Мусорная ДНК. Путешествие в темную материю генома - Несса Кэри

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

8. См., напр.: Hedges SB, Blair JE, Venturi ML, Shoe JL. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol. 2004 Jan 28;4:2.

9. Цит. no: Wilson DN. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nat Rev Microbiol. 2014 Jan; 12(1):35—48.

10. http://www.genenames.org/rna/TRNA#MTTRNA.

11. Если хотите узнать об этом побольше, можете снова обратиться к упомянутому выше хорошему учебнику по молекулярной биологии: Molecular Biology of the Cell, 5th Edition, авторы: Alberts, Johnson, Lewis, Raff, Roberts и Walter, 2012.

12. McFarland R, Schaefer AM, Gardner JL, Lynn S, Hayes CM, Barron MJ, Walker M, Chinnery PF, Taylor RW, Turnbull DM. Familial myopathy: new insights into the T14709C mitochondrial tRNA mutation. Ann Neurol. 2004 Apr; 55 (4):478-84.

13. Zheng J, Ji Y, Guan MX. Mitochondrial tRNA mutations associated with deafness. Mitochondrion. 2012 May; 12 (3):406-13.

14. Qiu Q, Li R, Jiang P, Xue L, Lu Y, Song Y, Han J, Lu Z, Zhi S, Mo JQ, Guan MX. Mitochondrial tRNA mutations are associated with maternally inherited hypertension in two Han Chinese pedigrees. Hum Mutât. 2012 Aug; 33(8):1285-93.

15. Giordano C, Perli E, Orlandi M, Pisano A, Tuppen HA, He L, lerinô R, Petruzziello L, Terzi A, Au tore C, Petrozza V, Gallo P, Taylor RW, d’Amati G. Cardiomyopathies due to homoplasmic mitochondrial tRNA mutations: morphologic and molecular features. Hum Pathol. 2013 Jul; 44(7); 1262—70.

16. Lincoln TA, Joyce GF. Self-sustained replication of an RNA enzyme. Science. 2009 Feb 27;323(5918):1229-32.

17. Sczepanski JT, Joyce GF. A cross-chiral RNA polymerase ribozyme. Nature. Опубликовано онлайн 29 октября 2014.

1. Обзор, посвященный роли Мус и важному значению хромосомных реаранжировок, см. в: Ott G, Rosenwald A, Campo Е. Understanding MYC-driven aggressive В-cell lymphomas: pathogenesis and classification. Blood. 2013 Dec 5;122(24):3884-91.

2. http://www.nlm.nih.gov/medlineplus/ency/article/001308.htm.

3. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee Tl, Young RA. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013 Apr 11;153(2):307-19.

4. Ostuni R, Piccolo V, Barozzi 1, PollettiS, Termanini A, BonifacioS, Curina A, Prospering E, Ghisletti S, Natoli G. Latent enhancers activated by stimulation in differentiated cells. Cell. 2013 Jan 17; 152(1-2): 157-71.

5. Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Baiasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012 May 11;336(6082):736-9.

6. 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.

7. Описание этих типов длинных некоднрующих РНК см. в: Ørom UA, Shiekhattar R. Long noncoding RNAs usher in a new era in the biology of enhancers. Cell. 2013 Sep 12; 154(6): 1190—3.

8. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010 Oct 1;143(1):46-58.

9. De Santa F, Barozzi 1, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010 May 11;8(5):e1000384.

10. Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013 Aug; 23(8):1210-23.

11. Lai F, Ørom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature. 2013 Feb 28;494(7438):497-501.

12. Risheg H, Graham JM Jr, Clark RD, Rogers RC, Opitz JM, Moeschler JB, Peiffer AP, May M, Joseph SM, Jones JR, Stevenson RE, Schwartz CE, Friez MJ. A recurrent mutation in MED12 leading to R961W causes Opitz-Kaveggia syndrome. Nat Genet. 2007 Apr; 39(4):451-3.

13. Роль суперэнхансеров в плюрипотентных клетках впервые выявлена в: Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA. Master transcription factors and mediator establish super-enhancers at key cell identity. Cell. 2013 Apr 11;153(2):307-19.

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.

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.

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.

9. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tänzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatiin J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigô R, Gingeras TR. Landscape of transcription in human cells. Nature. 2012 Sep 6:489(7414): 101-8.

10. Впервые я употребила это описание в своем посте на Huffington Post, рассуждая о проекте ENCODE. Оно мне настолько понравилось, что я решила использовать его и здесь. Вот ссылка на блог: http://www. huffingtonpost.com/nessa-carey/the-value-of-encode_b_1909153.html.

11. Хороший пример такой фотографии: http://blog.art21.org/ 2009/03/06/on-representations-of-the-artist-at-work-part-2/#.UyDZjZZFDIU.

12. Ward LD, Kellis M. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science. 2012 Sep 28:337(6102): 1675-8.