An evolving view of epigenetic complexity in the brain

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 369, Issue 1652, 2014, Pages

  Qureshi, Irfan A ^a   Mehler, Mark F ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Chromatin; DNA methylation; Epigenetic; Histone modification; Non coding RNA

Indexed keywords

BRAIN; GENE EXPRESSION; HOMEOSTASIS; MITOCHONDRIAL DNA; PROTEIN;

HISTONE; UNTRANSLATED RNA;

BIOLOGICAL MODEL; BRAIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; GENETIC EPIGENESIS; HUMAN; METABOLISM; PHYSIOLOGY;

BRAIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; MODELS, NEUROLOGICAL; RNA, UNTRANSLATED;

EID: 84906083342     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2013.0506     Document Type: Review

References (104)

1. Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S. 2009 Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J. Comp. Neurol. 513, 532-541. (doi:10.1002/ cne.21974)
2. Spalding KL et al. 2013 Dynamics of hippocampal neurogenesis in adult humans. Cell 153, 1219-1227. (doi:10.1016/j.cell.2013.05.002)
3. Mehler MF. 2008 Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog. Neurobiol. 86, 305-341. (doi:10.1016/j.pneurobio.2008.10.001)
4. Amaral PP, Dinger ME, Mercer TR, Mattick JS. 2008 The eukaryotic genome as an RNA machine. Science 319, 1787-1789. (doi:10.1126/science.1155472)
5. Bernstein BE et al. 2012 An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74. (doi:10.1038/nature11247)
6. Heyn H, Esteller M. 2012 DNA methylation profiling in the clinic: applications and challenges. Nat. Rev. Genet. 13, 679-692. (doi:10.1038/nrg3270)
7. Portela A, Esteller M. 2010 Epigenetic modifications and human disease. Nat. Biotechnol. 28, 1057-1068. (doi:10.1038/nbt.1685)
8. Kohli RM, Zhang Y. 2013 TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472-479. (doi:10.1038/nature12750)
9. Kriaucionis S, Heintz N. 2009 The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930. (doi:10.1126/science.1169786)
10. Shi L, Lin Q, Su B. 2013 Human-specific hypomethylation of CENPJ, a key brain size regulator. Mol. Biol. Evol. 31, 594-604. (doi:10. 1093/molbev/mst231)
11. Hernando-Herraez I et al. 2013 Dynamics of DNA methylation in recent human and great ape evolution. PLoS Genet. 9, e1003763. (doi:10.1371/ journal.pgen.1003763)
12. Xu H, Wang F, Liu Y, Yu Y, Gelernter J, Zhang H. 2013 Sex-biased methylome and transcriptome in human prefrontal cortex. Hum. Mol. Genet. 23, 1260-1270. (doi:10.1093/hmg/ddt516)
13. Qureshi IA, Mehler MF. 2010 Genetic and epigenetic underpinnings of sex differences in the brain and in neurological and psychiatric disease susceptibility. Prog. Brain Res. 186, 77-95. (doi:10.1016/B978-0-444-53630-3.00006-3)
14. Kozlenkov A et al. 2013 Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Res. 42, 109-127. (doi:10.1093/ nar/gkt838)
15. Guo JU et al. 2013 Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat. Neurosci. 17, 215-222. (doi:10.1038/nn.3607)
16. Lister R et al. 2013 Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905. (doi:10.1126/ science.1237905)
17. Day JJ, Childs D, Guzman-Karlsson MC, Kibe M, Moulden J, Song E, Tahir A, Sweatt JD. 2013 DNA methylation regulates associative reward learning. Nat. Neurosci. 16, 1445-1452. (doi:10.1038/ nn.3504)
18. Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, Faull KF, Jaenisch R, Tsai LH. 2013 Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron 79, 1109-1122. (doi:10.1016/j.neuron.2013. 08.003)
19. Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming GL, King JR, Song H, Sweatt JD. 2013 TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron 79, 1086-1093. (doi:10.1016/j.neuron.2013.08.032)
20. Dias BG, Ressler KJ. 2013 Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat. Neurosci. 17, 89-96. (doi:10.1038/nn.3594)
21. Molina-Serrano D, Kirmizis A. 2013 Beyond the histone tail: acetylation at the nucleosome dyad commands transcription. Nucleus 4, 343-348. (doi:10.4161/nucl.26051)
22. Tropberger P et al. 2013 Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 152, 859-872. (doi:10. 1016/j.cell.2013.01.032)
23. Mueller-Planitz F, Klinker H, Becker PB. 2013 Nucleosome sliding mechanisms: new twists in a looped history. Nat. Struct. Mol. Biol. 20, 1026-1032. (doi:10.1038/nsmb.2648)
24. Mazzoni EO et al. 2013 Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals. Nat. Neurosci. 16, 1191-1198. (doi:10. 1038/nn.3490)
