Книга: Мусорная ДНК. Путешествие в темную материю генома

Примечания

Примечания

1. Информацию об этом заболевании и его генетике см. в: www. omim.org record #160900.

2. Подробнее см. в: http://ghr.nlm.nih.gov/condition/myotonic-dystrophy.

3. Подробнее см. в: http://www.ninds.nih.gov/disorders/friedre-ichs_ataxia/detail_friedreichs_ataxia.htm.

4. Подробнее см. в: http://ghr.nlm.nih.gov/condition/facioscapulo-humeral-muscular-dystrophy.

1. http://www.escapistmagazine.com/news/view/113307-Virtual-Typewriter-Monkeys-Pen-Complete-Works-of-Shakespeare-Almost.

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3. Bidichandani SI, Ashizawa T, Patel PI. The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA. Am J Hum Genet. 1998 Jan; 62(1 ):111-21.

4. Babcock M, de Silva D, Oaks R, Davis-Kaplan S, Jiralerspong S, Montermini L, Pandolfo M, Kaplan J. Regulation of mitochondrial iron accumulation by Yfh1p, a putative homolog of frataxin. Science. 1997 Jun 13; 276(5319): 1709-12.

5. Kremer EJ, Pritchard M, Lynch M, YuS, Holman K, Baker E, Warren ST, Schlessinger D, Sutherland GR, Richards RI. Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p () n. Science. 1991 Jun 21; 252(5013):1711-4

6. Verkerk AJ, Pieretti M, Sutcliffe JS, Fu YH, Kuhl DP, Pizzuti A, Reiner O, Richards S, Victoria MF, Zhang FP, et al. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell. 1991 May 31; 65(5):905 14.

7. Pieretti M, Zhang FP, Fu YH, Warren ST, Oostra BA, Caskey CT, Nelson DL. Absence of expression of the FMR-1 gene in fragile X syndrome. Cell. 1991 Aug 23;66(4):817-22.

8. Qin M, Kang J, Burlin TV, JiangC, Smith CB. Postadolescent changes in regional cerebral protein synthesis: an in vivo study in the FMR1 null mouse. J Neurosci. 2005 May 18;25(20):5087-95.

9. Цит. по: Echeverria GV, Cooper TA. RNA-binding proteins in microsatellite expansion disorders: mediators of RNA. Brain Res. 2012 Jun 26; 1462:100-11.

1. http://www.genome.gov/11006943.

2. Если не оговорено обратное, основная часть информации в этой главе почерпнута из номера Nature, вышедшего 15 февраля 2001 года и содержащего результаты, полученные консорциумом, работавшим при помощи государственного финансирования, и их анализ. Прежде всего следует сослаться на текст «Initial sequencing and analysis of the human genome», автором которого является международный консорциум «Геном человека» (International Human Genome Sequencing Consortium). Дополнительные комментарии можно найти в том же номере Nature.

3. http://partners.nytimes.com/library/national/science/062700sci-genome-text.html.

4. http://news.bbc.co.uk/1/hi/sci/tech/807126.stm.

5. http://news.bbc.co.uk/1/hi/sci/tech/807126.stm.

6. http://www.genome.gov/sequencingcosts.

7. http://www.wired.co.uk/news/archive/2014-01/15/1000-dollar-genome.

8. Необыкновенные подробности этого случая см. в: Gura, Nature, 2012, Volume 483, 20-22.

9. http://www.cancerresearchuk.org/cancer-help/about-cancer/treatment/cancer-drugs/Crizotinib/crizotinib.

10. https://genographic.nationalgeographic.com/human-journey.

11. http://publications.nigms.nih.gov/insidelifescience/genetics-numbers.html.

12. Aparicio et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Aug 23: 297(5585): 1301-10.

13. Baltimore D. Our genome unveiled. Nature. 2001 Feb 15;409(6822):814-6.

14. Данные Американского онкологического общества: http://www.cancer.org/cancer/skincancer-melanoma/detailedguide/melanoma-skin-cancer-key-statistics.

1. Если не оговорено обратное, основная часть информации в этой главе почерпнута из номера Nature, вышедшего 15 февраля 2001 года и содержащего результаты, полученные консорциумом, работавшим при помощи государственного финансирования, и их анализ. Прежде всего следует сослаться на текст «Initial sequencing and analysis of the human genome», автором которого является международный консорциум «Геном человека» (International Human Genome Sequencing Consortium). Представляют интерес и комментарии, которые делают в том же номере David Baltimore, а также Li и др. Эти комментарии, пожалуй, наиболее приемлемы по стилю и содержанию.

2. Vlangos CN, Siuniak AN, Robinson D, Chinnaiyan AM, Lyons RH Jr, Cavalcoli JD, Keegan CE. Next-generation sequencing identifies the Danforth’s short tail mouse mutation as a retrotransposon insertion affecting Ptf1a expression. PLoS Genet. 2013;9(2):e1003205.

