Genome-wide gene expression analysis of 45 days pregnant fetal cotyledons vis-a-vis non-pregnant caruncles in buffalo (Bubalus bubalis).

The crosstalk between fetus and mother starts with the onset of placental attachment to the uterus. The cotyledons and caruncles are the two anatomically distinct structures that play a crucial role in this physiological communication. Using Agilent Gene Chip Genome microarray, we measured the expression profile of pregnancy cotyledons in comparison to caruncular reminiscence of the uteri in non-pregnant buffalo (Bubalus bubalis) for the detection of the early post-pregnancy rapid changes in cellular expression of mRNA transcripts. We identified a total of 497 up- and 578 down-regulated genes with <0.05 the FDR corrected p-values using 4 replicates in each group (cotyledons and caruncles) and their role in pregnancy. Deep bioinformatics analysis of data revealed the cluster of genes involved at the placentome level for various functions such as fetus attachment, transport of nutrition, and immune response. Importantly, the pathways like Hedgehog/Calcium/Wnt signalling, cell cycle regulation and immune responses regulatory functions were highly enriched by the differentially identified genes. A very highly up-regulated IL-2 specific gene showed the role of interleukin-2 signalling in the attachment of the embryo. It was observed that the genes responsible for immune response were downregulated, suggesting an immune suppressive environment which is required to adopt the semiallogeneic fetus for a successful pregnancy. To further evaluate and validate the data, we have performed qRT-PCR analysis of twenty-one genes. The present study highlights the repertoire of active transcripts in the junction of cotyledons and caruncles, which are essential for a successful onset and completion of pregnancy.