Junk DNA: A Journey Through the Dark Matter of the Genome (44 page)

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, Haussler 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, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C. Expression of a noncoding RNA 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 Dis
. 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
. For a useful review, see for example Wahlestedt C. 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

Chapter 9

  
1
. If you want to learn more about this topic, have a read of my first book,
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, Gómez 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, Cao Q, 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 Sci U S A
. 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 B-cell lymphomas.
Proc Natl Acad Sci U S A
. 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 O, 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
. For a recent major paper on this see Davidovich C, 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
. For a slightly more accessible summary of the above paper, see 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’Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation.
Nature
. 2013 Nov 21;503(7476):371–6

13
. For an overview of all the complex stages in this process see 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 methylation state and is influenced by parental lineage.
Genes Dev
. 1994 Jun 15;8(12):1463–72

Chapter 10

  
1
. For a contemporaneous review of the work see Surani MA, 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
. An online depository of imprinted mouse sequences can be found at
http://www.mousebook.org/catalog.php?catalog=imprinting

  
3
. For a useful review see 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
. For a recent review of imprinting in marsupials see 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
. Reviewed in 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. Methylation and imprinting: from host defense to gene regulation?
Science
. 1993 Apr 16;260(5106):309–10

11
. Reviewed in 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
. A description of the actions of these proteins in the methylation of the maternal ICE can be found in Bourc’his D, Proudhon C. Sexual dimorphism in parental imprint ontogeny and contribution to embryonic development.
Mol Cell Endocrinol
. 2008 Jan 30;282(1–2):87–94

13
. The paper that demonstrated the importance of this protein for maintaining the maternal imprint is Hirasawa R, Chiba H, Kaneda M, Tajima S, Li E, Jaenisch R, Sasaki H. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation 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 methylation at imprinted genes.
Mol Cell Biol
. 2006 Nov;26(22):8347–56

15
. 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

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
. Reviewed in 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
. For a review of this aspect, see Frost JM, Moore GE. The importance of imprinting in the human placenta.
PLoS Genet
. 2010 Jul 1;6(7):e1001015

19
. For a full description see
http://omim.org/entry/176270

20
. For a full description see
http://omim.org/entry/105830

21
. de Smith AJ, Purmann C, Walters RG, Ellis RJ, Holder SE, Van Haelst MM, Brady AF, Fairbrother UL, Dattani M, Keogh JM, Henning E, Yeo GS, O’Rahilly S, Froguel P, Farooqi IS, 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 EV, Person RE, Mahadevan S, Alliman S, Thompson R, Traylor R, Bejjani BA, Shaffer LG, Rosenfeld JA, Lamb AN, Sahoo T. Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome.
Eur J 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
. For a full description see
http://omim.org/entry/180860

25
. For a full description see
http://omim.org/entry/130650