DNA sequence and analysis of human chromosome 9

Humphray, Sean; Oliver, Karen; Hunt, A. R.; Plumb, Robert; Loveland, Jane; Howe, Kerstin; Andrews, T. Daniel; Searle, S.; Hunt, Sarah; Scott, Carol; Jones, Matt; Ainscough, R.; Almeida, J. P.; Ambrose, K. D.; Ashwell, R. I. S.; Babbage, Anne; Babbage, S.; Bagguley, C. L.; Bailey, J.; Banerjee, Ruby; Barker, Darren; Barlow, K. F.; Bates, K.; Beasley, Helen; Beasley, O.; Bird, Christine P.; Bray-Allen, S.; Brown, Andrew; Brown, J. Y.; Burford, D. C.; Burrill, W.; Burton, John H.; Carder, C.; Carter, N. P.; Chapman, J C; Chen, Y.; Clarke, Geraldine M.; Clark, S. Y.; Clee, Christopher M.; Clegg, S.; Collier, R. E.; Corby, N.; Crosier, Moira; Cummings, A. T.; Davies, Joy; Dhami, Pawandeep; Dunn, Matt; Dutta, I.; Dyer, Lauren; Earthrowl, M. E.; Faulkner, L.; Fleming, Colin; Frankish, Adam; Frankland, J.; French, Lisa; Fricker, David; Garner, P.; Garnett, J.; Ghori, Jilur; Gilbert, James; Glison, C.; Grafham, Darren; Gribble, Susan; Griffiths, Chris; Griffiths‐Jones, Sam; Grocock, Russell; Guy, JH; Hall, R. E.; Hammond, S.; Harley, Joanna; Harrison, Elliot; Hart, Elizabeth A.; Heath, P. D.; Henderson, Caroline; Hopkins, Barbara; Howard, P. J.; Howden, Philip; Huckle, Elizabeth J.; Johnson, Chénel; Johnson, David J.; Joy, A. A.; Kay, Mike; Keenan, Stephen; Kershaw, J. K.; Kimberley, A. M.; King, Andrew G.; Knights, Andrew; Laird, Gavin K.; Langford, C.; Lawlor, Stephanie; Leongamornlert, Daniel; Leversha, Margaret; Lloyd, Christine; Lloyd, D. M.; Lovell, J.; Martin, Sancha; Mashreghi-Mohammadi, M.; Matthews, Lucy; McLaren, Stuart; McLay, Kirsten; McMurray, Amanda; Milne, Sarah; Nickerson, T.; Nisbett, James; Nordsiek, Gabriele; Pearce, A. V.; Peck, A. I.; Porter, Keith; Pandian, Richard; Pelan, Sarah; Phillimore, Benjamin; Povey, S.; Ramsey, Y. H.; Rand, Vikki; Scharfe, Maren; Sehra, Harminder; Shownkeen, Ratna; Sims, Sarah; Skuce, C. D.; Smith, Michelle; Steward, Charles A.; Swarbreck, David; Sycamore, Neil; Tester, J.; Thorpe, A.; Tracey, Alan S.; Tromans, A.; Thomas, Duncan W.; Wall, M.; Wallis, J. M.; West, Anthony P.; Whitehead, Sally; Willey, David L.; Williams, S. A.; Wilming, Laurens G.; Wray, Paul; Young, Lynn; Ashurst, Jennifer; Coulson, Alan; Blöcker, Helmut; Durbin, Richard; Sulston, John; Hubbard, Tim; Jackson, Michael; Bentley, David; Beck, Stephan; Rogers, Jane; Dunham, Ian

doi:10.1038/nature02465

Cited by 317 publications

(79 citation statements)

References 52 publications

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“…This band is known to be involved in constitutional pericentric inversions of chromosome 9, which occurs with a frequency of about 2% in the general population (37). Additionally, this region is known to be breakpoint prone and carries segmental duplications (38). Our own studies showed that the constitutional pericentric inversions of chromosome 9 are not due to one or two founder mutations but that they differ on a molecular level (8,39; our own unpublished data).…”

Section: Alignment Of Breakpoints With Segmental Duplicationsmentioning

confidence: 99%

Forty-eight new cases with infertility due to balanced chromosomal rearrangements: Detailed molecular cytogenetic analysis of the 90 involved breakpoints

Manvelyan¹,

Schreyer²,

I³

et al. 2007

Int J Mol Med

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Abstract. A molecular cytogenetic study was performed on 48 infertile patients who were identified as carriers of balanced translocations (40 cases), inversions (6 cases) or insertions (2 cases) by means of banding cytogenetics. Cases with a Robertsonian translocation or pericentric inversion 2 or 9 were not included. In summary, 100 break-events occurred in these patients, and 90 different chromosomal regions were involved. Thus, this study confirmed the presence of abnormal karyotypes in a subgroup of patients seeking infertility treatment. Breaks were demonstrated to appear preferentially in GTG-light bands in these patients. Furthermore, the observed breakpoints were associated with genomic regions prone to instability due to the presence of segmental duplications. Nonetheless, further detailed molecular analysis will be necessary in the future to characterize the mechanisms and genetic basis for this phenomenon.

