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M. T. Ross,
D. V. Grafham,
A. J. Coffey,
S. Scherer,
K. McLay,
D. Muzny,
M. Platzer,
G. R. Howell,
C. Burrows,
C. P. Bird, [......],
A. Coulson,
D. L. Nelson,
G. Weinstock,
J. E. Sulston,
R. Durbin,
T. Hubbard,
R. A. Gibbs,
S. Beck,
J. Rogers,
D. R. Bentley
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ABSTRACT: The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
Nature 03/2005; 434:325-37. · 36.28 Impact Factor
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Nature 01/2004; · 36.28 Impact Factor
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R H Waterston,
L W Hillier,
L A Fulton,
R S Fulton,
T A Graves,
K H Pepin,
P Bork,
M Suyama,
D Torrents,
A T Chinwalla,
E R Mardis,
J D McPherson,
R K Wilson
Cold Spring Harbor Symposia on Quantitative Biology 02/2003; 68:13-22.
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ABSTRACT: We report the identification of several putative muscle-specific regulatory elements, and genes which are expressed preferentially in the muscle of the nematode Caenorhabditis elegans. We used computational pattern finding methods to identify cis-regulatory motifs from promoter regions of a set of genes known to express preferentially in muscle; each motif describes the potential binding sites for an unknown regulatory factor. The significance and specificity of the identified motifs were evaluated using several different control sequence sets. Using the motifs, we searched the entire C. elegans genome for genes whose promoter regions have a high probability of being bound by the putative regulatory factors. Genes that met this criterion and were not included in our initial set were predicted to be good candidates for muscle expression. Some of these candidates are additional, known muscle expressed genes and several others are shown here to be preferentially expressed in muscle cells by using GFP (green fluorescent protein) constructs. The methods described here can be used to predict the spatial expression pattern of many uncharacterized genes.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 02/2002;
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genesis 01/2002; 31(4):137-41. · 2.53 Impact Factor
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01/2002
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ABSTRACT: Comparative sequence analysis has facilitated the discovery of protein coding genes and important functional sequences within proteins, but has been less useful for identifying functional sequence elements in nonprotein-coding DNA because the relatively rapid rate of change of nonprotein-coding sequences and the relative simplicity of non-coding regulatory sequence elements necessitates the comparison of sequences of relatively closely related species. We tested the use of comparative DNA sequence analysis to aid identification of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Saccharomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA sequence of a few specific promoters and RNA genes of several Saccharomyces species to determine the degree of conservation of known functional elements within the genome. Our results lead us to conclude that comparative DNA sequence analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.
Genome Research 08/2001; 11(7):1175-86. · 13.61 Impact Factor
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ABSTRACT: Single nucleotide polymorphisms (SNPs) are valuable genetic markers of human disease. They also comprise the highest potential density marker set available for mapping experimentally derived mutations in model organisms such as Caenorhabditis elegans. To facilitate the positional cloning of mutations we have identified polymorphisms in CB4856, an isolate from a Hawaiian island that shows a uniformly high density of polymorphisms compared with the reference Bristol N2 strain. Based on 5.4 Mbp of aligned sequences, we predicted 6,222 polymorphisms. Furthermore, 3,457 of these markers modify restriction enzyme recognition sites ('snip-SNPs') and are therefore easily detected as RFLPs. Of these, 493 were experimentally confirmed by restriction digest to produce a snip-SNP map of the worm genome. A mapping strategy using snip-SNPs and bulked segregant analysis (BSA) is outlined. CB4856 is crossed into a mutant strain, and exclusion of CB4856 alleles of a subset of snip-SNPs in mutant progeny is assessed with BSA. The proximity of a linked marker to the mutation is estimated by the relative proportion of each form of the biallelic marker in populations of wildtype and mutant genomes. The usefulness of this approach is illustrated by the rapid mapping of the dyf-5 gene.