3. Bogdanik LP, Chapman HD, Miers KE, Serreze DV, Burgess RW. A MusD retrotransposon insertion in the mouse Slc6a5 gene causes alterations in neuromuscular junction maturation and behavioral phenotypes. PLoS One. 2012;7(1):e30217.

4. Schneuwly S, Klemenz R. Gehring WJ. Redesigning the body plan of Drosophila by ectopic expression of the homeotic gene Antennapedia. Nature. 1987 Feb 26 — Mar 4;325(6107):816-8.

5. Mortlock DP, Post LC, Innis JW. The molecular basis of hypodactyly (Hd): a deletion in Hoxa 13 leads to arrest of digital arch formation. Nat Genet. 1996 Jul; 13(3):284-9.

6. Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Spitz F, Constam DB, Trono D. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature. 2010 Jan 14;463(7278):237-40.

7. Young GR, Eksmond U, Salcedo R, Alexopoulou L, Stoye JP, Kassiotis G. Resurrection of endogenous retroviruses in antibody-deficient mice. Nature. 2012 Nov 29;491(7426):774-8.

8. http://www.emedicinehealth.com/heart_and_lung_transplant/article_em.htm

9. Недавно вышел интересный обзор, посвященный ксенотрансплантации: Cooper DK. A brief history of cross-species organ transplantation. Proc (Bayl Univ Med Cent). 2012 Jan; 25(1):49-57.

10. Patience C, Takeuchi Y, Weiss RA. Infection of human cells by an endogenous retrovirus of pigs. Nat Med. 1997 Mar; 3(3):282-6.

11. Di Nicuolo G, D’Alessandro A, Andria B, Scuderi V, Scognamiglio M, Tammaro A, Mancini A, Cozzolino S, Di Florio E, Bracco A, Calise F, Chamuleau RA. Long-term absence of porcine endogenous retrovirus infection in chronically immunosuppressed patients after treatment with the porcine cell-based Academic Medical Center bioartificial liver. Xenotransplantation. 2010 Nov — Dec; 17(6):431-9.

12. Недавно появился полезный обзор исследований эффектов такого удвоения сегментов генетического материала, в том числе и при аномальном кроссинговере: Rudd МК, Keene J, Bunke В, Kaminsky ЕВ, Adam MP, Mulle JG, Ledbetter DH, Martin CL. Segmentai duplications mediate novel, clinically relevant chromosome rearrangements. Hum Mol Genet. 2009 Aug 15;18(16):2957-62.

13. Подробнее об этом заболевании и его причинах см. в: http:// www.ninds.nih.gov/disorders/charcot_marie_tooth/detail_charcot_marie_tooth.htm.

14. Подробнее об этом заболевании и его причинах см. в: http:// www.nlm.nih.gov/mediineplus/ency/article/001116.htm.

15. Mombaerts Р. The human repertoire of odorant receptor genes and pseudogenes. Annu Rev Genomics Hum Genet. 2001;2:493-510.

16. http://www.innocenceproject.org/know, по состоянию на 1 января 2014.

1. Сведения о сборах даются по: http://www.imdb.com.

2. Цит. по: Boxer LM, Dang CV. Translocations involving c-myc and c-myc function. Oncogene. 2001 Sep 20(40):5595-610.

3. Moyzis RK, Buckingham JM, Cram LS, Dani M, Deaven LL, Jones MD, Meyne J, Ratliff RL, Wu JR. A highly conserved repetitive DNA sequence, (TTAGGG) n, present at the telomeres of human chromosomes. Proc Natl Acad Sci USA. 1988 Sep; 85(18):6622-6.

4. Vaziri H, Sch?chter F, Uchida I, Wei L, Zhu X, Effros R, Cohen D, Harley CB. Loss of telomeric DNA during aging of normal and trisomy 21 human lymphocytes. Am J Hum Genet. 1993 Apr; 52(4):661-7.

5. Hayfick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961 Dec; 25:585-621.

6. Harley CB, Futcher AB, Greider CW. Telomeres shorten during ageing of human fibroblasts. Nature. 1990 May 31;345(6274):458-60.

7. Bodnar AG, Ouellette M, Frolkis M, Holt SE, Chiu CP, Morin GB, Harley CB, Shay JW, Lichtsteiner S, Wright WE. Extension of life-span by introduction of telomerase into normal human cells. Science. 1998 Jan 16;279(5349):349-52.

8. Полезное обсуждение проблемы см. в: Armanios M, Blackburn EH. The telomere syndromes. Nat Rev Genet. 2012 Oct; 13(10):693-704.

9. Полезный обзор см. в: Armanios М, Blackburn EH. The telomere syndromes. Nat Rev Genet. 2012 Oct; 13(10):693-704.

10. Wright WE, Piatyszek MA, Rainey WE, Byrd W, Shay JW. Telomerase activity in human germline and embryonic tissues and cells. Dev Genet. 1996;18(2):173-9.

