Книга Мусорная ДНК. Путешествие в темную материю генома - Несса Кэри

14. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006 Aug 25;126(4):663-676.

15. http://www.nobelprize.org/nobel_prizes/medicine/laureates/2012.

16. Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Celt. 2013 Apr 11 ; 153(2):320—34.

17. Обзор различных молекулярных причин см. в: Skibbens RV, Colquhoun JM, Green MJ, Molnar CA, Sin DN, Sullivan BJ, Tanzosh EE. Cohesinopathies of a feather flock together. PLoS Genet. 2013 Dec; 9(12):e1004036.

18. http://www.cdls.org.uk/information-centre.

19. Sanyal A, Lajoie BR. Jain G, Dekker J. The long-range interactionj-landscapeof gene promoters. Nature. 2012 Sep 6;489(7414):109-13.

20. Jackson DA, Hassan AB, Errington RJ, Cook PR. Visualization of focal sites of transcription within human nuclei. EMBO J. 1993 Mar; 12(3):1059-65.

21. Отличный обзор на эту тему: Rieder D, Trajanoski Z, McNally JG. Transcription factories. Front Genet. 2012 Oct 23;3:221. doi: 10.3389/fgene.2012.00221.eCollection 2012.

22. Iborra FJ, Pombo A, Jackson DA, Cook PR. Active RNA polymerases are localized within discrete transcription «factories» in human nuclei. J Cell Set. 1996 Jun; 109(Pt 6):1427-36.

23. Jackson DA, Iborra FJ, Manders EM, Cook PR. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell. 1998 Jun; 9 (6):1523-36

24. Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR. Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol. 2010 Jul 13;8(7):e1000419.

25. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet. 2004 Oct; 36(10):1065-71.

26. Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P. Мус dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 2007 Aug; 5(8):e192.

Глава 13

1. Установить, кто впервые использовал это описание, трудно. См. обсуждение этого вопроса: http://engiish.stackexchange.com/questions/ 103851/where-does-the-phrase-of-boredom-punctuated-by-moments-of-terror-come-from.

2. Обзор на эту тему: Molto Е, Fernandez A, Montoliu L. Boundaries in vertebrate genomes: different solutions to adequately insulate gene expression domains. Brief Fund Genomic Proteomic. 2009 Jul; 8(4):283-96.

3. Ishihara K, Oshimura M, Nakao M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Celt. 2006 Sep 1;23(5):733-42.

4. Lutz M, Burke LJ, Barreto G, Goeman F, Greb H, Arnold R, Schultheiss H, Brehm A, Kouzarides T, Lobanenkov V, Renkawitz R. Transcriptional repression by the insulator protein CTCF involves histone deacetylases. Nucleic Acids Res. 2000 Apr 15;28(8):1707-13.

5. Lunyak W, Prefontaine GG, Nuftez E, Cramer T, Ju BG, Ohgi KAr|-Hutt K, Roy R, Garria-Dfaz A, Zhu X, Yung Y, Montoliu L, Glass CK, Rosenfeld MG. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science. 2007 Jul 13;317(5835):248-51.

6. Цит. no: Kirkland JG, Raab JR, Kamakaka RT. TFIIIC bound DNA elements in nuclear organization and insulation. Biochim Biophys Acta. 2013 Mar—Apr; 1829(3-4):418-24.

7. Так называемый синдром Тёрнера. Подробнее см. в: http://www. nhs.uk/Conditions/Turners-syndrome/Pages/Introduction.aspx.

8. Подробнее см. в: http://ghr.nlm.nih.gov/condition/triple-x-syn-drome.

9. Так называемый синдром Клайнфельтера. Подробнее см. в: http://ghr.nlm.nih.gov/condition/klinefelter-syndrome.

10. Star Trek: First Contact [«Звездный путь. Первый контакт«] (1996). Несомненно, лучший фильм из всего цикла — во всяком случае, до того, как Дж.Дж. Адамс взялся за перезагрузку проекта.

11. См. https://ghr.nlm.nih.gov/gene/SHOX.

12. Hemani G, Yang J, Vinkhuyzen A, Powell JE, Willemsen G, Hottenga JJ, Abdellaoui A, Mangino M, Valdes AM, Medland SE, Madden PA, Heath AC, Henders AK, Nyholt DR, deGeusEJ, Magnusson PK, Ingelsson E, Montgomery GW, Spector TD, Boomsma DI, Pedersen NL, Martin NG, Visscher PM. Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs. Am J Hum Genet. 2013 Nov 7;93(5):865-875.

Глава 14

1. Массу информации о проекте ENCODE, в том числе ряд интервью с некоторыми из его ведущих специалистов, см. в: http://www.nature.com/encode.

2. http://www.theguardian.com/science/2012/sep/05/genes-genome-junk-dna-encode.

3. http://edition.cnn.com/2012/09/05/health/encode-human-genome/index. html?hpt-hp_bn 12.

4. http://www.telegraph.co.uk/science/science-news/9524165/Worldwide-army-of-scientists-cracks-the-junk-DNA-code.html.

5. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

6. Mattick JS. A new paradigm for developmental biology. J Exp Biol. 2007 May; 210(Pt 9):1526-47.

7. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012 Sep 6;489(7414):109-13.

8. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MTif-Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie В, Lee BK, Lee К, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Saf A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, VongS, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82.