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Section: Alignment Of Breakpoints With Segmental Duplicationsmentioning

confidence: 99%

Forty-eight new cases with infertility due to balanced chromosomal rearrangements: Detailed molecular cytogenetic analysis of the 90 involved breakpoints

Manvelyan¹,

Schreyer²,

I³

et al. 2007

Int J Mol Med

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“…Interestingly, chromosome 9, which is orthologous to large parts of the chicken Z, is highly structurally polymorphic in humans (Humphray et al, 2004). Trisomies of human 9p (Wilson et al, 1985), and monosomies of 5q and 18q (which all share homology with the chicken Z), survive to birth (Nusbaum et al, 2005;Boultwood et al, 2010).…”

Section: Does Dosage Insensitivity Predispose An Autosome To Evolve Smentioning

confidence: 99%

The origin and evolution of vertebrate sex chromosomes and dosage compensation

2011

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In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome.

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“…1 Human ATGL (also called PNPLA2 or PLPL2) encodes adipose triglyceride lipase (ATGL, also known as desnutrin or PNPLA2) and is localizedPNPLA4 (PLPL4, X chromosome); 5 PNPLA6 (PLPL6 or NTE) (neuropathy target esterase, chromosome 19); 6,7 PNPLA7 (PLPL7, chromosome 9); 8 and PNPLA8 (PLPL8 or IPLA2G, calcium-independent phospholipase A2-gamma, chromosome 7). [9][10][11] ATGL catalyzes the first step in the hydrolysis of triglycerides in adipocytes and lipid droplets in other tissues of the body, and also acts as an acylglycerol transacylase.…”

Section: Introductionmentioning

confidence: 99%

Comparative studies of adipose triglyceride lipase genes and proteins: an ancient gene in vertebrate evolution

Holmes¹

2012

OAB

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At least eight families of mammalian patatin-like phospholipase domain-containing proteins (EC 3.1.1.3) catalyze the hydrolysis of triglycerides, including adipose triglyceride lipase (ATGL), which functions in triglyceride lipase metabolism in the body, especially in adipose tissue. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures, and gene locations for ATGL genes and encoded proteins using data from several vertebrate genome projects. ATGL genes usually contained nine coding exons for each of the vertebrate genomes examined, whereas the invertebrate sea squirt (Ciona intestinalis) ATGL gene contained a single exon. Vertebrate ATGL subunits contained 473-504 residues, shared .46% sequence identities, and exhibited sequence alignments and identities for key amino acid residues and predicted motifs: an N-terminal lipid binding region (residues 7-29 for human ATGL); a patatin "motif " (residues 10-179); a putative active site oxyanion "hole" (Cys15, Gly16, and Leu18); and catalytic dyad active site residues (Ser47 and Asp166). Predicted tertiary structures for the ATGL patatin "motif " were similar to those reported for potato patatin, suggesting that this structure is strongly conserved during animal and plant evolution. Human ATGL contained a CpG131 island within the gene promoter; miR-124/506 and miR-108 binding sites within the mRNA 3′-noncoding region; several transcription factor binding sites, including PPARA and PPARG, which are key regulators of genes encoding enzymes of lipid metabolism; and exhibited wide tissue expression at a higher than average level (2.2×). Phylogenetic analyses of vertebrate PNPLA-like gene families suggest that ATGL is an ancient gene in vertebrate evolution which has been derived from an ancestral ATGL gene (encoding adipose triglyceride lipase) and undergone successive gene duplication events, forming ancestral genes for vertebrate PNPLA1, ATGL, PNPLA3, PNPLA4, and PNPLA5 gene families.

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DNA sequence and analysis of human chromosome 9

Cited by 317 publications

References 52 publications

Forty-eight new cases with infertility due to balanced chromosomal rearrangements: Detailed molecular cytogenetic analysis of the 90 involved breakpoints

Forty-eight new cases with infertility due to balanced chromosomal rearrangements: Detailed molecular cytogenetic analysis of the 90 involved breakpoints

The origin and evolution of vertebrate sex chromosomes and dosage compensation

Comparative studies of adipose triglyceride lipase genes and proteins: an ancient gene in vertebrate evolution

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