11. Kim NW, Piatyszek MA, Prowse KR, Harley CB, West MD, Ho PL, Coviello GM, Wright WE, Weinrich SL, Shay JW. Specific association of human telomerase activity with immortal cells and cancer. Science. 1994 Dec 23;266(5193):2011-5.

12. http://www.nlm.nih.gov/medlineplus/ency/anatomyvideos/000104.htm.

13. Chiu CP, Dragowska W, Kim NW, Vaziri H, Yui J, Thomas ТЕ, Harley CB, Lansdorp PM. Differential expression of telomerase activity in hematopoietic progenitors from adult human bone. Stem Cells. 1996 Mar; 14(2):239-48.

14. Vaziri H, Dragowska W, Allsopp RC, Thomas ТЕ, Harley CB, Lansdorp PM. Evidence for a mitotic clock in human hematopoietic stem cells: loss of telomeric DNA with age. Proc Natl Acad Set USA. 1994 Oct ll;91(21):9857-60.

15. Armanios M, Blackburn EH. The telomere syndromes. Nat Rev Genet. 2012 Oct; 13(10):693-704.

16. Armanios M, Blackburn EH. The telomere syndromes. Nat Rev Genet. 2012 Oct; 13(10):693-704.

17. Отличное клиническое описание и полезные иллюстрации см. в: Calado RT, Young NS. Telomere diseases. N Engl J Med. 2009 Dec 10;361(24):2353-65.

18. Alder JK, Chen JJ, Lancaster L, Danoff S, Su SC, Cogan JD, Vulto I, Xie M, Qi X, Tuder RM, Phillips JA 3rd, Lansdorp PM, Loyd JE, Armanios MY. Short telomeres are a risk factor for idiopathic pulmonary fibrosis. Proc Natl Acad Sci USA. 2008 Sep 2;105(35):13051-6.

19. Armanios MY, Chen JJ, Cogan JD, Alder JK, Ingersoll RG, Markin C, Lawson WE, Xie M, Vulto I, Phillips JA 3rd, Lansdorp PM, Greider CW, Loyd JE. Telomerase mutations in families with idiopathic pulmonary fibrosis. N Engl J Med. 2007 Mar 29;356(13):1317-26.

20. Tsakiri KD,CronkhiteJT, Kuan PJ, XingC, RaghuG, Weissler JC, Rosenblatt RL, Shay JW, Garcia CK. Adult-onset pulmonary fibrosis caused by mutations in telomerase. Proc Natl Acad Sei USA. 2007 May 1;104(18):7552-7.

21. Cronkhite JT, Xing C, Raghu G, Chin KM, Torres F, Rosenblatt RL, Garcia CK. Telomere shortening in familial and sporadic pulmonary fibrosis. Am J Respir Crit Care Med. 2008 Oct 1;178(7):729-37.

22. Полезное описание см. в: see http://www.patient.co.uk/doctor/aplastic-anaemia.

23. de la Fuente J, Dokal I. Dyskeratosis congenita: advances in the understanding of the telomerase defect and the role of stem cell transplantation. Pediatr Transplant. 2007 Sep; 11(6):584-94.

24. Armanios M, Chen JL, Chang YP, Brodsky RA, Hawkins A, Griffin CA, Eshleman JR, Cohen AR, Chakravarti A, Hamosh A, Greider CW. Haploinsufficiency of telomerase reverse transcriptase leads to anticipation in autosomal dominant dyskeratosis congenita. Proc Natl Acad Sci USA. 2005 Nov 1;102(44):15960-4.

25. http://www.who.int/mediacentre/factsheets/fs339/en.

26. Alder JK, Guo N, Kembou F, Parry EM, Anderson CJ, Gorgy AI, Walsh MF, Sussan T, Biswal S, Mitzner W, Tuder RM, Armanios M. Telomere length is a determinant of emphysema susceptibility. Am J Respir Crit Care Med. 2011 Oct 15;184(8):904-12.

27. Цит. no: Sahin E, Depinho RA. Linking functional decline of telomeres, mitochondria and stem cells during ageing. Nature. 2010 Mar 25;464(7288):520-528.

28. Статистика дается по данным American Heart Association on Older Americans & Cardiovascular Diseases (Американской ассоциации изучения сердца пожилых американцев и сердечно-сосудистых заболеваний), 2013.

29. http://www.rcpsych.ac.uk/healthadvice/problemsdisorders/depressioninolderadults.aspx.

30. Valdes AM, Andrew T, Gardner JP, Kimura M, Oelsner E, Cherkas LF, Aviv A, Spector TD. Obesity, cigarette smoking, and telomere length in women. Lancet. 2005 Aug 20-26;366(9486):662-4.

