mrna EDITING Watson et al., BIOLOGIA MOLECOLARE DEL GENE, Zanichelli editore S.p.A. Copyright 2005

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1 mrna EDITING

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3 mrna EDITING

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5 The number of A to I sites in the human transcriptome >15;000 the vast majority of these sites occurring in Alu repeats 6

6 glutamate receptor serotonin (5-HT) receptor-2c Ion-channel receptors that contain the edited GluR2 subunit are impermeable to Ca2+ the potency of the agonist-stimulated G-protein coupling activity of the fully edited receptor isoform (Val-Gly-Val) is reduced by 20-fold compared with the unedited receptor

7 RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1 Whole transcriptome sequence analysis from various human tissues identified over 200 possible A to I editing sites in non repeat sequences, including a site predicted to cause recoding in the mrna for the DNA repair enzyme NEIL1 (lysine 242 AAA codon edited to AIA codon for arginine) NEIL1 plays a key role in the initiation of base excision repair of oxidized base lesions by catalyzing the cleavage of the N-glycosidic linkage to the 2 -deoxyribose

8 Known substrates for the base excision repair glycosylase NEIL1.

9 NEIL1 mrna sequencing mrna Editing A to G AAA to AIA (AGA) R to K

10 (A) Superposition of human NEIL1 structure (dark gray) with that of E. coli Fpg (green) bound to 8-oxoguanine-containing DNA. Red open arrow indicates lesion recognition loop of Fpg. (B) B) Sequence alignment of Fpg/Nei family of DNA repair glycosylases indicating the position of the hneil1 recoding site and lesion recognition loop. Editing of the pre-mrna for the DNA repair enzyme NEIL1 causes a lysine to arginine change in the lesion recognition loop of the protein.

11 Three human ADAR (adenosine deaminase acting on RNA)-family members cytoplasm nucleoplasm and nucleolus ADAR1L is detected mainly in the, whereas ADAR1S localizes in the s40,44,45. ADAR2 localizes predominantly in the nucleolus44,46

12 Sequence of products from reaction of 1 µm human ADAR central A and third A of K242 codon Editing of the pre-mrna for the DNA repair enzyme NEIL1 causes a lysine to arginine change in the lesion recognition loop of the protein.

13 NEIL1 editing in response to IFN-α. (Left) Sequence at the recoding site in NEIL1 cdna from U87 human glioblastoma cells cultured in the absence of IFN-α. (Right) NEIL1 cdna sequence from U87 cells treated with IFN-α.

14 Known substrates for the base excision repair glycosylase NEIL1. thymine glycol guanidinohydantoin

15 The two forms of NEIL1 have distinct enzymatic properties. The edited form removes thymine glycol from duplex DNA 30 times more slowly than the form encoded in the genome, whereas editing enhances repair of the guanidinohydantoin lesion by NEIL1.

16 ADAR1-catalyzed editing of the NEIL1 mrna causes the genomically encoded AAA lysine codon, corresponding to amino acid position 242 in the lesion recognition loop of the protein, to be converted to a codon for arginine. The two forms of the NEIL1 protein (edited and unedited) have distinct enzymatic properties with changes observed for both glycosylase activity and lesion specificity. Editing occurs in a hairpin duplex structure formed near the intron 5/exon 6 boundary in the NEIL1pre-mRNA. Furthermore, NEIL1 mrna recoding is regulated extracellularly by interferon, as predicted for an ADAR1-catalyzed reaction. These results suggest a unique regulatory mechanism for DNA repair and extend our understanding of the impact of RNA editing.

17 Regulation of microrna processing and expression by RNA editing

18 Extensive A I RNA editing of non-coding repeat sequences

19 Extensive A I RNA editing of non-coding repeat sequences

20 RNA EDITING RNA editing in trypanosomes creates functional mitochondrial mrnas by extensive uridylate (U) insertion and deletion The precursors of messenger RNAs (pre-mrnas) have their coding information remodeled by RNA editing Pre-mRNAs are encoded in the maxicircle DNA RNA editing creates initiation and termination codons, corrects frameshifts and even builds entire open-reading frames from nonsense sequences. The edited transcripts are translated into components of the oxidative phosphorylation: subunits of complex I (NADH-UQ reductase), III (Cyt bc1), IV (cyt oxidase) and V (ATP synthase) Minicircles encode guide RNAs (grnas) that specify the editing. Other types of editing includes changes in nucleotide identity. It occurs in other protozoa, mammals, plants and viruses. 1

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22 mrna EDITING

23 The RNA editing process. The catalysis cycle of editing

24 the APOBEC3 (A3) family of cytidine deaminases has specificity for singlestranded DNA (ssdna). APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding

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