The theory of RNA-mediated gene evolution

Epigenetics

Volumn 10, Issue 1, 2015, Pages 1-5

  Morris, Kevin V ^a,b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Deamination; DNA methylation; Epigenetic; Gene editing; IncRNA; RNA

Indexed keywords

CYTOSINE; DNA GLYCOSYLTRANSFERASE; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 3A; GENOMIC DNA; HISTONE DEACETYLASE; RNA; THYMINE; TRANSCRIPTION FACTOR EZH2; UNTRANSLATED RNA; LONG UNTRANSLATED RNA;

ARTICLE; CPG ISLAND; DEAMINATION; DNA METHYLATION; DNA REPAIR; DNA REPLICATION; EPIGENETIC REPRESSION; EPIGENETICS; EVOLUTION; GENE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE MUTATION; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; INHERITANCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; THEORY; ANIMAL; GENETIC EPIGENESIS; GENETICS; MOLECULAR EVOLUTION;

ANIMALS; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; HUMANS; RNA, LONG NONCODING;

EID: 84924429089     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.1080/15592294.2014.995536     Document Type: Article

References (49)

1. Banfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Jr., Kundaje A, Gunawardena HP, Yu Y, Xie L, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 2012; 22:1646-57; PMID: 22955977; http://dx.doi.org/10.1101/gr.134767.111
2. St Laurent G, 3rd, Shtokalo D, Tackett M, Yang Z, Eremina T, Wahlestedt C, Inchima SU, Seilheimer B, McCaffrey TA, Kapranov P. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 2012; 13:504; PMID: 23006825; http://dx.doi.org/10.1186/1471-2164-13-504
3. Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, et al. ENCODE whole-genome data in the UCSC Genome browser: update 2012. Nucleic Acids Res 2012; 40:D912-7; PMID:22075998; http://dx.doi.org/10.1093/nar/gkr1012
4. Pennisi E. Genomics. ENCODE project writes eulogy for junk DNA. Science 2012; 337:1159, 61; PMID:22955811; http://dx.doi.org/10.1126/science.337.6099.1159
5. Ohno S. So much "junk" DNA in our genome. Brookhaven Sym Biol 1972; 23:366-70; PMID:5065367
6. Ohno S, Yomo T. The grammatical rule for all DNA: junk and coding sequences. Electrophoresis 1991; 12:103-8; PMID:2040257; http://dx.doi.org/10.1002/elps.1150120203
7. Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet 2014; 15:423-37; PMID:24776770; http://dx.doi.org/10.1038/nrg3722
8. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 2005; 309:1559-63; PMID:16141072; http://dx.doi.org/10.1126/science.1112014
9. Malecova B, Morris KV. Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs. Curr Opin Mol Ther 2010; 12:214-22; PMID:20373265
10. Turner AM, Morris KV. Controlling transcription with noncoding RNAs in mammalian cells. Biotechniques 2010; 48; PMID:20569216; http://dx.doi.org/10.2144/000113442
11. Allis CD, Jenuwein T, Reinberg D. Epigenetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2007.
12. Rechavi O, Minevich G, Hobert O. Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans. Cell 2011; 147:1248-56; PMID: 22119442; http://dx.doi.org/10.1016/j.cell.2011.10.042
13. Braunschweig M, Jagannathan V, Gutzwiller A, Bee G. Investigations on transgenerational epigenetic response down the male line in F2 pigs. PLoS ONE 2012; 7: e30583; PMID:22359544; http://dx.doi.org/10.1371/journal.pone.0030583
14. Franklin TB, Russig H, Weiss IC, Graff J, Linder N, Michalon A, Vizi S, Mansuy IM. Epigenetic transmission of the impact of early stress across generations. Biol Psychiatry 2010; 68:408-15; PMID:20673872; http://dx.doi.org/10.1016/j.biopsych.2010.05.036
15. Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A 2008; 105:17046-9; PMID:18955703; http://dx.doi.org/10.1073/pnas.0806560105
16. Barry G. Lamarckian evolution explains human brain evolution and psychiatric disorders. Front Neurosci 2013; 7:224; PMID:24324395; http://dx.doi.org/10.3389/fnins.2013.00224
17. Hawkins PG, Santoso S, Adams C, Anest V, Morris KV. Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res 2009; 37:2984-95; PMID:19304753; http://dx.doi.org/10.1093/nar/gkp127
18. Morris KV. Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells. Epigenetics 2009; 4:296-301; PMID:19633414; http://dx.doi.org/10.4161/epi.4.5.9282
19. Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Grander D, Morris KV. A pseudogene longnoncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 2013; 20:440-6; PMID:23435381; http://dx.doi.org/10.1038/nsmb.2516
20. Weinberg MS, Villeneuve LM, Ehsani A, Amarzguioui M, Aagaard L, Chen ZX, Riggs AD, Rossi JJ, Morris KV. The antisense strand of small interferingRNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 2006; 12:256-62; PMID: 16373483; http://dx.doi.org/10.1261/rna.2235106
21. Ross JP, Suetake I, Tajima S, Molloy PL. Recombinant mammalian DNA methyltransferase activity on model transcriptional gene silencing short RNA-DNA heteroduplex substrates. Biochem J 2010; 432:323-32; PMID: 20846120; http://dx.doi.org/10.1042/BJ20100579
22. Turner AM, De La Cruz J, Morris KV. Mobilizationcompetent lentiviral vector-mediated sustained transcriptional modulation of HIV-1 expression. Mol Ther 2009; 17:360-8; PMID:19066594; http://dx.doi.org/10.1038/mt.2008.268
23. Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006; 439:871-4; PMID:16357870; http://dx.doi.org/10.1038/nature04431
24. Wijesinghe P, Bhagwat AS. Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G. Nucleic Acids Res 2012; 40:9206-17; PMID:22798497; http://dx.doi.org/10.1093/nar/gks685
25. Carpenter MA, Li M, Rathore A, Lackey L, Law EK, Land AM, Leonard B, Shandilya SM, Bohn MF, Schiffer CA, et al. Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J Biol Chem 2012; 287:34801-8; PMID:22896697; http://dx.doi.org/10.1074/jbc.M112.385161
26. Suspene R, Aynaud MM, Vartanian JP, Wain-Hobson S. Efficient deamination of 5-methylcytidine and 5-substituted cytidine residues in DNA by human APOBEC3A cytidine deaminase. PLoS ONE 2013; 8: e63461; PMID:23840298; http://dx.doi.org/10.1371/journal.pone.0063461
27. Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X. Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Res 2012; 40:10203-14; PMID:22962365; http://dx.doi.org/10.1093/nar/gks845
28. Jacobs AL, Schar P. DNA glycosylases: in DNA repair and beyond. Chromosoma 2012; 121:1-20; PMID:22048164; http://dx.doi.org/10.1007/s00412-011-0347-4
29. Lutsenko E, Bhagwat AS. Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications. Mutat Res 1999; 437:11-20; PMID:10425387; http://dx.doi.org/10.1016/S1383-5742(99)00065-4
30. Shen JC, Rideout WM, 3rd, Jones PA. The rate of hydrolytic deamination of 5-methylcytosine in doublestranded DNA. Nucleic Acids Res 1994; 22:972-6; PMID:8152929; http://dx.doi.org/10.1093/nar/22.6.972
31. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6-21; PMID:11782440; http://dx.doi.org/10.1101/gad.947102
32. Neddermann P, Gallinari P, Lettieri T, Schmid D, Truong O, Hsuan JJ, Wiebauer K, Jiricny J. Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase. J Biol Chem 1996; 271:12767-74; PMID:8662714; http://dx.doi.org/10.1074/jbc.271.48.30986
33. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, et al. Signatures of mutational processes in human cancer. Nature 2013; 500:415-21; PMID: 23945592; http://dx.doi.org/10.1038/nature12477
34. Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M. CpG deamination creates transcription factor-binding sites with high efficiency. Genome biology and evolution 2011; 3:1304-11; PMID:22016335; http://dx.doi.org/10.1093/gbe/evr107
35. Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, Vertino PM, Zhang X, Cheng X. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res 2012; 40:4841-9; PMID:22362737; http://dx.doi.org/10.1093/nar/gks155
36. Kondo E, Gu Z, Horii A, Fukushige S. The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16(INK4a) and hMLH1 genes. Mol Cell Biol 2005; 25:4388-96; PMID:15899845; http://dx.doi.org/10.1128/MCB.25.11.4388-4396.2005
37. Kemmerich K, Dingler FA, Rada C, Neuberger MS. Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung-/-Msh2-/- mice. Nucleic Acids Res 2012; 40:6016-25; PMID:22447450; http://dx.doi.org/10.1093/nar/gks259
38. Budworth H, McMurray CT. Bidirectional transcription of trinucleotide repeats: roles for excision repair. DNA repair 2013; 12:672-84; PMID:23669397; http://dx.doi.org/10.1016/j.dnarep.2013.04.019
39. Morris KV. RNA-directed transcriptional gene silencing and activation in human cells. Oligonucleotides 2009; 19:299-306.PMID:19943804; http://dx.doi.org/10.1089/oli.2009.0212
40. Turner AM, Ackley AM, Matrone MA, Morris KV. Characterization of an HIV-targeted transcriptional gene-silencing RNA in primary cells. Hum Gene Ther 2012; 23:473-83; PMID:22122263; http://dx.doi.org/10.1089/hum.2011.165
41. Weinberg MS, Morris KV. A new world order: tailored gene targeting and regulation using CRISPR. Mol Ther 2014; 22:893; PMID:24787973; http://dx.doi.org/10.1038/mt.2014.54
42. Qiu P, Shandilya H, D’Alessio JM, O’Connor K, Durocher J, Gerard GF. Mutation detection using Surveyor nuclease. Biotechniques 2004; 36:702-7; PMID: 15088388
43. Johnsson P, Lipovich L, Grander D, Morris KV. Evolutionary conservation of long noncoding RNAs; sequence, structure, function. Biochim Biophys Acta 2013; PMID:24184936; http://dx.doi.org/10.1016/j.bbagen.2013.10.035
44. Holz-Schietinger C, Reich NO. RNA modulation of the human DNA methyltransferase 3A. Nucleic Acids Res 2012; 40:8550-7; PMID:22730298; http://dx.doi.org/10.1093/nar/gks537
45. Jeffery L, Nakielny S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J Biol Chem 2004; 279:49479-87; PMID: 15342650; http://dx.doi.org/10.1074/jbc.M409070200
46. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451:202-6; PMID:18185590; http://dx.doi.org/10.1038/nature06468
47. Hawkins PG, Morris KV. Transcriptional regulation of oct4 by a long non-coding RNA antisense to oct4-pseudogene 5. Transcription 2010; 1:165-75; PMID: 21151833; http://dx.doi.org/10.4161/trns.1.3.13332
48. Morris KV, Santoso S, Turner AM, Pastori C, Hawkins PG. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 2008; 4:e1000258; PMID:19008947; http://dx.doi.org/10.1371/journal.pgen.1000258
49. Morris KV. Non-coding RNAs, epigenetic memory, and the passage of information to progeny. RNA Biol 2009; 6:242-7; PMID:19305164; http://dx.doi.org/10.4161/rna.6.3.8353