Nature Genetics 07/2001; 28(2):160-4. · 35.53 Impact Factor
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E S Lander,
L M Linton,
B Birren,
C Nusbaum,
M C Zody,
J Baldwin,
K Devon,
K Dewar,
M Doyle,
W FitzHugh, [......],
K A Wetterstrand,
A Patrinos,
M J Morgan,
P de Jong,
J J Catanese,
K Osoegawa,
H Shizuya,
S Choi,
Y J Chen,
J Szustakowki
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ABSTRACT: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Nature 03/2001; 409(6822):860-921. · 36.28 Impact Factor
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C A Tilford,
T Kuroda-Kawaguchi,
H Skaletsky,
S Rozen,
L G Brown,
M Rosenberg,
J D McPherson,
K Wylie,
M Sekhon,
T A Kucaba, R H Waterston,
D C Page
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ABSTRACT: The non-recombining region of the human Y chromosome (NRY), which comprises 95% of the chromosome, does not undergo sexual recombination and is present only in males. An understanding of its biological functions has begun to emerge from DNA studies of individuals with partial Y chromosomes, coupled with molecular characterization of genes implicated in gonadal sex reversal, Turner syndrome, graft rejection and spermatogenic failure. But mapping strategies applied successfully elsewhere in the genome have faltered in the NRY, where there is no meiotic recombination map and intrachromosomal repetitive sequences are abundant. Here we report a high-resolution physical map of the euchromatic, centromeric and heterochromatic regions of the NRY and its construction by unusual methods, including genomic clone subtraction and dissection of sequence family variants. Of the map's 758 DNA markers, 136 have multiple locations in the NRY, reflecting its unusually repetitive sequence composition. The markers anchor 1,038 bacterial artificial chromosome clones, 199 of which form a tiling path for sequencing.
Nature 03/2001; 409(6822):943-5. · 36.28 Impact Factor
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J D McPherson,
M Marra,
L Hillier, R H Waterston,
A Chinwalla,
J Wallis,
M Sekhon,
K Wylie,
E R Mardis,
R K Wilson, [......],
A Shimizu,
K Shibuya,
J Kudoh,
S Minoshima,
J Ramser,
P Seranski,
C Hoff,
A Poustka,
R Reinhardt,
H Lehrach
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ABSTRACT: The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.
Nature 03/2001; 409(6822):934-41. · 36.28 Impact Factor
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ABSTRACT: Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitude analysis indicates library depth is of secondary importance compared to the other variables, especially as clone size diminishes. In such cases, the well-known Poisson coverage law is a good approximation. Parameters derived from these models are used to examine performance for the specific case of sequencing random human BAC clones. We compare coverage and redundancy rates for libraries possessing uniform and nonuniform clone distributions. Results are measured against data from map-based human-chromosome-2 sequencing. We conclude that the map-based approach outperforms random clone sequencing, except early in a project. However, simultaneous use of both strategies can be beneficial if a performance-based estimate for halting random clone sequencing is made. Results further show that the random approach yields maximum effectiveness using nonbiased rather than biased libraries.
Genome Research 03/2001; 11(2):274-80. · 13.61 Impact Factor
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R Sachidanandam,
D Weissman,
S C Schmidt,
J M Kakol,
L D Stein,
G Marth,
S Sherry,
J C Mullikin,
B J Mortimore,
D L Willey, [......],
D Reich,
J Higgins,
M J Daly,
B Blumenstiel,
J Baldwin,
N Stange-Thomann,
M C Zody,
L Linton,
E S Lander,
D Altshuler
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ABSTRACT: We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.
Nature 03/2001; 409(6822):928-33. · 36.28 Impact Factor
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Journal of nematology 01/2001; 32(4):331-3. · 0.52 Impact Factor
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ABSTRACT: The precise arrangement of molecules within the thick filament, as well as the mechanisms by which this arrangement is specified, remains unclear. In this article, we have exploited a unique genetic interaction between one isoform of myosin heavy chain (MHC) and paramyosin in Caenorhabditis elegans to probe the molecular interaction between MHC and paramyosin in vivo. Using chimeric myosin constructs, we have defined a 322-residue region of the MHC A rod critical for suppression of the structural and motility defects associated with the unc-15(e73) allele. Chimeric constructs lacking this region of MHC A either fail to suppress, or act as dominant enhancers of, the e73 phenotype. Although the 322-residue region is required for suppression activity, our data suggest that sequences along the length of the rod also play a role in the isoform-specific interaction between MHC A and paramyosin. Our genetic and cell biological analyses of construct behavior suggest that the 322-residue region of MHC A is important for thick filament stability. We present a model in which this region mediates an avid interaction between MHC A and paramyosin in parallel arrangement in formation of the filament arms.
