Junk DNA: A Journey Through the Dark Matter of the Genome (41 page)

  
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. 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

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

Chapter 3

  
1
.
http://www.genome.gov/11006943

  
2
. Unless otherwise stated, the majority of the information in this chapter is from the edition of
Nature
published on 15th February 2001 which contained the data and analyses from the publicly funded consortium. The major reference
is Initial sequencing and analysis of the human genome
, authored by the International Human Genome Sequencing Consortium. Readers may also find the accompanying commentaries in the same issue of interest.

  
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
. For a fascinating case history, see Gura,
Nature
, 2012, Volume 483, pp20–22

  
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
. Data from the American Cancer Society
http://www.cancer.org/cancer/skincancer-melanoma/detailedguide/melanoma-skin-cancer-key-statistics

Chapter 4

  
1
. Unless otherwise stated, the majority of the information in this chapter is from the edition of
Nature
published on 15th February 2001 which contained the data and analyses from the publicly funded consortium. The major reference
is Initial sequencing and analysis of the human genome
, authored by the International Human Genome Sequencing Consortium. The accompanying commentaries by David Baltimore and by Li et al in the same issue are also of interest, and rather more accessible in style and content.

  
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 homoeotic 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
. For an interesting recent review of the field of xenotransplanation, see 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
. For a useful recent review of the effects of segmental duplication, including abnormal crossing-over, see Rudd MK, Keene J, Bunke B, Kaminsky EB, Adam MP, Mulle JG, Ledbetter DH, Martin CL. Segmental duplications mediate novel, clinically relevant chromosome rearrangements.
Hum Mol Genet
. 2009 Aug 15;18(16):2957–62

13
. For more information on this condition and its causes, see
http://www.ninds.nih.gov/disorders/charcot_marie_tooth/detail_charcot_marie_tooth.htm

14
. For more information on this condition and its causes, see
http://www.nlm.nih.gov/medlineplus/ency/article/001116.htm

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

16
.
http://www.innocenceproject.org/know/
retrieved 1 January 2014

Chapter 5

  
1
. Gross takings as cited by
http://www.imdb.com

  
2
. Reviewed in 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 U S A
. 1988 Sep;85(18):6622–6

  
4
. Vaziri H, Schächter 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
. Hayflick 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
. There is a useful discussion of this problem in Armanios M, Blackburn EH. The telomere syndromes.
Nat Rev Genet
. 2012 Oct;13(10):693–704

  
9
. Armanios M, Blackburn EH. The telomere syndromes.
Nat Rev Genet
. 2012 Oct;13(10):693–704 provides a useful overview.

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 TE, Harley CB, Lansdorp PM. Differential expression of telomerase activity in hematopoietic progenitors from adult human bone marrow.
Stem Cells
. 1996 Mar;14(2):239–48

14
. Vaziri H, Dragowska W, Allsopp RC, Thomas TE, Harley CB, Lansdorp PM. Evidence for a mitotic clock in human hematopoietic stem cells: loss of telomeric DNA with age.
Proc Natl Acad Sci U S A
. 1994 Oct 11;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
. For an excellent clinical description, and useful pictures, see 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 U S A
. 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, Cronkhite JT, Kuan PJ, Xing C, Raghu G, Weissler JC, Rosenblatt RL, Shay JW, Garcia CK. Adult-onset pulmonary fibrosis caused by mutations in telomerase.
Proc Natl Acad Sci U S A
. 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