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Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome dynamics

ABSTRACT: Understanding chromatin dynamics is a key to other related processes, including DNA replication, transcription and recombination. As a first step, recently, an increasing amount of effort has been devoted to precisely define nucleosome positioning in different organisms. The most popular method to do so is digestion by Micrococcal nuclease (MNase), nowadays followed by ultrasequencing of the generated fragments. Although the sequence bias of MNase has been known for a long time, a data-based way of correcting this bias for sequencing experiments is still missing. Here we provide such a method, based on the digestion of naked DNA and the use of the bioinformatic tool DANPOS. Using Saccharomyces cerevisiae as a model, we demonstrate that the overall quality of the data is better after the correction proposed here. The characteristics of the method make it perfectly applicable to any other organism. Moreover, we find that the correction affects more to TATA containing genes than to TATA-like genes. Importantly, the correction uncovers a new role for TFIIS in chromatin dynamics. The absence of TFIIS caused a general increase in nucleosome fuzziness, and a higher peak of the -1 nucleosome at some promoters

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE94313 | GEO | 2017/11/28

SECONDARY ACCESSION(S): PRJNA369331

REPOSITORIES: GEO

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

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Project description:In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription. Yet the structural features that distinguish enhancers and promoters are unclear. Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers. We find that prior MNase genomic studies have an overdigestion bias and that low-level MNase digestion, coupled with mapping core histones, reveals two classes of MNase-hypersensitive sites: at active promoters, which are nucleosome depleted, and at tissue-specific enhancers, which retain core histones and co-bound transcription factors substantially more than promoters. Hypersensitivity of active enhancer nucleosomes may reflect their preferential exposure in chromatin and can be maintained by pioneer transcription factors such as FoxA. These findings unveil fundamental differences in the chromatin structure of active enhancers and promoters.

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