Junk DNA: A Journey Through the Dark Matter of the Genome (45 page)

26
. Data collated in 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):237–42

28
. For a detailed review of the inheritance and clinical characteristics of various human imprinting disorders, see the review by Ishida M, Moore GE. The role of imprinted genes in humans.
Mol Aspects Med
. 2013 Jul-Aug;34(4):826–40

29
. Press release on 14 October 2013 from American Society for Reproductive Medicine
http://www.asrm.org/Five_Million_Babies_Born_with_Help_of_Assisted_Reproductive_Technologies/

30
. This is discussed in some detail in Ishida M, Moore GE. The role of imprinted genes in humans.
Mol Aspects Med
. 2013 Jul–Aug;34(4):826–40

Chapter 11

  
1
. Reviewed in Moss T, Langlois F, Gagnon-Kugler T, Stefanovsky V. A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis.
Cell Mol Life Sci
. 2007 Jan;64(1):29–49

  
2
. For more information on ribosomes and rRNAs it is easiest to refer to a good molecular biology textbook such as
Molecular Biology of the Cell, 5th Edition
by Alberts, Johnson, Lewis, Raff, Roberts and Walter, 2012.

  
3
.
http://www.nobelprize.org/educational/medicine/dna/a/translation/trna.html

  
4
.
http://www.bscb.org/?url=softcell/ribo

  
5
. Reviewed in Zentner GE, Saiakhova A, Manaenkov P, Adams MD, Scacheri PC. Integrative genomic analysis of human ribosomal DNA.
Nucleic Acids Res
. 2011 Jul;39(12):4949–60

  
6
. This whole area of diseases caused by defects in ribosomal proteins is interestingly, if occasionally rather provocatively reviewed in Narla A, Ebert BL. Ribosomopathies: human disorders of ribosome dysfunction.
Blood
. 2010 Apr 22;115(16):3196–205

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

  
8
. See for example 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
. Reviewed in 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
. Once again I would recommend a good molecular biology textbook if you would like to learn more, such as
Molecular Biology of the Cell, 5th Edition
by Alberts, Johnson, Lewis, Raff, Roberts and 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 Mutat
. 2012 Aug;33(8):1285–93

15
. Giordano C, Perli E, Orlandi M, Pisano A, Tuppen HA, He L, Ierinò R, Petruzziello L, Terzi A, Autore 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
. Published online 29 October 2014

Chapter 12

  
1
. An overview of MYC’s role, and the importance of chromosomal rearrangements can be found in Ott G, Rosenwald A, Campo E. Understanding MYC-driven aggressive B-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 TI, 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 I, Polletti S, Termanini A, Bonifacio S, Curina A, Prosperini 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, Balasubramanian 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
. For a description of these types of long non-coding RNAs see 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 I, 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
. The role of super-enhancers in pluripotent cells was first identified in 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 genes.
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):663–76

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.
Cell
. 2013 Apr 11;153(2):320–34

17
. For an overview of the various molecular causes see 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 interaction landscape of 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
. For an excellent review of this topic see 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 Sci
. 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. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh.
PLoS Biol
. 2007 Aug;5(8):e192

Chapter 13

  
1
. It’s difficult to find a definitive first use of this description, as discussed in
http://english.stackexchange.com/questions/103851/where-does-the-phrase-of-boredom-punctuated-by-moments-of-terror-come-from