25. Yu Y et al. 2013 Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation. Cell 152, 248-261. (doi:10.1016/j. cell.2012.12.006)
26. Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG. 2013 CAST-ChIP maps celltype-specific chromatin states in the Drosophila central nervous system. Cell Rep. 5, 271-282. (doi:10.1016/j.celrep.2013.09.001)
27. Nott A et al. 2013 S-nitrosylation of HDAC2 regulates the expression of the chromatinremodeling factor Brm during radial neuron migration. Proc. Natl Acad. Sci. USA 110, 3113-3118. (doi:10.1073/pnas.1218126110)
28. Di Meglio T et al. 2013 Ezh2 orchestrates topographic migration and connectivity of mouse precerebellar neurons. Science 339, 204-207. (doi:10.1126/science.1229326)
29. Ito H, Sato K, Koganezawa M, Ote M, Matsumoto K, Hama C, Yamamoto D. 2012 Fruitless recruits two antagonistic chromatin factors to establish singleneuron sexual dimorphism. Cell 149, 1327-1338. (doi:10.1016/j.cell.2012.04.025)
30. Chatoo W, Abdouh M, David J, Champagne MP, Ferreira J, Rodier F, Bernier G. 2009 The polycomb group gene Bmi1 regulates antioxidant defenses in neurons by repressing p53 pro-oxidant activity. J. Neurosci. 29, 529-542. (doi:10.1523/JNEUROSCI. 5303-08.2009)
31. Sando 3rd R, Gounko N, Pieraut S, Liao L, Yates 3rd J, Maximov A. 2012 HDAC4 governs a transcriptional program essential for synaptic plasticity and memory. Cell 151, 821-834. (doi:10.1016/j.cell. 2012.09.037)
32. Kerimoglu C et al. 2013 Histone-methyltransferase MLL2 (KMT2B) is required for memory formation in mice. J. Neurosci. 33, 3452-3464. (doi:10.1523/ JNEUROSCI.3356-12.2013)
33. Vogel-Ciernia A et al. 2013 The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat. Neurosci. 16, 552-561. (doi:10.1038/nn.3359)
34. Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S. 2010 Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc. Natl Acad. Sci. USA 107, 8824-8829. (doi:10.1073/ pnas.1001702107)
35. Volle C, Dalal Y. 2014 Histone variants: the tricksters of the chromatin world. Curr. Opin. Genet. Dev. 25C, 8-14. (doi:10.1016/j.gde.2013.11.006)
36. Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. 2013 Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol. 14, R121. (doi:10.1186/gb-2013-14-10-r121)
37. Michod D, Bartesaghi S, Khelifi A, Bellodi C, Berliocchi L, Nicotera P, Salomoni P. 2012 Calciumdependent dephosphorylation of the histone chaperone DAXX regulates H3.3 loading and transcription upon neuronal activation. Neuron 74, 122-135. (doi:10.1016/j.neuron.2012.02.021)
38. Schwartzentruber J et al. 2012 Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482, 226-231. (doi:10.1038/nature10833)
39. Sturm D et al. 2012 Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 22, 425-437. (doi:10.1016/j.ccr.2012.08.024)
40. Wu G et al. 2012 Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and nonbrainstem glioblastomas. Nat. Genet. 44, 251-253. (doi:10.1038/ng.1102)
41. Chan KM et al. 2013 The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev. 27, 985-990. (doi:10.1101/gad.217778.113)
42. Newhart A et al. 2013 Single cell analysis of RNA-mediated histone H3.3 recruitment to a cytomegalovirus promoter-regulated transcription site. J. Biol. Chem. 288, 19 882-19 899. (doi:10. 1074/jbc.M113.473181)
43. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. 2002 Largescale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919. (doi:10.1126/science. 1068597)
44. Birney E et al. 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. (doi:10.1038/nature05874)
45. Kapranov P et al. 2007 RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488. (doi:10. 1126/science.1138341)
46. Kapranov P, Willingham AT, Gingeras TR. 2007 Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 8, 413-423. (doi:10.1038/nrg2083)
47. Qureshi IA, Mehler MF. 2012 Emerging roles of noncoding RNAs in brain evolution, development, plasticity and disease. Nat. Rev. Neurosci. 13, 528-541. (doi:10.1038/nrn3234)
48. Gerstein MB et al. 2007 What is a gene, post-ENCODE? History and updated definition. Genome Res. 17, 669-681. (doi:10.1101/gr.6339607)
49. Kapranov P et al. 2010 The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol. 8, 149. (doi:10.1186/1741-7007-8-149)
50. Xie C et al. 2014 NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 42, D98-D103. (doi:10.1093/nar/gkt1222)
