DNA bendability regulates transcription factor binding to nucleosomes [MNase-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1242366 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA bendability regulates transcription factor binding to nucleosomes
| PRJNA1244853 | ENA
Project description:Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here, we developed PIONEAR-seq, a high-throughput biochemical assay to characterize pioneer binding to nucleosomes. We used PIONEAR-seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by TFs' recognition motifs, senses the broader nucleosome sequence context and that TFs previously found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences exhibit exclusively end binding to nucleosomes based on genomic sequences. We propose a model where the nucleosome exploits the local bendability of the DNA sequence to position pioneer binding, revealing another cis-regulatory layer in eukaryotes.
2025-05-01 | GSE293024 | GEO
Project description: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.
2016-12-15 | GSE83123 | GEO
Project description:DNA bendability regulates transcription factor binding to nucleosomes [PIONEAR-seq and SELEX-seq]
| PRJNA1244796 | ENA
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.
2011-01-24 | E-GEOD-26412 | biostudies-arrayexpress
Project description:We showed that topoisomerase II synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin. To study the consequences of this on transcription factors, we performed MNase-seq on light digest of native chromatin in Brg1 conditional knockout embryonic stem (ES) cells. We found that spacing of nucleosomes flanking pluripotency factor binding sites specifically partially collapsed upon Brg1 deletion, indicating that pluripotency factor binding is likely lost.
2017-03-01 | GSE94040 | GEO
Project description:Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here, we developed PIONEAR-seq, a high-throughput biochemical assay to characterize pioneer binding to nucleosomes. We used PIONEAR-seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by TFs' recognition motifs, senses the broader nucleosome sequence context and that TFs previously found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences exhibit exclusively end binding to nucleosomes based on genomic sequences. We propose a model where the nucleosome exploits the local bendability of the DNA sequence to position pioneer binding, revealing another cis-regulatory layer in eukaryotes.
2025-05-01 | GSE293487 | GEO
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
2011-01-24 | GSE26412 | GEO
Project description:Nucleosomes are the most basic units of chromatin and are regulators of genome integrity and gene expression. The fundamental mechanism how nucleosomes are dynamically regulated is one of the main questions in chromatin organization; most of the study has, however, focused on its positioning. Here we performed HiLo-MNase-seq, which involves limit and partial digestion of chromatin by micrococcal nuclease (MNase) to identify the positioning of nucleosome array along with the kinetics of MNase digestion. We identified a subset of unique nucleosomes with fast digestion kinetics at the transcription factor binding sites that have been characterized as nucleosome depleted regions (NDRs). By inhibiting RNA polymerase II, we also showed that those nucleosomes changed its sensitivity to MNase in a context-dependent manner. These findings implicated a self-reinforcing regulatory network involving nucleosomes, Pol II, and transcription factors for fine-tuning of gene expression.
2020-02-01 | GSE77526 | GEO
Project description:We employed an MNase-Transcription Start Site Sequence Capture method to map and determine the accessibility of all nucleosomes during immune stimulus, at high coverage for all human Pol II promoters. We uncovered features of nucleosomal organization and sensitivity to MNase digestion in B-lymphoblastoid cells. We also find that transcription factor binding is associated with sensitive nucleosomes.
2020-01-01 | GSE139224 | GEO