Chromatin accessibility conservation across four livestock species

International audience

English. Within the FAANG consortium, the FR-AgENCODE pilot project has generated transcriptome (RNA-seq) and chromatin accessibility (ATAC-seq) data in the liver and immune cells of 2 males and 2 females of 4 vertebrate species (cattle, goat, chicken and pig), in addition to Hi-C data (see abstract #79896 by S. Foissac et al.). The first single-assay and integrative analyses performed on these data were mostly done on each species separately. Although these analyses provided several interesting insights (https://www.biorxiv.org/content/10.1101/316091v1), they did not take full advantage of our data richness, namely the availability of the same kind of functional data on species belonging to different parts of the phylogenetic tree. Here we have investigated the relationship between chromatin accessibility conservation across vertebrates and functionality. We first defined orthologous accessible regions by projecting accessible regions from our four species to the human genome. Two accessible regions are called orthologous if their projection on the human genome overlap. In doing so we identified 19,982, 7,877 and 1,083 regions shared between 2, 3 and 4 species, respectively. Our main results are: The level of accessibility of a region, measured by ATAC-seq, increases with the number of shared accessibility-orthologues Regions with more shared accessibility-orthologues are more likely to be close to gene promoters The functional conservation of an accessible region, measured by the number of species exhibiting a tissue-differential accessibility, is correlated to sequence conservation, measured by phastCons. This confirms and reinforces previous findings in human and mouse A hierarchical clustering of ATAC-seq samples based on the correlation between the accessibility of the 1083 orthologous regions shared between 4 species shows that clustering occurs first by species and then by tissue. This is different from what we found for RNA-seq (i.e. all liver samples clustering together). Based on these findings, we are currently working to define more precisely the functional regulatory relationships in liver and immune cells in light of their conservation during evolution. We anticipate that the comparison of these relationships to known QTLs should provide interesting results.