RNA EDITING

RNA editing
Some mRNA are edited before translation.

This can involve the addition, deletion, or

alteration of the nucleotides in the RNA that affect the meaning of the transcript when it is translated. Addition and deletion mostly occurs in the mitochondria or chloroplast genomes. A special class of the RNA with sequence complementary to the edited mRNA called guide RNAs (gRNAs) act as template.

 RNA editing occurs by two distinct mechanisms A. Insertion/Deleting edition: these alterations are

mediated by guide RNA molecules B. Substitution editing: these alterations are catalysed by enzymes that recognise a specific target sequence of nucleotides.
1. Cytidine deaminase:

2. Adenosine deaminase:

Editing by insertion
Cytochrome oxidase subunit II in protist

mitochondria (Tryanosoma brucei.). A post transcriptional editing process inserts four U residues that shift the translational reading frame.

1. gRNAs are found in the kinetoplastids. 2. The gRNA forms part of the editosome and contains sequences that hybridize to matching sequences in the mRNA. 3. This RNA editing is mediated by a guide RNA (gRNA) that pairs with the mRNA, cleaving it, adding the Us and ligating it.

 If deamination of the A residue forming I (ionosine) in the

A to I editing

coding region of the mRNA, I is recognised as G during translation. The enzymes that catalyse A-I editing are members of a family of adenosine deaminase that act on RNA ADAR genes Three mammalian (ADARs). give rise to four known isoforms
1. 2. 3. 4. ADAR1p150 ADAR1p110 ADAR2 ADAR3

 The enzymes that catalyse C to U

C to U editing

are called cytosine deaminases that interact on RNA (CDARs) All ADARs and CDARs belong to the super family RNA dependent deaminases that also includes tRNA-specific deaminases (ADATs) or Activation induced deaminase(AID). All 3 types of deaminases (zinc coordinating catalytic domain) likely arose from an ancestral cytidine deaminase via acquisition of RNAbinding domains. The common feature is that the deaminase domain of the conserved residues that are

 A to I editing occurs in more

RNAs than does C to U editing. Most of the A to I editing occurs in nervous system. Examples: transcripts of
Ionotropic glutamate

receptors (GluRs) family Serotonin receptor subunit 2C (5-HT2CR)

In the above two the

deamination leads to the change in the single aminoacid in the resulting protein.

Significance of RNA editing

Transcript of GluA2 (GluR2) subunit of (2-amino-

3hydroxy 5 methyl 4 isoxazolepropionic acid) AMPA receptor. The editing for this mRNA occurs at sites termed Q/R (glutamine for arginine) and R/G (arginine for glycine) sites. Q/R- exon 11 and resides within the second transmembrane domain (TMII) of the protein. R/G- exon 13 and downstream intron. Edited transcript R/G: splicing favors inclusion of exon 15 over that of exon 14. Edited transcript Q/R: profound effect on calcium permeability of the resulting AMPA receptor.

 Calcium permeability of all AMPA receptor

isoforms is controlled by GluA2 subunit Unedited GluA2: the presence of Q residue allows Ca2+ permeability whereas the edited amino acid does not. Almost all the GluA2 present in the human brain is edited. The importance of GluA2 mRNA editing can be demonstrated by the phenotype of ADAR2 knockout mice. These mice have significantly reduced editing of the Q/R site which causes them to be highly seizure prone and they die within 3 weeks of birth.

C to U editing
It requires ssRNA template, cofactors that

assemble into a functional complex referred to as a holoenzyme or editosome. The functional complex includes a minimal core composed of APOBEC-1, the catalytic deaminase and competence factor, APOBEC-1 complementation factor (ACF) that function as an adaptor protein by binding both the deaminase and mRNA substrate.

 First report in mRNA encoding apolipoproten B

C to U editing

(apoB). Editing of the apoB mRNA changes CAA/UAA translational stop codon leading to premature termination of protein synthesis. Full length apoB is translated in liver called apoB100 (VLDL particles produced and secreted by the liver). Edited mRNA is in intestinal enterocytes resulting in the generation of apoB-48 (associated with chylomicrons and released into the lymphatic system)

 Other example include site specific deamination

of CGA to UGA codon in neurofibromatosis type 1 (NF1) mRNA. NF1 mRNA encodes a protein neurofibromin. Editing results in introduction of the stop codon at 3916 that results in truncated NF1 protein which loss critical domain involved in GTPase activation which is found in peripheral nerve sheath tumors from patients with type1 neurofibromatosis.

 Another example NAT1 (also called p97, DAP5, elF4G2) which is a

translation repressor that may be involved in repression of global translation. In experimental animals when APOBEC-1 is over expressed NAT1 underwent C to U editing at multiple sites and created stop codons that in turn reduced the abundance of the NAT1 protein. NAT1-negative embryos die during gastrulation, NAT 1 has crucial role in early embryogenesis. The mechanism by which elevated APOBEC-1 activity leads to dysplasia and cancer is not yet refined.

 The adenosine deaminases that act on RNA (ADARs)

which promote A to I are common in primates transcripts. 90 percent of the editing occurs in the short interspersed elements (SINES) called Alu elements. There are about million 300bp Alu elements in human DNA. these are concentrated near protein coding genes, often appearing in introns and untranslated regions at the 3 and 5 ends of transcripts. The ADAR enzymes bind to and promote A to I editing only in duplex region of RNA. Some of the editing affects the coding sequences of genes. Defects in the ADAR function have been associated with a variety of human neurological conditions including amyotrophic lateral sclerosis (ALS),

 THE END

Clinical significance of Alternative and Aberrant splicing

Presence of introns can protect the genetic

makeup of an organism from genetic damage by outside influences such as chemical and radiation. An aditionally important function of introns is to allow alternative splicing to occur thereby increasing the genetic diversity of the genome without increasing the overall number of genes Alternative splicing can occur either at specific developmental stages or at different cell types.

miRN A
Involved in gene regulation. 22 nts long & complementary

to particular region of mRNAs They regulate mRNA by cleaving the mRNA or suppressing its translation Upto 1% of the human genome encode miRNA. 1/3 of mRNA in humans are targeted by miRNA. To protect form invading RNA viruses. To control the activity of transposons. In formation of heterochromatin (undefined).