Genetics 11/2000; 156(2):631-43. · 4.01 Impact Factor
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M R Emmert-Buck,
R L Strausberg,
D B Krizman,
M F Bonaldo,
R F Bonner,
D G Bostwick,
M R Brown,
K H Buetow,
R F Chuaqui,
K A Cole, [......],
M A Marra,
P J Munson,
D K Ornstein,
V V Prabhu,
C Prang,
G D Schuler,
M B Soares,
C M Tolstoshev,
C D Vocke, R H Waterston
Journal of Molecular Diagnostics 06/2000; 2(2):60-6. · 3.58 Impact Factor
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M R Emmert-Buck,
R L Strausberg,
D B Krizman,
M F Bonaldo,
R F Bonner,
D G Bostwick,
M R Brown,
K H Buetow,
R F Chuaqui,
K A Cole, [......],
M A Marra,
P J Munson,
D K Ornstein,
V V Prabhu,
C Prange,
G D Schuler,
M B Soares,
C M Tolstoshev,
C D Vocke, R H Waterston
American Journal Of Pathology 05/2000; 156(4):1109-15. · 4.89 Impact Factor
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R E Ellsworth,
D C Jamison,
J W Touchman,
S L Chissoe,
V V Braden Maduro,
G G Bouffard,
N L Dietrich,
S M Beckstrom-Sternberg,
L M Iyer,
L A Weintraub, [......],
I Korf,
K Pepin,
L Antonacci-Fulton,
R S Fulton,
P Minx,
L W Hillier,
R K Wilson, R H Waterston,
W Miller,
E D Green
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ABSTRACT: The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. For example, the latter might provide clues about the sequence elements responsible for the temporal and spatial regulation of CFTR expression. We thus sought to establish the sequence of the chromosomal segments encompassing the human CFTR and mouse Cftr genes, with the hope of identifying conserved regions of biologic interest by sequence comparison. Bacterial clone-based physical maps of the relevant human and mouse genomic regions were constructed, and minimally overlapping sets of clones were selected and sequenced, eventually yielding approximately 1.6 Mb and approximately 358 kb of contiguous human and mouse sequence, respectively. These efforts have produced the complete sequence of the approximately 189-kb and approximately 152-kb segments containing the human CFTR and mouse Cftr genes, respectively, as well as significant amounts of flanking DNA. Analyses of the resulting data provide insights about the organization of the CFTR/Cftr genes and potential sequence elements regulating their expression. Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr.
Proceedings of the National Academy of Sciences 03/2000; 97(3):1172-7. · 9.68 Impact Factor
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ABSTRACT: To accommodate the increasingly rapid rates of DNA sequencing we have developed and implemented an inexpensive, expeditious method for the purification of double-stranded plasmid DNA clones. The robust nature, high throughput, low degree of technical difficulty and extremely low cost have made it the plasmid DNA preparation method of choice in both our expressed sequence tag (EST) and genome sequencing projects. Here we report the details of the method and describe its application in the generation of more than 700 000 ESTs at a rate exceeding 16 000 per week.
Nucleic Acids Research 01/2000; 27(24):e37. · 8.03 Impact Factor
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ABSTRACT: In C. elegans, assembly of hypodermal hemidesmosome-like structures called fibrous organelles is temporally and spatially coordinated with the assembly of the muscle contractile apparatus, suggesting that signals are exchanged between these cell types to position fibrous organelles correctly. Myotactin, a protein recognized by monoclonal antibody MH46, is a candidate for such a signaling molecule. The antigen, although expressed by hypodermis, first reflects the pattern of muscle elements and only later reflects the pattern of fibrous organelles. Confocal microscopy shows that in adult worms myotactin and fibrous organelles show coincident localization. Further, cell ablation studies show the bodywall muscle cells are necessary for normal myotactin distribution. To investigate myotactin's role in muscle-hypodermal signaling, we characterized the myotactin locus molecularly and genetically. Myotactin is a novel transmembrane protein of approximately 500 kd. The extracellular domain contains at least 32 fibronectin type III repeats and the cytoplasmic domain contains unique sequence. In mutants lacking myotactin, muscle cells detach when embryonic muscle contraction begins. Later in development, fibrous organelles become delocalized and are not restricted to regions of the hypodermis previously contacted by muscle. These results suggest myotactin helps maintain the association between the muscle contractile apparatus and hypodermal fibrous organelles.
The Journal of Cell Biology 09/1999; 146(3):659-72. · 10.26 Impact Factor
