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Sperm chromatin and the evolution of chromatin architecture at regulatory regions in animal genomes

Final Report Summary - EVO-CHROMO (Sperm chromatin and the evolution of chromatin architecture at regulatory regions in animal genomes.)

The original objectives of the grant were to study the chromatin organization of promoters and enhancers in animal genomes and their evolution. To study the organization of chromatin at human promoters we analysed publicly available genomewide chromatin and gene expression datasets. More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications. We tested whether these two different types of promoters are associated with different chromatin profiles, after controlling for gene expression. Ours results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription- associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates (Vavouri and Lehner, Genome Biology, 2012). We also tested whether the two types of promoters are packaged differently in human sperm. We found that CpG island promoters retain a mixture of nucleosomes and subnucleosomal structures in mature sperm cells (Castillo et al, Mol Hum Reprod, 2014). We also studied the organization and evolution of distal enhancers at the base of the chordate lineage. Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. We used genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non- coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity (Doglio et al, PLoS Genetics, 2013). Last, we tested whether chromatin organization is involved in intergenerational epigenetic inheritance. In a fruitfly model of intergenerational obesity, we found that paternal high sugar diet causes derepression of genes encoded in H3K27me3 and H3K9me3 heterochromatin in the early embryo and also sperm (Ost et al, Cell, 2014).