Discovery and characterization of 91 novel transcripts expressed in cattle placenta

Kumar, Charu G.; Larson, Joshua H.; Band, Mark; Lewin, Harris A.

doi:10.1186/1471-2164-8-113

Cited by 9 publications

(22 citation statements)

References 63 publications

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“…As we and others have shown, the placenta is a rich source of expressed LSGs and rapidly diverging genes [2,3,57-60]. Such genes are candidates for adaptive placental functions acquired by the ruminant lineage.…”

Section: Discussionmentioning

confidence: 99%

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

et al. 2010

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BackgroundThe diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis.ResultsClusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development.ConclusionsThe placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.

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Section: Discussionmentioning

confidence: 99%

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

et al. 2010

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“…Trophoblastic cells of the ruminant placenta express various tissue-specific proteins during pregnancy, such as PAGs, which play a key role in fetal-maternal signaling and communication [31,32]. Within this family of PAG genes, the incorporation of different repetitive and transposable elements like Art2A and BovA2 has been reported [62].…”

Section: Tags Exclusively In Samples Of Pregnant Cowsmentioning

confidence: 98%

“…During pregnancy in ruminants, different molecules are produced in the trophoblastic cells of the placenta, such as progesterone, lactogenes, pregnancy-associated glycoproteins (PAGs), and prolactins, that play a key role in fetal-maternal signaling and communication [31,32] and are measurable in the cow's circulation [33]. The aim of the present study was the identification and characterization of circulating DNA in serum samples of pregnant dairy cows that are present in early gestation.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Circulating DNA Distribution in Pregnant and Nonpregnant Dairy Cows1

Mayer

Beck²,

Soller

et al. 2013

Biology of Reproduction

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Circulating nucleic acids (CNAs) are free-floating, cell-free DNA and RNA molecules in the circulation of healthy and diseased humans and animals. The aim of this study was to identify differences in CNA distribution in serum samples from multiparous pregnant (n = 24) and nonpregnant (n = 16) dairy cows at different days of gestation (Days 0, 20, and 40). A modified serial analysis of gene expression procedure was used to generate concatemerized short sequence tags from isolated serum DNA. A total of 6.1 × 10(6) tags were recovered from analyzed samples (n = 40). Significant differences between the pregnant and nonpregnant groups were detected in chromosomal regions, protein-coding sequences, and single genes (P < 0.05). Approximately 23% (1.4 × 10(6) tags) of the total sequence pool were present exclusively in the analyzed serum samples of pregnant cows. Of these tag sequences, seven originated from genomic regions and 13 from repetitive elements. Comparative BLAST analysis identified the repetitive tags as BovB (non-long terminal repeat retrotransposons/long interspersed nuclear elements), Art2A, BovA2, and Bov-tA2 (short interspersed nuclear elements). To our knowledge, this is the first study to comprehensively characterize the circulating, cell-free DNA profile in sera from pregnant and nonpregnant cows across early gestation.

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“…However, these oocyte-exclusive genes and their functions have not yet been extensively characterized. To this end, the mining of public sequence and library databases has been of great value for discovering gene expression patterns (4,5), as well as new genes or gene variants (6,7). The genes Oogenesin-2 and Oogenesin-3 were previously characterized as being specifically expressed in mouse oocytes (8).…”

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confidence: 99%

Messenger RNA expression of Pabpnl1 and Mbd3l2 genes in oocytes and cleavage embryos

Biase

Martelli

Puga

et al. 2010

Fertility and Sterility

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Discovery and characterization of 91 novel transcripts expressed in cattle placenta

Cited by 9 publications

References 63 publications

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

Analysis of Circulating DNA Distribution in Pregnant and Nonpregnant Dairy Cows1

Messenger RNA expression of Pabpnl1 and Mbd3l2 genes in oocytes and cleavage embryos

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