51. Somel M, Liu X, Khaitovich P. 2013 Human brain evolution: transcripts, metabolites and their regulators. Nat. Rev. Neurosci. 14, 112-127. (doi:10.1038/nrn3372)
52. Babiarz JE, Hsu R, Melton C, Thomas M, Ullian EM, Blelloch R. 2011 A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA 17, 1489-1501. (doi:10.1261/rna.2442211)
53. Khudayberdiev SA, Zampa F, Rajman M, Schratt G. 2013 A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons. Front. Mol. Neurosci. 6, 43. (doi:10.3389/ fnmol.2013.00043)
54. Fernandez-Valverde SL, Taft RJ, Mattick JS. 2010 Dynamic isomiR regulation in Drosophila development. RNA 16, 1881-1888. (doi:10.1261/ rna.2379610)
55. Marti E, Pantano L, Banez-Coronel M, Llorens F, Minones-Moyano E, Porta S, Sumoy L, Ferrer I, Estivill X. 2010 A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 38, 7219-7235. (doi:10.1093/nar/ gkq575)
56. Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. 2006 RNA editing of human microRNAs. Genome Biol. 7, R27. (doi:10.1186/gb-2006-7-4-r27)
57. Boudreau RL, Jiang P, Gilmore BL, Spengler RM, Tirabassi R, Nelson JA, Ross CA, Xing Y, Davidson BL. 2014 Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron 81, 294-305. (doi:10.1016/j.neuron.2013.10.062)
58. Li JH, Liu S, Zhou H, Qu LH, Yang JH. 2014 starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92-D97. (doi:10.1093/nar/gkt1248)
59. Orom UA, Nielsen FC, Lund AH. 2008 MicroRNA-10a binds the 50UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell 30, 460-471. (doi:10.1016/j.molcel.2008.05.001)
60. Hawkins PG, Morris KV. 2008 RNA and transcriptional modulation of gene expression. Cell Cycle 7, 602-607. (doi:10.4161/cc.7.5.5522)
61. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. 2013 Natural RNA circles function as efficient microRNA sponges. Nature 495, 384-388. (doi:10.1038/nature11993)
62. Kishore S, Stamm S. 2006 The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230-232. (doi:10.1126/ science.1118265)
63. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER. 2012 A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149, 693-707. (doi:10.1016/j.cell.2012.02.057)
64. Saxena A, Tang D, Carninci P. 2012 piRNAs warrant investigation in Rett syndrome: an omics perspective. Dis. Markers 33, 261-275. (doi:10. 3233/DMA-2012-0932)
65. Qureshi IA, Mehler MF. 2013 Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics 10, 632-646. (doi:10.1007/s13311-013-0199-0)
66. St Laurent 3rd G, Wahlestedt C. 2007 Noncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci. 30, 612-621. (doi:10.1016/j.tins.2007.10.002)
67. Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. 2013 Cell-type specific features of circular RNA expression. PLoS Genet. 9, e1003777. (doi:10.1371/ journal.pgen.1003777)
68. Memczak S et al. 2013 Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338. (doi:10.1038/nature11928)
69. Derrien T et al. 2012 The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789. (doi:10.1101/gr.132159.111)
70. Lipovich L et al. 2013 Developmental changes in the transcriptome of human cerebral cortex tissue: long noncoding RNA transcripts. Cereb. Cortex 24, 1451-1459. (doi:10.1093/cercor/bhs414)
71. Ponjavic J, Oliver PL, Lunter G, Ponting CP. 2009 Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 5, e1000617. (doi:10.1371/journal.pgen.1000617)
72. Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, Green ED, Molnar Z, Ponting CP. 2010 Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 11, R72. (doi:10.1186/ gb-2010-11-7-r72)
73. Belgard TG et al. 2011 A transcriptomic atlas of mouse neocortical layers. Neuron 71, 605-616. (doi:10.1016/j.neuron.2011.06.039)
74. Sauvageau M et al. 2013 Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife 2, e01749. (doi:10.7554/ eLife.01749)
75. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. 2012 Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 30, 99-104. (doi:10.1038/nbt.2024)
76. Rais Y et al. 2013 Deterministic direct reprogramming of somatic cells to pluripotency. Nature 502, 65-70. (doi:10.1038/nature12587)
77. Jung BP, Zhang G, Nitsch R, Trogadis J, Nag S, Eubanks JH. 2003 Differential expression of methyl CpG-binding domain containing factor MBD3 in the developing and adult rat brain. J. Neurobiol. 55, 220-232. (doi:10.1002/neu.10199)
78. Di Ruscio A et al. 2013 DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 503, 371-376. (doi:10.1038/nature12598)