31. Cawthon RM, Smith KR, O’Brien E, Sivatchenko A, Kerber RA. Association between telomere length in blood and mortality in people aged 60 years or older. Lancet. 2003 Feb 1;361(9355):393-5.

32. Fitzpatrick AL, Kronmal RA, Kimura M, Gardner JP, Psaty BM, Jenny NS, Tracy RP, Hardikar S, Aviv A. Leukocyte telomere length and mortality in the Cardiovascular Health Study. J Gerontol A Biol Sci MedSci. 2011 Apr; 66<4):421-9.

33. Atzmon G, Cho M, Cawthon RM, Budagov T, Katz M, Yang X, Siegel G, Bergman A, Huffman DM, Schechter CB, Wright WE, Shay JW, Barzilai N, Govindaraju DR, Suh Y. Evolution in health and medicine Sackler colloquium: Genetic variation in human telomerase is associated with telomere length in Ashkenazi centenarians. Proc Natl Acad Sci USA. 2010 Jan 26;107 Suppl 1:1710-7.

34. Segerstrom SC, Miller GE. Psychological stress and the human immune system: a meta-analytic study of 30 years of inquiry. Psychol Bull. 2004 Jul; 130(4):601-30.

35. Epel ES, Blackburn EH, Lin J, Dhabhar FS, Adler NE, Morrow JD, Cawthon RM. Accelerated telomere shortening in response to life stress. Proc Natl Acad Sci USA. 2004 Dec 7; 101(49): 17312-5.

36. http://www.who.int/mediacentre/factsheets/fs311/en/index.html.

37. Полезное введение в эту область см. в: Tennen RI, Chua KF. Chromatin regulation and genome maintenance by mammalian SIRT6. Trends Biochem Sci. 2011 Jan; 36(l):39-46.

38. Valdes AM, Andrew T, Gardner JP, Kimura M, Oelsner E, Cherkas LF, Aviv A, Spector TD. Obesity, cigarette smoking, and telomere length in women. Lancet. 2005 Aug 20-26;366(9486):662-4.

39. UNFPA report on Ageing in The Twenty-First Century (Доклад Фонда ООН в области народонаселения «Старение в XXI веке»), 2012.

40. Jennings BJ, Ozanne SE, Dorling MW, Hales CN. Early growth determines longevity in male rats and may be related to telomere shortening in the kidney. FEBS Lett. 1999 Apr 1;448(1):4-8.

1. Из: The King and I («Король и я»), 1956, автор сценария Ernest Lehman, 20th Century Fox.

2. Хороший обзор типов центромер различных ветвей эволюционного древа см. в: Ogiyama Y, Ishii К. The smooth and stable operation of centromeres. Genes Genet Syst. 2012;87(2):63-73.

3. Полезный обзор: Verdaasdonk JS, Bloom K. Centromeres: unique chromatin structures that drive chromosome segregation. Nat Rev Mol Cell Biol. 2011 May; 12(5):320-32.

4. Palmer DK, O’Day K, Wener MH, Andrews BS, Margolis RL. A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol. 1987 Apr; 104(4):805-15.

5. Takahashi К, Chen ES, Yanagida M. Requirement of Mis6 centromere connector for localizing a CENP-A-like protein in fission yeast. Science. 2000 Jun 23;288(5474):2215-9.

6. Blower MD, Karpen GH. The role of Drosophila CID in kinetochore formation, cell-cycle progression and heterochromatin interactions. Nat Cell Biot. 2001 Aug; 3(8):730-9.

7. Hori T, Amano M, Suzuki A, Backer CB, Welburn JP, Dong Y, McEwen BF, Shang WH, Suzuki E, Okawa K, Cheeseman IM, Fukagawa T. CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell. 2008 Dec 12;135(6):1039-52.

8. Heun P, Erhardt S, Blower MD, Weiss S. Skora AD, Karpen GH?f-Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores. Dev Cell. 2006 Mar; 10(3):303-15.

9. Van Hooser AA, Ouspenski II, Gregson HC, Starr DA, Yen TJ, Goldberg ML, Yokomori K, Earnshaw WC, Sullivan KF, Brinkley BR. Specification of kinetochore-forming chromatin by the histone H3 variant CENP-A. J Cell Sci. 2001 Oct; 114(Pt 19):3529-42.

10. Zuccolo M, Alves A, Galy V, Bolhy S, Formstecher E, Racine V, Sibarita JB, Fukagawa T, Shiekhattar R, Yen T, Doye V. The human Nupl07-160 nuclear pore subcomplex contributes to proper kinetochore functions. EMBO J. 2007 Apr 4;26(7): 1853-64.

11. Palmer DK, O’Day K, Wener MH, Andrews BS, Margolis RL. A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol. 1987 Apr; 104(4):805-15.

12. Sekulic N, Bassett EA, Rogers DJ, Black BE. The structure of (CENP-A-H4) (2) reveals physical features that mark centromeres. Nature. 2010 Sep 16;467(7313):347-51.

