Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library

Z., R.; Eijk, Michiel J. T. van; Beever, Jonathan E.; Guérin, Gérard; Mummery, Christine L.; Lewin, Harris A.

doi:10.1007/s003359900816

Cited by 52 publications

(37 citation statements)

References 20 publications

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“…The COMPASS strategy (Ma et al 1998;Rebeiz and Lewin 2000;Larkin et al 2003) was used to target more than 900 new Comparative length of chromosome is the total length minus area of telomere, centromere, and heterochromatin regions. The full length of the chromosome is given in parentheses.…”

Section: Discussionmentioning

confidence: 99%

“…Markers were selected for mapping using the COMPASS strategy (Ma et al 1998;Band et al 2000;Rebeiz and Lewin 2000;Larkin et al 2003). All of the 47,787 cattle ESTs in the April 2000 GenBank release were used as a resource for filling gaps in the firstgeneration comparative map (Band et al 2000).…”

Section: Methods Marker Selection and Mapping Strategymentioning

confidence: 99%

“…Our goal for the second-generation wholegenome cattle RH map was to fill in existing gaps in the cattlehuman comparative map as well as segments of the map with large distances between markers. To clarify these ambiguous regions of the cattle-human comparative map, the COMPASS bioinformatics strategy (Ma et al 1998;Rebeiz and Lewin 2000;Larkin et al 2003) was employed for targeted selection of expressed sequence tags (ESTs) for RH mapping. In addition, human genome sequence coordinates were used to construct the comparative chromosome maps.…”

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confidence: 99%

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A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Wind¹,

Kata²,

Band³

et al. 2004

Genome Res.

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139

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A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle–human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH5000 panel to 1913. Of these, 1463 have significant BLASTN hits (E < e–5) against the human genome sequence. A cattle–human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle–human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Methods Marker Selection and Mapping Strategymentioning

confidence: 99%

mentioning

confidence: 99%

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A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Wind¹,

Kata²,

Band³

et al. 2004

Genome Res.

Self Cite

139

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“…Expressed sequence tag (EST) analysis of gene expression in specific tissues is widely used to characterise gene function and tissue physiology [13]. This approach has been used to accelerate gene discovery in a variety of bovine tissues including the ovary [14], mammary gland [15], embryo [16], foetus [17], and multiple tissues [18]. In addition, a recent study reported the identification and mapping of 11 gene sequences preferentially expressed in the bovine CL [19].…”

Section: Introductionmentioning

confidence: 99%

Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs

Casey

Fitzpatrick

McInerney

et al. 2004

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expres

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To gain new insights into gene identity and gene expression in the bovine corpus luteum (CL) a directionally cloned CL cDNA library was constructed, screened with a total CL cDNA probe and clones representing abundant and rare mRNA transcripts isolated. The 5V-terminal DNA sequence of 960 cDNA clones, composed of 192 abundant and 768 rare mRNA transcripts was determined and clustered into 351 non-redundant expressed sequence tag (EST) groups. Bioinformatic analysis revealed that 309 (88%) of the ESTs showed significant homology to existing sequences in the protein and nucleotide public databases. Several previously unidentified bovine genes encoding proteins associated with key aspects of CL function including extracellular matrix remodelling, lipid metabolism/steroid biosynthesis and apoptosis, were identified. Forty-two (12%) of the ESTs showed homology with human or with other uncharacterised ESTs, some of these were abundantly expressed and may therefore play an important role in primary CL function. Tissue-specificity and temporal CL gene expression of selected clones previously unidentified in bovine CL tissue was also examined. The most interesting finds indicated that mRNA encoding squalene epoxidase was constitutively expressed in CL tissue throughout the oestrous cycle and 7-fold down-regulated ( P < 0.05) in late luteal tissue, concomitant with the disappearance of systemic progesterone, suggesting that de novo cholesterol biosynthesis plays an important role in steroidogenesis. The mRNA encoding the growth factor, insulin-like growth factor-binding protein-related protein 1 (IGFBP-rP1), remained constant during the oestrous cycle and was 1.8-fold up-regulated ( P < 0.05) in late luteal tissue implying a role in CL regression. D

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“…A new strategy of comparative mapping by annotation and sequence similarity (COMPASS; ref. 18) has accelerated the comparative gene-mapping process (19,20). By using this approach, more than 1,000 markers were assigned and presented in a combined first generation cattle WGRH 5,000 and cattle͞human whole-genome comparative map (21).…”

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confidence: 99%

A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice

Goldammer

Kata²,

Brunner³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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A comprehensive radiation hybrid (RH) map and a high resolution comparative map of Bos taurus (BTA) chromosome 18 were constructed, composed of 103 markers and 76 markers, respectively, by using a cattle-hamster somatic hybrid cell panel and a 5,000 rad whole-genome radiation hybrid (WGRH) panel. These maps include 65 new assignments (56 genes, 3 expressed-sequence tags, 6 microsatellites) and integrate 38 markers from the first generation WGRH5,000 map of BTA18. Fifty-nine assignments of coding sequences were supported by somatic hybrid cell mapping to markers on BTA18. The total length of the comprehensive map was 1666 cR5,000. Break-point positions within the chromosome were refined and a new telomeric RH linkage group was established. Conserved synteny between cattle, human, and mouse was found for 76 genes of BTA18 and human chromosomes (HSA) 16 and 19 and for 34 cattle genes and mouse chromosomes (MMU) 7 and 8. The new RH map is potentially useful for the identification of candidate genes for economically important traits, contributes to the expansion of the existing BTA18 gene map, and provides new information about the chromosome evolution in cattle, humans, and mice.

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Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library

Cited by 52 publications

References 20 publications

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Analysis of gene expression in the bovine corpus luteum through generation and characterisation of 960 ESTs

A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice

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