79. Kfoury N, Kapatos G. 2009 Identification of neuronal target genes for CCAAT/enhancer binding proteins. Mol. Cell. Neurosci. 40, 313-327. (doi:10.1016/j. mcn.2008.11.004)
80. Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP. 2014 The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J. 33, 296-311. (doi:10.1002/embj.201386225)
81. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R. 2013 Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 494, 497-501. (doi:10.1038/nature11884)
82. Hacisuleyman E et al. 2014 Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat. Struct. Mol. Biol. 21, 198-206. (doi:10.1038/nsmb.2764)
83. Qureshi IA, Mehler MF. 2010 Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states. Ann. NY Acad. Sci. 1204(Suppl.), E20-E37. (doi:10.1111/j.1749-6632. 2010.05718.x)
84. Mercer TR, Mattick JS. 2013 Understanding the regulatory and transcriptional complexity of the genome through structure. Genome Res. 23, 1081-1088. (doi:10.1101/gr.156612.113)
85. Light WH, Brickner JH. 2013 Nuclear pore proteins regulate chromatin structure and transcriptional memory by a conserved mechanism. Nucleus 4, 357-360. (doi:10.4161/nucl.26209)
86. Capra JA, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS. 2013 Many human accelerated regions are developmental enhancers. Phil. Trans. R. Soc. B 368, 20130025. (doi:10.1098/rstb.2013.0025)
87. Kamm GB, Pisciottano F, Kliger R, Franchini LF. 2013 The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol. Biol. Evol. 30, 1088-1102. (doi:10.1093/molbev/mst023)
88. Jacques PE, Jeyakani J, Bourque G. 2013 The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 9, e1003504. (doi:10.1371/journal.pgen.1003504)
89. Poduri A, Evrony GD, Cai X, Walsh CA. 2013 Somatic mutation, genomic variation, and neurological disease. Science 341, 1237758. (doi:10.1126/science. 1237758)
90. Reilly MT, Faulkner GJ, Dubnau J, Ponomarev I, Gage FH. 2013 The role of transposable elements in health and diseases of the central nervous system. J. Neurosci. 33, 17 577-17 586. (doi:10.1523/ JNEUROSCI.3369-13.2013)
91. McConnell MJ et al. 2013 Mosaic copy number variation in human neurons. Science 342, 632-637. (doi:10.1126/science.1243472)
92. Li W, Prazak L, Chatterjee N, Gruninger S, Krug L, Theodorou D, Dubnau J. 2013 Activation of transposable elements during aging and neuronal decline in Drosophila. Nat. Neurosci. 16, 529-531. (doi:10.1038/nn.3368)
93. Perrat PN, DasGupta S, Wang J, Theurkauf W, Weng Z, Rosbash M, Waddell S. 2013 Transposition-driven genomic heterogeneity in the Drosophila brain. Science 340, 91-95. (doi:10.1126/science.1231965)
94. Abbasi-Moheb L et al. 2012 Mutations in NSUN2 cause autosomal-recessive intellectual disability. Am. J. Hum. Genet. 90, 847-855. (doi:10.1016/j. ajhg.2012.03.021)
95. Hussain S et al. 2013 NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 4, 255-261. (doi:10.1016/j.celrep.2013.06.029)
96. Lapinaite A, Simon B, Skjaerven L, Rakwalska-Bange M, Gabel F, Carlomagno T. 2013 The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature 502, 519-523. (doi:10.1038/ nature12581)
97. Hess ME et al. 2013 The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat. Neurosci. 16, 1042-1048. (doi:10.1038/nn.3449)
98. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. 2012 Comprehensive analysis of mRNA methylation reveals enrichment in 30 UTRs and near stop codons. Cell 149, 1635-1646. (doi:10.1016/j.cell.2012.05.003)
99. Xu D et al. 2013 Top3beta is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat. Neurosci. 16, 1238-1247. (doi:10.1038/nn.3479)
100. Stoll G et al. 2013 Deletion of TOP3beta, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders. Nat. Neurosci. 16, 1228-1237. (doi:10.1038/nn.3484)
101. Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SM. 2011 DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc. Natl Acad. Sci. USA 108, 3630-3635. (doi:10.1073/pnas. 1012311108)
102. Landerer E et al. 2011 Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells. Cell Oncol. (Dordr.) 34, 297-305. (doi:10.1007/ s13402-011-0018-8)
103. Lung B, Zemann A, Madej MJ, Schuelke M, Techritz S, Ruf S, Bock R, Huttenhofer A. 2006 Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res. 34, 3842-3852. (doi:10.1093/nar/gkl448)
104. Chen H, Dzitoyeva S, Manev H. 2012 Effect of valproic acid on mitochondrial epigenetics. Eur. J. Pharmacol. 690, 51-59. (doi:10.1016/j.ejphar. 2012.06.019)