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: Gonz?lez-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.

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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, Lafreni?re 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.

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

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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.

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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.

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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 m?thylation 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.

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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.

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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.

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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 Mut?t. 2012 Aug; 33(8):1285-93.

15. Giordano C, Perli E, Orlandi M, Pisano A, Tuppen HA, He L, lerin? 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.

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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.

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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: rom 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. rom 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, rom 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. Lov?n 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, T?nzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatiin J, Williams BA, Zaleski C, Rozowsky J, R?der 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, Guig? 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.

13. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 6;489(7414).

14. Потрясающий пример межпоколенческого эпигенетического наследования с передачей реакции страха от родителя к детенышам изложен в: Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci. 2014 Jan; 17(1):89—96.

15. Graur D, Zheng Y, Price N, Azevedo KB, Zufall RA, Elhaik E. On the immortality of television sets: «function» in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 2013;5(3):578-90.

1. http://womenshistory.about.eom/od/mythsofwomenshistory/a/ Did-Anne-Boleyn-Really-Have-Six-Fingers-On-One-Hand.htm.

2. Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, Oostra BA, Goode D, Elgar G, Hill RE, de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 2003 Jul 15;12(14): 1725-35.

3. www.hemingwayhome.com/cats.

4. Lettice LA, Hill AE, Devenney PS, Hill RE. Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly. Hum Mol Genet. 2008 Apr 1;17(7):978-85.

5. Подробнее см. в: http://www.genome.gov/12512735.

6. Jeong Y, Leskow PC, El-Jaick K, Roessler E, Muenke M, Yocum A, Du bourg C, Li X, Geng X, Oliver G, Epstein DJ. Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat Genet. 2008 Nov; 40(ll):1348-53.

7. Подробнее см. в: http://rarediseases.info.nih.gov/gard/10874/pancreatic-agenesis/resources/1.

8. Lan go Allen H, Flanagan SE, Shaw-Smith C, De Franco E, Akerman I, Caswell R; International Pancreatic Agenesis Consortium, Ferrer J, Hattersley AT, Ellard S. GATA6 haploinsufficiency causes pancreatic agenesis in humans. Nat Genet. 2011 Dec 11;44(1):20-2.

9. SellickGS, BarkerKT,Stolte-DijkstraI,FleischmannC,Coleman RJ, Garrett C, Gloyn AL, Edghill EL, Hattersley AT, Wellauer PK, Goodwin G, Houlston RS. Mutations in PTF1A cause pancreatic and cerebellar agenesis. Nat Genet. 2004 Dec; 36(12):1301-5.

10. Weedon MN, Cebola I, Patch AM, Flanagan SE, De Franco E, Caswell R, Rodriguez-Segui SA, Shaw-Smith C, Cho CH, Lango Allen H, Houghton JA, Roth CL, Chen R, Hussain K, Marsh P, Vallier L, Murray A; International Pancreatic Agenesis Consortium, Ellard S, Ferrer J, Hattersley AT. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet. 2014 Jan; 46(1):61 —4.

11. Обзор на эту тему: Sturm RA. Molecular genetics of human pigmentation diversity. Hum Mol Genet. 2009 Apr 15;18(R1):R9-17.

12. Durham-Pierre D, Gardner JM, Nakatsu Y, King RA, Francke U, Ching A, Aquaron R, del Marmol V, Brilliant MH. African origin of an intragenic deletion of the human P gene in tyrosinase positive oculoeutane^-ous albinism. Nat Genet. 1994 Jun; 7(2): 176—9.

13. Visser M, Kayser M, Palstra RJ. HERC2 rsl2913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res. 2012 Mar; 22(3):446 455.

14. Наиболее современный каталог см. в: www.genome.gov/gwas-tudies.

15. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential ?tiologie and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Set USA. 2009 Jun 9;106(23):9362-7.

16. Gorkin DU, Ren B. Genetics: Closing the distance on obesity culprits. Nature. 2014 Mar 20;507(7492):309-10.

17. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, Perry JR, Elliott KS, Lango H, Rayner NW, Shields B, Harries LW, Barrett JC, Ellard S, Groves CJ, Knight B, Patch AM, NessAR, Ebrahim S, Lawlor DA, Ring SM, Ben-Shlomo Y, Jarvelin MR, Sovio U, Bennett AJ, Melzer D, Ferrucci L, Loos RJ, Barroso I, Wareham NJ, Karpe F, Owen KR, Cardon LR, Walker M, Hitman GA, Palmer CN, Doney AS, Morris AD, Smith GD, Hattersley AT, McCarthy MI. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science. 2007 May 11;316(5826):889-94.

18. Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, Najjar S, Nagaraja R, Orr? M, UsalaG, Dei M, LaiS, Maschio A, BusoneroF, Mulas A, Ehret GB, Fink AA, Weder AB, Cooper RS, Galan P, Chakravarti A, Schlessinger D, Cao A, Lakatta E, Abecasis GR. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoSGenet. 2007 Jul; 3(7):e115.

