub- recently, Wellner et al. [51] recently demonstrated that
unit within PRC2, are elevated in cancers relative to an EMT-related miRNA, miR-203, targets Bmi-1. This
nding suggests that EMT mechanisms include the reg-
Table 2. miRNAs targeting genes that are involved in epigenetic ulation of epigenetic regulators by miRNAs.
regulatory pathways. The letters c and p with respect to miRNA
binding site numbers indicate that the miRNA binding sites are the
conserved region and poorly conserved region among verte- Yin Yang 1 (YY1)
brates, according to the TargetScan database (http://www.target-
scan.org ). YY1 is a transcription factor that contributes to vari-
ous biological processes, including embryogenesis, the
Target genes miRNAs Binding sites References cell cycle, apoptosis, inammation, carcinogenesis and
EZH2 miR-26a 249c [6466,68] epigenetics. In the epigenetic context, YY1 is a PRC-
miR101 58p, 113ca binding protein that recruits PRC2 and HDAC to a
miR-214 172p specic genome locus to induce chromatin remodeling.
Bmi1 miR-128 481c [51,71] NF-jB-mediated miR-29b c repression reactivates
miR-203 1443c YY1 protein expression from post-transcriptional
YY1 miR-29b 774c [73]
silencing induced by these two miRs. In addition, YY1
HDAC1 miR-449 459p [94]
HDAC4 miR-1 2333c, 3513ca, 3546ca [95]
also represses miR-29b c. This NF-jB-miR-29-YY1
DNMT3A miR-29 855c [79,80] regulatory circuit is also involved in myogenesis and
DNMT3B miR-29 1202c [7981] tumorigenesis, probably via chromatin remodeling [73].
miR-148 1424c and 2384c in
coding region
MeCP2 miR-132 6886c [96] HDACs
a
SNPs are located within the miRNA binding sites (not only the In human cells, PRC2 physically associates with
seed sequence regions, but also an approximately 23 bp region), HDACs 1 and 2 [74]. If H3K27 is pre-acetylated,
which may affect the affinity of miRNA with the binding sites. methylation at an H3K27 residue by PRC2 may
1604 FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS
F. Sato et al. MicroRNAs and epigenetics
require deacetylation by HDACs. Thus, both acetyla- indicates that miRNAs can regulate gene expression
tion and deacetylation of histones is involved in the uniquely among different gene isoforms by targeting a
transcriptional regulation of target genes. In addition, coding exon.
recent studies have demonstrated that HDACs target As described above and illustrated in Fig. 1, a num-
not only histone proteins, but also nonhistone pro- ber of miRNAs are regulated epigenetically. At the
teins: p53 and Myo-D are targeted by HDAC-1, same time, a variety of miRNAs regulate epigenetic
whereas Bcl-6, Stat3 and YY1 are targeted by HDAC- pathway-related molecules, most notably polycomb
2. By regulating both histone and nonhistone proteins, group proteins, HDACs and DNA methyltransferases.
HDACs 1 and 2, classied as class I HDACs, are Taken together, post-transcriptional regulation by
implicated in cell proliferation, apoptosis and chemore- miRNAs and transcriptional control machinery by epi-
sistance. The expression of HDACs 1 and 2 is elevated genetics cooperate with each other to organize the
in various cancers [75]. However, the mechanism of whole gene expression prole and to maintain physio-
HDAC overexpression remains unclear. Dysregulation logical functions in cells. Once this miRNAepigenetics
of miRNAs may contribute to the overexpression of regulatory circuit is disrupted, normal physiological
HDACs observed in cancer cells. In prostate cancer, functions are interfered with, contributing to various
HDAC-1 is a direct target of miR-449a, and downre- disease processes. A comprehensive elucidation of this
gulation of miR-449a causes overexpression of regulatory network still remains to be completed.
HDAC-1. Thus, aberrant expression of miR-449a may Therefore, continual studies on dysregulation of the
contribute to the abnormal epigenetic patterns occur- miRNAepigenetics regulatory circuitry would be
ring in prostate cancer. highly benecial for deepening our understanding of
diseases.
DNMT 3A and 3B
Materials and methods
DNMTs 1, 3A, and 3B are key DNA methylation
enzymes. Recent studies in human cells have demon-
Typing of miRNAs by positional relationship to
strated that PRC2 and DNMTs are physically and
mRNA transcripts
functionally linked [76], and that DNMT-mediated
DNA methylation lies downstream of PRC2-mediated Information about the localization and strand direction of
H3K27 methylation [76,77]. Thus, these two key epige- 939 miRNAs, 35245 Refseq genes and 283708 mRNAs
netic repression systems cooperate in the silencing of was retrieved from the genome browser of University of
target genes. Dysregulation of DNMTs has been California Santa Cruz [82] on 31 January 2011. Because the
linked to various disease processes, including cancer original data table of refseq genes included miRNA genes,
and congenital disorders. These DNMTs are predicted these miRNA data were excluded from the Refseq data set.
to be potential targets of miRNAs [78]. Fabbri et al. Using matlab, version 2011a (Mathworks, Natick, MA,
[79] showed that members of the miR-29 family USA), we compared localization and strand direction
between miRNAs and transcripts (Refseq genes and
directly target DNMTs 3A and 3B, and that exoge-
mRNAs). Intragenic and intergenic miRNAs were dened
nous miR-29 species can reactivate methylation-
by whether the miRNAs are overlapped by transcripts, or
silenced tumor suppressor genes by restoring normal
not, respectively. In addition, intragenic miRNAs were
patterns of DNA methylation in nonsmall cell lung
divided into three different types, which are overlapped by
cancer cells. Another study reported similar ndings in
transcripts only in the same strand direction, only in oppo-
acute myeloid leukemia [80]. Thus, miRNAs may be site direction, or in both directions, respectively. The com-
involved in the establishment and or maintenance of plete results of this typing analysis are provided in
DNA methylation. In addition, some isoforms of Table S1.
DNMT3B are targeted at the penultimate exon of their
coding regions by miR-148 [81]. DNMT3B exhibits
several splicing isoforms, of which DNMT3B-1 and -3 References
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Supporting information
oRNA miR-196a-2 and breast cancer: a genetic and epi- The following supplementary material is available:
genetic association study and functional analysis. Table S1. miRNAs and overlapping transcripts.
Cancer Res 69, 59705977. This supplementary material can be found in the
90 Kim S, Lee UJ, Kim MN, Lee EJ, Kim JY, Lee MY, online version of this article.
Choung S, Kim YJ & Choi YC (2008) MicroRNA Please note: As a service to our authors and readers,
miR-199a* regulates the MET proto-oncogene and the
this journal provides supporting information supplied
downstream extracellular signal-regulated kinase 2
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(ERK2). J Biol Chem 283, 1815818166.
may be re-organized for online delivery, but are not
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copy-edited or typeset. Technical support issues arising
YH, Tsuchiya KD, Washington MK, Paraskeva C,
from supporting information (other than missing les)
Willson JK, Kaz AM et al. (2008) Epigenetic silencing
of the intronic microRNA hsa-miR-342 and its host
should be addressed to the authors.
FEBS Journal 278 (2011) 15981609 2011 The Authors Journal compilation 2011 FEBS 1609