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Discovery and characterization of 91 novel transcripts expressed in cattle placenta.

Kumar CG, Larson JH, Band MR, Lewin HA - BMC Genomics (2007)

Bottom Line: These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence.Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome.The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Mammalian Genome Biology, Department of Animal Sciences, University of Illinois at Urbana-Champaign, 210 Edward R. Madigan Laboratory, Urbana, IL 61801, USA. cgkumar@uiuc.edu <cgkumar@uiuc.edu>

ABSTRACT

Background: Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.

Results: A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

Conclusion: The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.

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Preferential expression of 39 NTs in 18 sampled tissues. Orange bars indicate NTs with no ORF and preferential expression in more than one tissue. Yellow bars indicate NTs with ORFs and preferential expression in more than one tissue. Blue bars represent NTs with no ORF and preferential expression in a single tissue. Purple bars represent NTs with ORFs and preferential expression in a single tissue. M.L.; mesenteric lymph node.
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Figure 5: Preferential expression of 39 NTs in 18 sampled tissues. Orange bars indicate NTs with no ORF and preferential expression in more than one tissue. Yellow bars indicate NTs with ORFs and preferential expression in more than one tissue. Blue bars represent NTs with no ORF and preferential expression in a single tissue. Purple bars represent NTs with ORFs and preferential expression in a single tissue. M.L.; mesenteric lymph node.

Mentions: Expression levels of the NTs were analyzed in 17 tissues from a one week-old Jersey calf and a term placentome. Expression of 86/91 NTs could be analyzed (5 had no representative cDNA element on the microarray). The expressed NTs were categorized with respect to the presence or absence of ORF(s) as well as with expression levels classified as high, moderate or low on the basis of an arbitrary scale (Table 5). Among the 60 expressed NTs with ORFs, 55% were expressed at a low level in all 18 tissues, and 45% were expressed at moderate or high levels in one or more tissues (Table 5). A similar distribution of expression levels in tissues was found among the NTs without ORFs. Tissue-preference in expression patterns of NTs was analyzed further by determining those NTs that were expressed greater than two-fold in any one tissue compared to at least 13 out of 17 other tissues (Figure 5; Additional file 2). A total of 39 NTs show tissue preference in their expression pattern. Of these, 28 were preferentially expressed in a single tissue. Six NTs were preferentially expressed in placentome, of which two were predicted to be ncRNAs. Ten different tissues showed exclusive expression of one or more of the NTs, with placentome and thymus having the largest number.


Discovery and characterization of 91 novel transcripts expressed in cattle placenta.

Kumar CG, Larson JH, Band MR, Lewin HA - BMC Genomics (2007)

Preferential expression of 39 NTs in 18 sampled tissues. Orange bars indicate NTs with no ORF and preferential expression in more than one tissue. Yellow bars indicate NTs with ORFs and preferential expression in more than one tissue. Blue bars represent NTs with no ORF and preferential expression in a single tissue. Purple bars represent NTs with ORFs and preferential expression in a single tissue. M.L.; mesenteric lymph node.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1884150&req=5

Figure 5: Preferential expression of 39 NTs in 18 sampled tissues. Orange bars indicate NTs with no ORF and preferential expression in more than one tissue. Yellow bars indicate NTs with ORFs and preferential expression in more than one tissue. Blue bars represent NTs with no ORF and preferential expression in a single tissue. Purple bars represent NTs with ORFs and preferential expression in a single tissue. M.L.; mesenteric lymph node.
Mentions: Expression levels of the NTs were analyzed in 17 tissues from a one week-old Jersey calf and a term placentome. Expression of 86/91 NTs could be analyzed (5 had no representative cDNA element on the microarray). The expressed NTs were categorized with respect to the presence or absence of ORF(s) as well as with expression levels classified as high, moderate or low on the basis of an arbitrary scale (Table 5). Among the 60 expressed NTs with ORFs, 55% were expressed at a low level in all 18 tissues, and 45% were expressed at moderate or high levels in one or more tissues (Table 5). A similar distribution of expression levels in tissues was found among the NTs without ORFs. Tissue-preference in expression patterns of NTs was analyzed further by determining those NTs that were expressed greater than two-fold in any one tissue compared to at least 13 out of 17 other tissues (Figure 5; Additional file 2). A total of 39 NTs show tissue preference in their expression pattern. Of these, 28 were preferentially expressed in a single tissue. Six NTs were preferentially expressed in placentome, of which two were predicted to be ncRNAs. Ten different tissues showed exclusive expression of one or more of the NTs, with placentome and thymus having the largest number.

Bottom Line: These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence.Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome.The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Mammalian Genome Biology, Department of Animal Sciences, University of Illinois at Urbana-Champaign, 210 Edward R. Madigan Laboratory, Urbana, IL 61801, USA. cgkumar@uiuc.edu <cgkumar@uiuc.edu>

ABSTRACT

Background: Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.

Results: A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

Conclusion: The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.

Show MeSH
Related in: MedlinePlus