Comparative Analysis of Super-enhancers Across Mammals Reveals Their High Function Conservation

BackgroundSuper-enhancers (SEs) are key positive regulatory elements in defining cells/tissues identity in mammals, yet their similarities and differences of sequence and function across mammals have been poor studied. To allow sequence and function comparison across mammalian SEs, we employ H3K27ac ChIP-seq data to six cell types/tissues across human, pig, and mouse, which represent different lineages of mammals in the evolutionary tree.ResultsOverall, a median of 848 human SEs, 888 pig SEs and 503 mouse SEs are identified across cells/tissues. These SEs are largely distributed in promoter regions for human (91.9% in median) and mouse (63.4% in median), while mostly in distal intergenic regions for pig (66.1% in median). Extremely higher unique orthologous SEs frequency (91.6%~92.1%) has been detected for the same cell/tissue across species. Consistently, their overlapping rates are very low for the same cell/tissue across species (0.1%~0.5%). For the SE-associated orthologous genes, they also show high unique frequency for species (63.3%~83.9%) and low overlapping rates (0.8%~1.3%) at inter-species comparison. However, orthologous SEs function comparisons across species have shown similar biological processes related to cells/tissues identity in the top 15 significant enriched terms for the same cell/tissue. Meanwhile, common core transcription factors that determine cells/tissues identity are determined for the same cell/tissue across mammals.ConclusionsThis study highlights the differences of SEs genomic distribution across mammals. It reveals low orthologous sequence overlapping but high function conservation of SEs across mammals. It would improve our understanding of regulation function cis-regulatory elements in mammals.

Identification of nuclear low-copy genes and their phylogenetic utility in rosids

By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eukaryotic orthologous groups) database, most of which were first used for phylogenetic analysis of angiosperms. The orthologous sequence datasets from completely sequenced genomes of rosids were assembled for the resolution of the position of the COM (Celastrales–Oxalidales–Malpighiales) clade in rosids. Our analysis revealed strong and consistent support for CM topology (the COM clade as sister to the malvids). Our results will contribute to further exploring the underlying cause of conflict between chloroplast, mitochondrial, and nuclear data. In addition, our study identified a few novel nuclear molecular markers with potential to investigate the deep phylogenetic relationship of plants or other eukaryotic taxonomical groups.