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

Abstract

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.

Novel SNPs and InDels discovered in two promoter regions of porcine pregnancy-associated glycoprotein 2-like subfamily (pPAG2-Ls) in crossbreed pigs

“…Presently, in crossbreed pigs, no SNPs were identified in the Ets2 binding site, although the identified SNPs in the GATA suggest the possibility of disturbance during pPAG2-L subfamily activation. In addition, the bovine microarrays (Kumar et al 2010 ) indicate a strong influence of the STAT Pax-2 (signal transducer and activator of transcription; paired homeobox 2) on the promoters of genes that are expressed in the placenta, e.g., bPAG2 , PTGS2 ( COX2 , PG – endoperoxide synthase 2 ) and LSG 34F , as a homologue of a secretory vesicle protein in the male (SSLP-1; seminal vesicle protein secreted ).…”

Modulation of Maternal Immune System During Pregnancy in the Cow

“…We compiled microarray data in gene expression of bovine endometrium into a list of genes expressed during the pre-implantation period (days 5 and 7 of pregnancy) (Forde et al 2011); at the window of implantation (from day 13 to day 20) (Bauersachs et al 2008;Mansouri-Attia et al 2009a,b;Salilew-Wondim et al 2010;Groebner et al 2011); and in the period after implantation (from day 35 to term) (Band et al 2002;Ishiwata et al 2003;Larson et al 2006;Hashizume 2007;Hashizume et al 2007;Kumar et al 2007Kumar et al , 2010. The compiled data were used for bioinformatics data analysis.…”

Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits

“…Transcription start sites were downloaded from the UCSC Genome Browser (refGene table for the cattle genome). Promoter extraction was performed as previously described (33). Polymorphisms in cattle promoters were analyzed to determine if TFBSs within the promoter region were disrupted by the allelic differences or resulted in the gain of a new TFBS.…”