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Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Oduru S, Campbell JL, Karri S, Hendry WJ, Khan SA, Williams SC - BMC Genomics (2003)

Bottom Line: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes.The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome.The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA. oduru.sreedhar@ttuhsc.edu

ABSTRACT

Background: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.

Results: 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.

Conclusion: The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

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Alignment of human, macaque, mouse and rat 7012 sequences. The sequenc es of predicted peptides for human (Hs), macaque (Mf), mouse (Mm) and rat (Rn) orthologues of 7012 were compared using AlignX. Portions of the human sequence were obtained from XP_059659, a peptide predicted from annotation of the human genome at NCBI. The macaque sequence was derived from Genbank entry BAB63112, the predicted translation product of a cDNA isolated from macaque testis. The mouse sequence was obtained by mapping the exon structure of the orthologous gene on the region of mouse chromosome 15. The rat coding sequence was constructed by assembling conserved exons on contigs RNOR01068092, RNOR01068093 and RNOR01068094 (Accession numbers AABR02034780 and AABR02122391). The sequence corresponding to the hamster clone obtained in this study is indicated with a dotted red underline in the human sequence.
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Figure 6: Alignment of human, macaque, mouse and rat 7012 sequences. The sequenc es of predicted peptides for human (Hs), macaque (Mf), mouse (Mm) and rat (Rn) orthologues of 7012 were compared using AlignX. Portions of the human sequence were obtained from XP_059659, a peptide predicted from annotation of the human genome at NCBI. The macaque sequence was derived from Genbank entry BAB63112, the predicted translation product of a cDNA isolated from macaque testis. The mouse sequence was obtained by mapping the exon structure of the orthologous gene on the region of mouse chromosome 15. The rat coding sequence was constructed by assembling conserved exons on contigs RNOR01068092, RNOR01068093 and RNOR01068094 (Accession numbers AABR02034780 and AABR02122391). The sequence corresponding to the hamster clone obtained in this study is indicated with a dotted red underline in the human sequence.

Mentions: This clone contained an ORF of 73 amino acids that detected a strong signal by Northern blotting in testis RNA (figure 1). Genome analysis permitted the mapping of a common set of 10 exons on human, mouse and rat chromosomes 5, 15 and 2, respectively (Table 2), assembly of which resulted in translation products of 579, 555 and 563 amino acids, respectively (figure 6). These predictions were also corroborated by a macaque cDNA (AB070167). The encoded proteins did not contain any recognizable functional motifs (figure 3) and were most similar to an uncharacterized human protein named B29 (figure 2). B29 was originally identified as a gene located on human chromosome 18q21 in a search for candidate tumor suppressor proteins in lung [28]. However, the function of B29 is unknown and it does not contain any obvious functional domains. Interestingly, the apparent size of the detected mRNA is significantly larger than that of the assembled sequences, suggesting that additional exons are likely to remain to be discovered. In this regard, gene prediction software identified an additional 35 exons in the mouse genomic sequence that were partly conserved in the rat but not present in the human sequence. Final mapping of the genomic structure of 7012 will await further refineme nt of each genomic sequence.


Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Oduru S, Campbell JL, Karri S, Hendry WJ, Khan SA, Williams SC - BMC Genomics (2003)

Alignment of human, macaque, mouse and rat 7012 sequences. The sequenc es of predicted peptides for human (Hs), macaque (Mf), mouse (Mm) and rat (Rn) orthologues of 7012 were compared using AlignX. Portions of the human sequence were obtained from XP_059659, a peptide predicted from annotation of the human genome at NCBI. The macaque sequence was derived from Genbank entry BAB63112, the predicted translation product of a cDNA isolated from macaque testis. The mouse sequence was obtained by mapping the exon structure of the orthologous gene on the region of mouse chromosome 15. The rat coding sequence was constructed by assembling conserved exons on contigs RNOR01068092, RNOR01068093 and RNOR01068094 (Accession numbers AABR02034780 and AABR02122391). The sequence corresponding to the hamster clone obtained in this study is indicated with a dotted red underline in the human sequence.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC161800&req=5

Figure 6: Alignment of human, macaque, mouse and rat 7012 sequences. The sequenc es of predicted peptides for human (Hs), macaque (Mf), mouse (Mm) and rat (Rn) orthologues of 7012 were compared using AlignX. Portions of the human sequence were obtained from XP_059659, a peptide predicted from annotation of the human genome at NCBI. The macaque sequence was derived from Genbank entry BAB63112, the predicted translation product of a cDNA isolated from macaque testis. The mouse sequence was obtained by mapping the exon structure of the orthologous gene on the region of mouse chromosome 15. The rat coding sequence was constructed by assembling conserved exons on contigs RNOR01068092, RNOR01068093 and RNOR01068094 (Accession numbers AABR02034780 and AABR02122391). The sequence corresponding to the hamster clone obtained in this study is indicated with a dotted red underline in the human sequence.
Mentions: This clone contained an ORF of 73 amino acids that detected a strong signal by Northern blotting in testis RNA (figure 1). Genome analysis permitted the mapping of a common set of 10 exons on human, mouse and rat chromosomes 5, 15 and 2, respectively (Table 2), assembly of which resulted in translation products of 579, 555 and 563 amino acids, respectively (figure 6). These predictions were also corroborated by a macaque cDNA (AB070167). The encoded proteins did not contain any recognizable functional motifs (figure 3) and were most similar to an uncharacterized human protein named B29 (figure 2). B29 was originally identified as a gene located on human chromosome 18q21 in a search for candidate tumor suppressor proteins in lung [28]. However, the function of B29 is unknown and it does not contain any obvious functional domains. Interestingly, the apparent size of the detected mRNA is significantly larger than that of the assembled sequences, suggesting that additional exons are likely to remain to be discovered. In this regard, gene prediction software identified an additional 35 exons in the mouse genomic sequence that were partly conserved in the rat but not present in the human sequence. Final mapping of the genomic structure of 7012 will await further refineme nt of each genomic sequence.

Bottom Line: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes.The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome.The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA. oduru.sreedhar@ttuhsc.edu

ABSTRACT

Background: Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.

Results: 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.

Conclusion: The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

Show MeSH
Related in: MedlinePlus