19. Church C, Moir L, McMurray F, Girard C, Banks GT, Teboul L, Wells S, Br?ning JC, Nolan PM, Ashcroft FM, Cox RD. Overexpression of Fto leads to increased food intake and results in obesity. Nat Genet. 2010 Dec; 42(12):1086 92.

20. Fischer J, Koch L, Emmerling C, Vierkotten J, Peters T, Br?ning JC, R?ther U. Inactivation of the Fto gene protects from obesity. Nature. 2009 Apr 16;458 (7240):894-8.

21. Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, G?mez-Marin C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK, Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC, Gomez-Skarmeta JL, N?brega MA. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014 Mar 20;507( 7492):371-5.

22. Недавний обзор работ в этой сфере: Trent RJ, Cheong PL, Chua EW, Kennedy MA. Progressing the utilisation of pharmacogenetics and pharma-cogenomics into clinical care. Pathology. 2013 Jun; 45(4):357-70.

23. http://www.nhs.uk/Conditions/Herceptin/Pages/Introduction.aspx.

24. http://www.nature.com/scitable/topicpage/gleevec-the-break-through-in-cancer-treatment-565.

25. http://www.cancer.gov/cancertopics/druginfo/fda-crizotinib.

1. Примеры таких случаев можно найти в: http://medicalmisdiagnosisresearch.wordpress.com/category/osteogeiiesis-imperfecta-misdiag-nosed-as-child-abuse.

2. Хорошее описание симптомов и генетики этого заболевания см. в: http://ghr.nlm.nih.gov/condition/osteogenesis-imperfecta.

3. Cho TJ, Lee KE, Lee SK, Song SJ, Kim KJ, Jeon D, Lee G, Kim HN, Lee HR, Eom HH, Lee ZH, Kim OH, Park WY, Park SS, Ikegawa S, Yoo WJ, Choi IH, Kim JW. A single recurrent mutation in the 5'-UTR of 1FITM5 causes osteogenesis imperfecta type V. Am J Hum Genet. 2012 Aug 10;91(2):343-8.

4. Semler O, Garbes L, Keupp K, Swan D, Zimmermann K, Becker J, Iden S, Wirth B, Eysel P, Koerber F, Schoenau E, BohlanderSK, Wollnik B, Netzer C. A mutation in the 5'-UTR of IFITM5 creates an in-frame start codon and causes autosomal-dominant osteogenesis imperfecta type V with hyperplastic callus. Am J Hum Genet. 2012 Aug 10;91(2):349-57.

5. Moffatt P, Gaumond MH, Salois P, Sellin К, Bessette MC, Godin E, de Oliveira PT, Atkins GJ, Nanci A, Thomas G. Bril: a novel bone-specific modulator of mineralization.«/ Bone Miner Res. 2008 Sep: 23(9): 1497-508.

6. Liu L, Dilworth D, Gao L, Monzon J, Summers A, Lassam N, Hogg D. Mutation of the CDKN2A 5' UTR creates an aberrant initiation codon and predisposes to melanoma. Nat Genet. 1999 Jan; 21(1):128-32.

7. Tietze JK, Pfob M, Eggert M, von Preu?en A, Mehraein Y, Ruzicka T, Herzinger T. A non-coding mutation in the 5' untranslated region of patched homologue 1 predisposes to basal cell carcinoma. Exp Dermatol. 2013 Dec; 22(12):834-5.

8. Полное описание см. в: http://omim.org/entry/309550.

9. Ashley CT Jr, Wilkinson KD, Reines D, Warren ST. FMR1 protein: conserved RNP family domains and selective RNA binding. Science. 1993 Oct 22;262(5133):563-6.

10. Qin M, Kang J, Burlin TV, Jiang C, Smith CB. Postadolescent changes in regional cerebral protein synthesis: an in vivo study in the FMR1 null mouse. J Neurosci. 2005 May 18;25(20):5087-95.

11. Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S. Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J Comp Neurol. 2009 Apr 10;513(5):532-41.

12. Drachman DA. Do we have brain to spare? Neurology. 2005 Jun 28;64(12):2004-5.

13. Darnell JC, Van DriescheSJ, ZhangC, Hung KY, Mele A, FraserCE, Stone EF, Chen C, Fak JJ, Chi SW, Licatalosi DD, Richter JD, Darnell RB. FMRP stalls ribosomal translocation on messenger RNAs linked to synaptic function and autism. Cell. 2011 Jul 22;146 (2):247-61.

14. Udagawa T, Farny NG, Jakovcevski M, Kaphzan H, Alarcon JM, Anilkumar S, Ivshina M, Hurt JA, Nagaoka K, Nalavadi VC, Lorenz LJ, Bassell GJ, Akbarian S, Chattarji S, Klann E, Richter JD. Genetic and acute CPEB1 depletion ameliorate fragile X pathophysiology. Nat Med. 2013 Nov; 19(11):1473-7.

