Precise genome-wide mapping of single nucleosomes and linkers in vivo

Chereji, Răzvan V.; Ramachandran, Srinivas; Bryson, Terri D.; Henikoff, Steven

doi:10.1186/s13059-018-1398-0

Cited by 147 publications

(187 citation statements)

References 105 publications

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“…TSSs, +1 NCPs, and TTSs are from Chereji et al (2018), and total nucleosome dyad positions are from Weiner et al (2015). Coordinates for rDNA and tRNA genes were from http://www.yeastgenome.org/.…”

Section: Published Data Setsmentioning

confidence: 99%

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

2018

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The FACT (FAcilitates Chromatin Transactions) complex is a conserved complex that maintains chromatin structure on transcriptionally active genes. Consistent with this, FACT is enriched on highly expressed genes, but how it is targeted to these regions is unknown. In vitro, FACT binds destabilized nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin through recognition of RNA polymerase (RNAP)-disrupted nucleosomes. In this study, we used high-resolution analysis of FACT occupancy in Saccharomyces cerevisiae to test this hypothesis. We demonstrate that FACT interacts with nucleosomes in vivo and that its interaction with chromatin is dependent on transcription by any of the three RNAPs. Deep sequencing of micrococcal nucleaseresistant fragments shows that FACT-bound nucleosomes exhibit differing nuclease sensitivity compared to bulk chromatin, consistent with a modified nucleosome structure being the preferred ligand for this complex. Interestingly, a subset of FACT-bound nucleosomes may be "overlapping dinucleosomes," in which one histone octamer invades the 147-bp territory normally occupied by the adjacent nucleosome. While the differing nuclease sensitivity of FACT-bound nucleosomes could also be explained by the demonstrated ability of FACT to alter nucleosome structure, transcription inhibition restores nuclease resistance, suggesting that it is not due to FACT interaction alone. Collectively, these results are consistent with a model in which FACT is targeted to transcribed genes through preferential interaction with RNAP-disrupted nucleosomes.

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Section: Published Data Setsmentioning

confidence: 99%

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

2018

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“…Transcription start and end sites were downloaded from the supplemental files of Chereji et al, 2018 65 . Transcribed genes were defined as genes in the top 3 quartiles for RNAPII ChIP-seq reads in 5' regions (TSS to +500 bp).…”

Section: Defining Genome Annoationsmentioning

confidence: 99%

“…For heatmaps, which were sorted by the change in RNAPII upon transcription inhibition, genes were considered irrespective of RNAPII enrichment, giving 5133 TSSs. For +2, +3, and +4 NCPs, called nucleosome positions from chemical mapping of dyads 66 were assigned a nucleosome position relative to the TSS 65 . Nucleosomes positions were then filtered by MNase-seq coverage, keeping nucleosomes in the middle two quartiles.…”

Section: Defining Genome Annoationsmentioning

confidence: 99%

The majority of histone acetylation is a consequence of transcription

Martin

Brind’Amour

Jensen

et al. 2019

Preprint

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Histone acetylation is a ubiquitous hallmark of transcriptional activity, but whether the link is of a causal or consequential nature is still a matter of debate. In this study we resolve this question. Using both immunoblot analysis and chromatin immunoprecipitation-sequencing (ChIP-seq) in S. cerevisiae, we show that the majority of histone acetylation is dependent on transcription. Loss of histone H4 acetylation upon transcription inhibition is partially explained by depletion of histone acetyltransferases (HATs) from gene bodies, implicating transcription in HAT targeting. Despite this, HAT occupancy alone poorly predicts histone acetylation, suggesting that HAT activity is regulated at a step postrecruitment. Collectively, these data show that the majority of histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases.

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“…Thus, using the chemical cleavage-based nucleosome map of Chereji et al (2018), which was based on the H3Q85C cleavage method, we also performed the same analysis. The profiles were generally similar to those obtained based on the MNase-seq-based map.…”

Section: Resultsmentioning

confidence: 99%

A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats

et al. 2018

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DNA sequences that read the same from 5′ to 3′ in either strand are called inverted repeat sequences or simply IRs. They are found throughout a wide variety of genomes, from prokaryotes to eukaryotes. Despite extensive research, their in vivo functions, if any, remain unclear. Using Saccharomyces cerevisiae, we performed genome-wide analyses for the distribution, occurrence frequency, sequence characteristics and relevance to chromatin structure, for the IRs that reportedly have a cruciform-forming potential. Here, we provide the first comprehensive map of these IRs in the S. cerevisiae genome. The statistically significant enrichment of the IRs was found in the close vicinity of the DNA positions corresponding to polyadenylation [poly(A)] sites and ~ 30 to ~ 60 bp downstream of start codon-coding sites (referred to as ‘start codons’). In the former, ApT- or TpA-rich IRs and A-tract- or T-tract-rich IRs are enriched, while in the latter, different IRs are enriched. Furthermore, we found a strong structural correlation between the former IRs and the poly(A) signal. In the chromatin formed on the gene end regions, the majority of the IRs causes low nucleosome occupancy. The IRs in the region ~ 30 to ~ 60 bp downstream of start codons are located in the + 1 nucleosomes. In contrast, fewer IRs are present in the adjacent region downstream of start codons. The current study suggests that the IRs play similar roles in Escherichia coli and S. cerevisiae to regulate or complete transcription at the RNA level.Electronic supplementary materialThe online version of this article (10.1007/s00294-018-0907-8) contains supplementary material, which is available to authorized users.

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Precise genome-wide mapping of single nucleosomes and linkers in vivo

Cited by 147 publications

References 105 publications

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

The majority of histone acetylation is a consequence of transcription

A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats

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