Мусорная ДНК. Путешествие в темную материю генома - Несса Кэри

26. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. The evolution of long-non-coding RNA repertoires and expression patterns in tetrapods. Nature. 2014 Jan 30;505(7485):635-40.

27. Любопытные критические замечания на сей счет см. в: Fatica А, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014 Jan; 15 (1):7—21.

28. Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010 Sep 15;29(18):3082-93.

29. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussier D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108): 167-72.

30. http://www.who.int/mental_health/publications/dementia_report_2012/en.

31. Faghihi MA, Modarresi F, Khali) AM, Wood DE, Sahagan BG, Morgan ТЕ, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C. Expression of a noncoding KNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 2008 Jul; 14(7):723-30.

32. Modarresi F, Faghihi MA, Patel NS, Sahagan BG, Wahlestedt C, Lopez-Toledano MA. Knockdown of BACE1-AS Nonprotein-Coding Transcript Modulates Beta-Amyloid-Related Hippocampal Neurogenesis. Int. J. Alzheimers Die. 2011;2011:929042.

33. Zhao X, Tang Z, Zhang H, Atianjoh FE, Zhao JY, Liang L, Wang W, Guan X, Kao SC, Tiwari V, Gao YJ, Hoffman PN, Cui H, Li M, Dong X, Tao YX. A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons. Nat Neurosci. 2013 Aug; 16(8):1024-31.

34. Полезный обзор см., например, в: Wahlestedt С. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov. 2013 Jun; 12(6):433-46.

35. Bird A. Genome biology; not drowning but waving. Cell. 2013 Aug 29;154(5):951-2.

1. Подробнее об этом см. в моей первой книге The Epigenetics Revolution.

2. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011 Aug 28;477(7364):295-300.

3. Guil S, Soler M, Portela A, Carrère J, Fonalleras E, Gômez A, Villanueva A, Esteller M. Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol. 2012 Jun 3;19(7):664-70.

4. Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, Ghosh D, Pienta KJ, Sewalt RG, Otte AP, Rubin MA, Chinnaiyan AM. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002 Oct 10;419(6907):624-9.

5. Kleer CG, CaoQ, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Set USA. 2003 Sep 30;100(20):11606-11.

6. Sneeringer CJ, Scott MP, Kuntz KW, Knutson SK, Pollock RM^-Richon VM, Copeland RA. Coordinated activities of wild type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human В-cell lymphomas. Proc Natl Acad Set USA. 2010 Dec 7;107 (49):20980-5.

7. http://clinicaltrials.gov/ct2/show/NCT01897571?term=7438&rank=1.

8. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 (INK4B) tumor suppressor gene. Oncogene. 2011 Apr 21;30(16):1956-62.

9. Tsai MC, Manor 0, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010 Aug 6;329(5992):689-93.

10. Недавно вышла программная статья на эту тему: Davidovich С, Zheng L, Goodrich KJ, Cech TR. Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol. 2013 Nov; 20(11):1250-7.

11. Статья, на которую дается ссылка выше, чуть более доступно изложена в: Goff LA, Rinn JL. Poly-combing the genome for RNA. Nat Struct Mol Biol. 2013 Dec; 20(12):1344-6.

12. Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D’Alô F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen ЕЮ. DNMTl-interacting RNAs block gene-specific DNA méthylation. Nature. 2013 Nov 21;503(7476):371-6.

13. Обзор всех сложных стадий процесса см. в: Froberg JE, Yang L, Lee JT. Guided by RNAs: X-inactivation as a model for long non-coding RNA function. J. Mol. Biol. 2013 Oct 9;425(19):3698-706.

14. Froberg JE, Yang L, Lee JT. Guided by RNAs: X-inactivation as a model for long non-coding RNA function. J Mol Biol. 2013 Oct 9;425(19):3698-706.

15. Michaud EJ, van Vugt MJ, Bultman SJ, Sweet HO, Davisson MT, Woychik RP. Differential expression of a new dominant agouti allele (Aiapy) is correlated with méthylation state and is influenced by parental lineage. Genes Dev. 1994 Jun 15;8(12):1463-72.

1. Довольно современный обзор исследований в этой области, см. в: Surani МА, Barton SC, Norris ML. Experimental reconstruction of mouse eggs and embryos: an analysis of mammalian development. Biol Reprod. 1987 Feb; 36(1):1-16.

2. Онлайн-хранилище импринтированных ДНК-последовательностей мыши: http://www.mousebook.org/catalog.php?catalog=imprinting.

3. Полезный обзор см. в: Guenzl PM, Barlow DP. Macro long non-coding RNAs: a new layer of cis-regulatory information in the mammalian genome. RNA Biol. 2012 Jun; 9(6):731-41.

4. Недавний обзор, посвященный импринтингу у сумчатых: Graves JA, Renfree MB. Marsupials in the age of genomics. Annu Rev Genomics Hum Genet. 2013;14:393-420.

5. Landers M, Bancescu DL, Le Meur E, Rougeulle C, Glatt-Deeley H, Brannan C, Muscatelli F, Lalande M. Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res. 2004 Jun 29;32 (11):3480-92

6. Terranova R, Yokobayashi S, Stadler MB, Otte AP, van Lohuizen M, Orkin SH, Peters AH. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell. 2008 Nov; 15(5):668-79.

7. Wagschal A, Sutherland HG, Woodfine K, Henckel A, Chebli K, Schulz R, Oakey RJ, Bickmore WA, Feil R. G9a histone methyltransferase contributes to imprinting in the mouse placenta. Mol Cell Biol. 2008 Feb; 28(3):1104-13.

8. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science. 2008 Dec 12;322(5908):1717-20.

9. Цит. no: Koerner MV, Pauler FM, Huang R, Barlow DP. The function of non-coding RNAs in genomic imprinting. Development. 2009 Jun; 136(11):1771—83.

10. Barlow DP. Methylationand imprinting: from host defense to gene regulation? Science. 1993 Apr 16;260(5106):309-10.

11. Цит. no: Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J. 2012 Dec; 53(3-4):341-58.

12. Описание действий этих белков в процессе метилирования материнской ОКИ см. в: Bourc’his D, Proudhon С. Sexual dimorphism in parental imprint ontogeny and contribution to embryonic development. Mol Cell Endocrinol. 2008 Jan 30;282(1-2):87-94.

13. Вот статья, продемонстрировавшая важную роль этого белка в поддержании материнского импринта: Hirasawa R, Chiba Н, Kaneda М, Tajima S. Li E, Jaenisch R, Sasaki H. Maternal and zygotic Dnmtl are necessary and sufficient for the maintenance of DNA methyl-ation imprints during preimplantation development. Genes Dev. 2008 Jun 15;22(12):1607-16.

14. Reinhart B, Paoloni-Giacobino A, Chaillet JR. Specific differentially methylated domain sequences direct the maintenance of méthylation at imprinted genes. Mol Cell Biol. 2006 Nov; 26(22):8347-56.

15. Skaar DA, Li Y, Bernal AJ, HoyoC, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J. 2012 Dec; 53(3-4):341-58.

16. Kawahara M, Wu Q, Takahashi N, Morita S, Yamada K, Ito M, Ferguson-Smith AC, Kono T. High-frequency generation of viable mice from engineered bi-maternal embryos. Nat Biotechnol. 2007 Sep; 25(9):1045-50.

17. Цит. no: Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014 Jan; 15(1):7-21.

18. Обзор данного аспекта проблемы см. в: Frost JM, Moore GE. The importance of imprinting in the human placenta. PLoS Genet. 2010 Jul 1;6(7):el001015.

19. Полное описание см. в: http://omim.org/entry/176270.

20. Полное описание см. в: http://omim.org/entry/105830.

21. de Smith AJ, Purmann C, Walters RG, Ellis RJ, Holder SE, Van Haclst MM, Brady AF, Fairbrother UL, Dattani M, Keogh JM, Henning E, Yeo GS, O’Rahilly S, Froguel P, Farooqi 1S, Blakemore AI. A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. Hum Mol Genet. 2009 Sep 1;18(17):3257-65.

22. Duker AL, Ballif BC, Bawle EY, Person RE, Mahadevan S, Alliman S, Thompson R, Traylor R, Bejjani BA, Shaffer LG, Rosenfeld JA, Lamb AN, SahooT. Paternally inherited microdeletion at 15qll.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome. EurJ Hum Genet. 2010 Nov; 18 (11):1196-201.

23. Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet. 2008 Jun; 40(6):719-21.

24. Полное описание см. в: http://omim.org/entry/180860.

25. Полное описание см. в: http://omim.org/entry/130650.

26. Данные собраны в: Kotzot D. Maternal uniparental disomy 14 dissection of the phenotype with respect to rare autosomal recessively inherited traits, trisomy mosaicism, and genomic imprinting. Ann Genet. 2004 Jul-Sep; 47(3):251-60.

27. Kagami M, Sekita Y, Nishimura G, Irie M, Kato F, Okada M, Yamamori S, Kishimoto H, Nakayama M, Tanaka Y, Matsuoka K, Takahashi T, Noguchi M, Tanaka Y, Masumoto K, Utsunomiya T, Kouzan H, Komatsu Y, Ohashi H, Kurosawa K, Kosaki K, Ferguson-Smith AC, Ishino F, Ogata T. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. Nat Genet. 2008 Feb; 40(2):237-242.

28. Подробный обзор, посвященный наследованию и клиническим особенностям различных заболеваний человека, связанных с импринтингом: Ishida М, Moore GE. The role of imprinted genes in humans. Mol. Aspects Med. 2013 Jul-Aug; 34(4):826-840.

29. Пресс-релиз Американского общества репродуктивной медицины от 14 октября 2013: http;//www.asrm.org/Five_Million_Babies Born with_Help_of_Assisted_Reproductive_Technologies.

30. Это довольно подробно обсуждается в: Ishida М, Moore GE. The role of imprinted genes in humans. Mol Aspects Med. 2013 Jul — Aug; 34(4):826-40.

1. Цит. no: Moss T, Langlois F, Gagnon-Kugler T, Stefanovsky V. A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell Mol LifeSci. 2007 Jan; 64(1):29-49.

2. Что касается более подробных сведений о рибосомах и рРНК, то проще всего сослаться на хороший учебник молекулярной биологии. Например, на: Molecular Biology of the Cell, 5th Edition, авторы: Alberts, Johnson, Lewis, Raff, Roberts и Walter, 2012.

3. http://www.nobelprize.org/educational/medicine/dna/a/translation/trna.html.

4. http://www.bscb.org/?url=softcell/ribo.

5. Цит. no: Zentner GE, Saiakhova A, Manaenkov P, Adams MD, Scacheri PC. Integrative genomic analysis of human ribosomal DNA. Nucleic Acids Res. 2011 Jul; 39(12):4949-60.

6. Интересный, хотя и несколько провокативный обзор, посвященный заболеваниям, вызванным дефектам рибосомных белков: Narla А, Ebert BL. Ribosomopathies: human disorders of ribosome dysfunction. Blood. 2010 Apr 22;115(16):3196-205.

7. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921.