15. Кратко изложено в: http://www.ncbi.nlm.nih.gov/books/NBK1165.

16. Jiang H, Mankodi A, Swanson MS, Moxley RT, Thornton CA. Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons. Hum Mol Genet. 2004 Dec 15;13(24):3079-88.

17. Savkur RS, Philips AV, Cooper ТА. Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy. Nat Genet. 2001 Sep; 29(1):40-7.

18. HoTH, Charlet-BN, Poulos MG, Singh G, Swanson MS, Cooper ТА. Muscleblind proteins regulate alternative splicing. EMBO J. 2004 Aug 4;23(15):3103-12.

19. Kino Y, Washizu C, Oma Y, Onishi H, Nezu Y, Sasagawa N, Nukina N, Ishiura S. MBNL and CELF proteins regulate alternative splicing of the skeletal muscle chloride channel CLCN1. Nucleic Acids Res. 2009 Oct; 37(19):6477-90.

20. Hanson EL, Jakobs PM, Keegan H,Coates K, BousmanS, Dienel NH, Litt M, Hershberger RE. Cardiac troponin T lysine 210 deletion in a family with dilated cardiomyopathy. J Card Fail. 2002 Feb; 8(1):28-32.

21. Цит. no: Michalova E, Vojtesek B, Hrstka R. Impaired pre-messenger RNA processing and altered architecture of 3' untranslated regions contribute to the development of human disorders. Int J Mol Sci. 2013 Jul 26; 14(8): 15681-94.

22. Полное описание синдрома см. в: http://ghr.nlm.nih.gov/ condition / immune-dysregulation-polyendocrinopathy-enteropa-thy-x-linked-syndrome.

23. Bennett CL, Brunkow ME, Ramsdell F, O’Briant КС, Zhu Q, Fuleihan RL, Shigeoka AO, Ochs HD, Chance PF. A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA-»AAUGAA) leads to the IPEX syndrome. Immunogenetics. 2001 Aug; 53(6):435-9.

24. Подробнее см. в: http://www.alsa.org.

25. Базу данных генов, которые, как полагают, играют какую-то роль в развитии БАС, можно найти здесь: http://alsod.iop.kcl.ac.uk.

26. Kwiatkowski TJ Jr, Bosco DA, Leclerc AL, Tamrazian E, Vanderburg CR, Russ C, Davis A, Gilchrist J, Kasarskis EJ, Munsat T, Valdmanis P, Rouleau GA, Hosier BA, Cortelli P, de Jong PJ, Yoshinaga Y, Haines JL, Pericak-Vance MA, Yan J, Ticozzi N, Siddique T, McKenna-Yasek D, Sapp PC, Horvitz HR, Landers JE, Brown RH Jr. Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophie lateral sclerosis. Science. 2009 Feb 27;323(5918):1205-8.

27. Vance C, Rogelj B, Hortob?gyi T, De Vos KJ, Nishimura AL, Sreedharan J, Hu X, Smith B, Ruddy D, Wright P, Ganesalingam J, Williams KL, Tripathi V, Al-Saraj S, Al-Chalabi A, Leigh PN, Blair IP, Nicholson G, de Belleroche J, Gallo JM, Miller CC, Shaw CE. Mutations in FUS, an RNA processing protein, cause familial amyotrophie lateral sclerosis type 6. Science. 2009 Feb27;323 (5918):1208-11.

28. Lai SL, Abramzon Y, Schymick JC, Stephan DA, Dunckley T, Dillman A, Cookson M, Calvo A, Battistini S, Giannini F, Caponnetto C, Mancardi GL, Spataro R, Monsurro MR, Tedeschi G, Marinou K, Sabatelli M, Conte A, Mandrioli J, Sola P, Salvi F, Bartolomei I, Lombardo F; ITALSGEN Consortium, Mora G, Restagno G, Chi? A, Traynor BJ. FUS mutations in sporadic amyotrophie lateral sclerosis. Neurobiol Aging. 2011 Mar; 32(3):550.el-4.

29. Sabatelli M, Moncada A, Conte A, battante S, Marangi G, Luigetti M, Lucchini M, Mirabelle M, Romano A, Del Grande A, Bisogni G, Doronzio PN, Rossini PM, Zollino M. Mutations in the 3' untranslated region of FUS causing FUS overexpression are associated with amyotrophic lateral sclerosis. Hum Moi Genet. 2013 Dec 1;22(23):4748-55.

1. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genomewide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003 Dec 19;302(5653):2141-4.

2. Цит. no: Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet. 2010 May; 11(5):345-55.

3. Эти стадии очень четко описаны в ряде обзоров. Напр.: WangGS, Cooper ТА. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet. 2007 Oct; 8(10):749-61.

