CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq)

ABSTRACT: One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE38563 | GEO | 2012/06/12

SECONDARY ACCESSION(S): PRJNA168377

REPOSITORIES: GEO