Genomics

Dataset Information

0

MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers


ABSTRACT: Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and Sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including transcription termination sites. However, they have high A/T-content, suggesting that MNase sensitivity does not indicate instability, but the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE83123 | GEO | 2016/12/15

SECONDARY ACCESSION(S): PRJNA324842

REPOSITORIES: GEO

Similar Datasets

2023-03-14 | GSE216057 | GEO
| E-GEOD-64061 | biostudies-arrayexpress
2016-10-18 | GSE79567 | GEO
2019-08-27 | GSE128689 | GEO
| E-GEOD-26412 | biostudies-arrayexpress
| E-GEOD-73337 | biostudies-arrayexpress
| E-GEOD-69177 | biostudies-arrayexpress
| E-GEOD-47073 | biostudies-arrayexpress
| E-GEOD-66185 | biostudies-arrayexpress
| E-GEOD-59523 | biostudies-arrayexpress