Department of Animal Sciences, University of Illinois at Urbana-Champaign, 210 Edward R Madigan Laboratory, 1201 W Gregory Dr, Urbana, IL 61801, USA.
BMC Genomics. 2010 Mar 9;11:161. doi: 10.1186/1471-2164-11-161.
The 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.
Clusters 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.
The 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.
哺乳动物目内和目间胎盘结构的多样性被认为是适应进化的结果。虽然这些差异的遗传基础尚不清楚，但有些可能是由快速分化和谱系特异性基因引起的。以前，我们从牛的胎盘中鉴定出了 91 个新的谱系特异性转录本（LST），它们是反刍动物谱系获得的适应性胎盘功能的优秀候选者。本研究的目的是使用共表达、启动子、途径和网络分析推断以前未表征的谱系特异性基因（LSG）的功能。
使用 49 个以前未表征的 LST 作为种子，发现了在肝脏、胎盘和胸腺中优先表达的共表达基因簇。然后，通过计算识别了聚类 LSGs 和已知基因启动子中复合转录因子结合位点（TFBS）的过度表达。使用共表达分析和途径分析工具推断了九个以前未表征的 LSG 的功能。我们的结果预测，这些 LSG 可能在细胞信号转导、甘油磷脂/脂肪酸代谢、蛋白质运输、核内调节过程以及启动分娩和免疫系统发育的过程中发挥作用。
胎盘是谱系特异性基因的丰富来源，这些基因在胎盘结构和功能的适应进化中发挥作用。我们已经表明，共表达、启动子和基因网络分析是推断具有未知功能的 LSG 功能的有用方法。我们的结果表明，许多 LSG 参与细胞识别和发育过程。此外，它们为验证 LSG 功能和研究其进化的实验方法提供了指导。
