Несса Кэри - Мусорная ДНК. Путешествие в темную материю генома

13. Warburton PE, Cooke CA, Bourassa S, Vafa O, Sullivan BA, Stetten G, Gimelli G, Warburton D, Tyler-Smith C, Sullivan KF, Poirier GG, Earnshaw WC. Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres. Curr Biol. 1997 Nov 1;7(11):901-904.

14. Очень хороший анализ этой модели см. в: Sekulic N, Black BE. Molecular underpinnings of centromere identity and maintenance. Trends Biochem Sci. 2012 Jun; 37(6):220-229.

15. Подробнее об этом процессе и об эпигенетических модификациях, которые играют в нем свою роль, см. в: Gonzàlez-Barrios R, Soto-Reyes Е, Herrera LA. Assembling pieces of the centromere epigenetics puzzle. Epigenetics. 2012 Jan 1;7(1):3-13.

16. Из песенки «Что-то хорошее» киноверсии «Звуков музыки» (The Sound of Music) 1965, 20th Century Fox.

17. Особенно важен в этом отношении белок HJURP. Подробнее см. в: Sekulic N, Black BE. Molecular underpinnings of centromere identity and maintenance. Trends Biochem Sci. 2012 Jun; 37(6):220-9.

18. Palmer DK, O’Day K, Margolis RL. The centromere specific histone CENP-A is selectively retained in discrete foci in mammalian sperm nuclei. Chromosoma. 1990 Dec; 100(l):32-6.

19. Schiff PB, Fant J, HorwitzSB. Promotion of microtubule assembly in vitro by taxol. Nature. 1979 Feb 2;277(5698):665-7.

20. http://www.cancerresearchuk.org/cancer-help/about-cancer/ treatment/cancer-drugs/paclitaxel.

21. Цифра приведена в: Rajagopalan H. Lengauer С. Aneupioidy and cancer. Nature. 2004 Nov 18;432(7015):338-41.

22. Обзор на эту тему: Pfau SJ, Amon A. Chromosomal instability and aneupioidy in cancer: from yeast to man. EM BO Rep. 2012 Jun 1;13(6):515-27.

23. Rehen SK, Yung YC, McCreight MP, Kaushal D, Yang AH, Almeida BS, Kingsbury MA, Cabral KM, McConnell MJ, Anliker B, Fontanoz M, Chun J. Constitutional aneupioidy in the normal human brain. J Neurosci. 2005 Mar 2;25(9):2176-80.

24. Rehen SK, McConnell MJ, Kaushal D, Kingsbury MA, Yang AH, Chun J. Chromosomal variation in neurons of the developing and adult mammalian nervous system. Proc Natl Acad Sci USA. 2001 Nov 6;98(23):13361-6.

25. Kingsbury MA, Friedman B, McConnell MJ, Rehen SK, Yang AH, Kaushal D, Chun J. Aneuploid neurons are functionally active and integrated into brain circuitry. Proc Natl Acad Sci USA. 2005 Apr 26; 102(17):6143-7.

26. Melchiorri C, Chieco P, Zedda AI, Coni P, Ledda-Columbano GM, Columbano A. Ploidy and nuclearity of rat hepatocytes after compensatory regeneration or mitogen-induced liver growth. Carcinogenesis. 1993 Sep; 14(9):1825-30.

27. Замечательный рассказ о бурных спорах вокруг того, кто первым идентифицировал причину синдрома Дауна (эти споры не утихают и сейчас, полвека спустя): http://www.nature.com/news/down-s-syn-drome-discovery-dispute- resurfaces-in-france-1.14690.

28. Медицинские и социальные аспекты синдрома Дауна подробно обсуждаются во многих группах поддержки пациентов. См., напр.: http://www.downs-syndrome.org.uk.

29. http://www.nhs.uk/conditions/edwards-syndrome/Pages/Introduction.aspx.

30. http://www.cafamily.org.uk/medical-inforination/conditions/p/patau-syndrome.

31. Toner JP, Grainger DA, Frazier LM. Clinical outcomes among recipients of donated eggs: an analysis of the U. S. national experience, 1996-1998. Fertil Steril. 2002 Nov; 78(5):1038-45.

1. Statistical Bulletin from the Office for National Statistics, 8 August 2013 Annual Mid-year Population Estimates, 2011 and 2012.

2. Вероятно, впервые важная роль этого гена продемонстрировала в: Berta Р, Hawkins JR, Sinclair АН, Taylor A, Griffiths BL, Goodfellow PN, Fellous M. Genetic evidence equating SRY and the testis-determining factor. Nature. 1990 Nov 29;348(6300):448-50.

3. Yamauchi Y, Riel JM, Stoytcheva Z, Ward MA. Two Y genes can replace the entire Y chromosome for assisted reproduction in the mouse. Science. 2014 Jan 3;343(6166):69-72.

4. Ross MT et al., The DNA sequence of the human X chromosome. Nature. 2005 Mar 17;434(7031):325-37.

5. Brown CJ, Lafreniere RG, Powers VE, Sebastio G, Ballabio A, Pettigrew AL, Ledbetter DH, Levy E, Craig IW, Willard HF. Localization of the X inactivation centre on the human X chromosome in Xq13. Nature. 1991 Jan 3;349(6304):82-84.

6. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature. 1991 Jan 3;349(6304):38-44.

7. Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell. 1992 Oct 30;71(3):527-42.

8. Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, SwiftS, Rastan S. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell. 1992 Oct 30;71(3):515-26.

9. Lee JT, Strauss WM, Dausman JA, Jaenisch R. A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell. 1996 Jul 12;86(1):83-94.

10. Всеобъемлющее описание данного процесса см. в: Lee JT. The X as model for RNA’s niche in epigenomic regulation. Cold Spring Harb Perspect Biol. 2010 Sep; 2(9):a003749.

11. Xu N, Tsai CL, Lee JT. Transient homologous chromosome pairing marks the onset of X inactivation. Science. 2006 Feb 24:311(5764):1149-52.

12. Удивительные подробности распространения гемофилии среди царствующих домов Европы см. в: http://www.hemophilia.org/NHFWeb/MainPgs/MainNHF.aspx?menuid=178&contentid=6.

13. Подробности об этом заболевании см. в: http://www.nhs.uk/con-ditions/Rett-syndrome/Pages/lntroduction.aspx.

14. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet. 1999 Oct; 23(2):185-8.

15. Подробности об этом заболевании см. в: http://www.nlm.nih.gov/medlineplus/ency/article/000705.htm.

16. Hoffman EP, Brown RH Jr, Kunkel LM. Dystrophin: the protein product of the Duchenne muscular dystrophy locus. Cell. 1987 Dec 24;51(6):919-28.

17. Pena SD, Karpati G, Carpenter S, Fraser FC. The cllnicafconse^ quences of X'chromosome inactivation: Duchenne muscular dystrophy in one of monozygotic twins. J Neurol Scl. 1987 Jul; 79(3):337-44.

18. Shin T, Kraemer D, Pryor J, Liu L, Rugila J, Howe L, Buck S, Murphy K, Lyons L, Westhusin M. A cat cloned by nuclear transplantation. Nature. 2002 Feb 21;415(6874):859.

1. Schmitt AM, Chang H Y. Gene regulation: Long RNAs wire up cancer growth. Nature. 2013 Aug 29;500(7464):536-7.

2. Volders PJ, Helsens K, Wang X, Menten В, Martens L, Gevaert К, Vandesompele J, Mestdagh P. LNCipcdia: a database for annotated human long-noncoding RNA transcript sequences and structures. Nucleic Acids Res. 2013 Jan; 41(Database issue):D246-51.

3. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham 1, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

4. Tay Y, Rinn J, Pandolf PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16;505(7483):344-52.

5. Derrien T, Johnson R, Bussotti G, Tänzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigô R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep; 22(9): 1775-89.

6. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of HncRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011 Dec 23;147(7): 1537-50.

7. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25( 18): 1915-27.

8. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschieb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP. Mouse Genome Sequencing Consortium. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol. 2009 May 5;7(5):el000112.

9. 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.

10. Wahlestedt C. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Dlscov. 2013 Jun; 12(6):433-46.

11. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA. 2008 Jan 15;105(2):716-21.

12. Очень полезный обзор этого класса, объясняющий, какую роль он играет среди длинных некодирующих РНК, см. в: Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell. 2013 Jul 3;154(1):26-46.

13. 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.

14. Wang КС, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011 Apr 7;472(7341): 120-4.

15. Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep. 2013 Oct 17;5(1):3—12.

16. Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol. 2013 Jul; 20(7):908-13.

17. Полезный обзор этой области см. в: Cheetham SW, Gruhl F, Mattick JS, Dinger ME. Long noncoding RNAs and the genetics of cancer. Br J Cancer. 2013 Jun 25;108(12):2419-25.

18. Yap KL, Li S, Mufloz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010 Jun 11;38(5):662-74.

19. 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.

20. Yang Z, Zhou L, Wu LM, Lai MC, Xie HY, Zhang F, Zheng SS. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann Surg Oncol. 2011 May; 18(5):1243-50.

21. Ishibashi M, Kogo R. Shibata K, Sawada G. Takahashi Y, Kurashige J, Akiyoshi S, Sasaki S, Iwaya T, Sudo T, Sugimachi K. Mi mo r і K, Wakabayashi G, Mori M. Clinical significance of the expression of long non-coding RNA HOTAIR in primary hepatocellular carcinoma. Oncol Rep. 2013 Mar; 29(3):946-50.

22. Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, Kim S, Safe S. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene. 2013 Mar 8;32(13): 1616-25.

23. Gupta RA, Shah N, Wang КС, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010 Apr 15;464(7291): 1071-6.

24. Yang L, Lin C, Jin C, Yang JC, Tanasa B, Li W, Merkurjev D, Ohgi KA, Meng D, Zhang J, Evans CP, Rosenfeld MG. Long-noncoding RNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature. 2013 Aug 29;500(7464):598-602.

25. Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM. The long noncoding RNA SChLAPl promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet. 2013 Nov; 45 (11):1392-8.