4. Подробнее о сплайсосоме см., напр., в: Padgett RA. New connections between splicing and human disease. Trends Genet. 2012 Apr; 28(4):147-54.

5. http://ghr.nlm.nih.gov/condition/retinitis-pigmentosa.

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1. Ameres SL, Zamore PD. Diversifying microRNA sequence and function. Nat Rev Mot Celt Biol. 2013 Aug; 14(8):475-88.

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3. Kang SG, Liu WH, Lu P, Jin HY, Lim HW, Shepherd J, Fremgen D, Verdin E, Oldstone MB, Qi H, Teijaro JR, Xiao C. MicroRNAs of the miR-17-92 family are critical regulators of T (FH) differentiation. Nat Immunol. 2013 Aug; 14 (8):849-57.

4. Baumjohann D, Kageyama R, Clingan JM, Morar MM, Patel S, de Kouchkovsky D, Bannard 0, Bluestone JA, Matloubian M, Ansel KM, Jeker LT. The microRNA cluster miR-17-92 promotes TFH cell differentiation and represses subset-inappropriate gene. Nat Immunol. 2013 Aug; 14(8):840-8.

5. Tassano E, Di Rocco M, Signa S, Gimelli G. De novo 13q31.1-q32.1 interstitial deletion encompassing the miR-17-92 cluster in a patient with Feingold syndrome-2. Am J Med Genet A. 2013 Apr; 161A(4):894-6.

6. Подробнее см. в: http://ghr.nlm.nih.gov/condition/feingold-syndrome.

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10. Subramanyam D, Lamouille S, Judson RL, Liu JY, Bucay N, Derynck R, Blelloch R. Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol. 2011 May; 29(5):443-8.

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1. Краткий перечень лекарств, активнее всего продававшихся за последние годы, см. в: http://www.fiercepharma.com/special-reports/ 15-best-selling-drugs-2012.

2. Этой сфере посвящено множество блогов. Напр.: http://biop-harmconsortium.com/rnai-therapeutics-stage-a-comeback.

3. Подробнее см. в: http://ghr.nlm.nih.gov/condition/transthyre-tin-amyloidosis.

4. http://investors.alnylam.com/releasedetail.cfm?ReleaseID-805999.

5. Все новости о данной программе можно найти здесь: http://mir-narx.com/pipeline/mirna-MRX34.html.

6. Koval ED, Shaner C, Zhang P, du Maine X, Fischer K, Tay J, Chau BN, Wu GF, Miller TM. Method for widespread microRNA-155 inhibition prolongs survival in ALS-model mice. Hum Mol Genet. 2013 Oct 15; 22(20):4127-35.

7. Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Celt. 2010 Dec 10; 143(6): 1018-29.

8. Очень хороший обзор, посвященный тому, как антисмысловая экспрессия может регулировать гены: Pelechano V, Stein me tz LM. Gene regulation by antisense transcription. Nat Rev Genet. 2013 Dec; 14(12):880-93.

9. http://www.dmgs.com/cons/fomivirsen-intraocular.html.

10. https://www.bhf.org.uk/heart-matters-online/august-septem-ber-2012/medical/familial-hypercholesterolaemia.aspx.

11. http://www.medscape.com/viewarticle/804574_5.

12. http://www.fda.gov/NewsEvents/Newsroom/PressAnnounceme nts/ucm337195.htm.

13. http://www.medscape.com/viewarticle/781317.

14. http://www.nature.com/nrd/journal/vl2/n3/full/nrd3963. html.

15. Lindow M, Kauppinen S. Discovering the first microRNA-targeted drug. J Cell Biot. 2012 Oct 29;199(3):407-12.

16. http://www.fiercebiotech.com/story/merck-writes-rnai-punts-sirna-alnylam-175m/2014-01-13.

17. http://www.ficrcebiotech.com/press-releases/rana-therapeu-tics-raises-207-milUon-harness-potential-long-non-coding-rna.

18. http://www.bostonglobe.com/business / 2014/01 /30/dicer-na-shares-soar-first-day-trading-after-biotech-raises-million-initial-public-offering/mbwMnXBSPsVCUVkGQLc64I/story.html.

19. http://www.dicerna.com/pipcline. php, по состоянию на 14 апреля 2014.

20. http://www.fiercebiotech.com/story/breaking-novartis-slams-brakes-rnai-development-efforts/2014-04-14.

1. Последняя история в этой книге сводит воедино различные находки, сделанные множеством исследователей. Вместо ссылок на каждую публикацию лучше дать ссылку на великолепную обзорную статью: van der Maarel SM, Miller DG, Tawil R, Filippova GN, Tapscott SJ. Facioscapulohumeral muscular dystrophy: consequences of chromatin relaxation. Curr Opin Neurol. 2012 Oct; 25(5):614-20.

2. Впервые это разграничение и это терминологическое новшество ввел Сидни Бреннер (Sidney Brenner).