EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation

Pradhan, Suman; Su, Trent; Yen, Linda; Jacquet, Karine; Huang, Chi‐Chun; Côté, Jacques; Kurdistani, Siavash K.; Carey, Michael

doi:10.1016/j.molcel.2015.10.039

Cited by 106 publications

(100 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…ChIP was performed as in (Pradhan et al, 2016) with minor adaptations. E14 cells grown in 150 cm 2 dishes were harvested at 70% confluency by trypsinization, followed by 1x DPBS wash.…”

Section: Star Methodsmentioning

confidence: 99%

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

et al. 2017

Self Cite

View full text Add to dashboard Cite

Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 colocalize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.

show abstract

“…ChIP was performed as in (Pradhan et al, 2016) with minor adaptations. E14 cells grown in 150 cm 2 dishes were harvested at 70% confluency by trypsinization, followed by 1x DPBS wash.…”

Section: Star Methodsmentioning

confidence: 99%

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…We used H3K4me1 and POL2B ChIP-seq peaks from GEO accession GSE73742 [48]. We used H3K4me3 and H3K27me3 ChIP-seq peaks from GSE35573 [49].…”

Section: Chip-seq and Dnase-seq Datamentioning

confidence: 99%

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

Mourad

Cuvier

2017

Preprint

View full text Add to dashboard Cite

Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of their origins. However, these techniques are costly and challenging. Hence, we devise a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are readily available from the ENCODE project. We achieve excellent prediction accuracy at high resolution. We identify chromatin accessibility, activity, and long-range contacts as the best predictors.

show abstract

“…GAGA recruits FACT and the Polybromo-associated Brm (PBAP) remodeling complex to chromatin boundaries; both complexes are required for boundary maintenance and H3.3 replacement at the boundaries [62]. In addition, EP400, a SWR1-class ATP-dependent chromatin remodeling protein that deposits H2A.Z variant in the Tip60-P400 complex, can also exchange H3.3 into canonical chromatin both in vitro and in cells, promoting gene activation [63]. Given the close correlation of H2A.Z with H3.3 in the genome, it awaits to see if other H2A.Z remodelers also have a role in regulating H3.3 deposition.…”

Section: Introductionmentioning

confidence: 99%

The Histone Variant H3.3 in Transcriptional Regulation and Human Disease

Shi

Wen

Shi

2017

Journal of Molecular Biology

View full text Add to dashboard Cite

Histone proteins wrap around DNA to form nucleosomes, which further compact into higher order structure of chromatin. In addition to the canonical histones, there are also variant histones that often have pivotal roles in regulating chromatin dynamics and the accessibility of the underlying DNA. H3.3 is the most common non-centromeric variant of histone H3 that differs from the canonical H3 by just 4–5 amino acids. Here we discuss the current knowledge of H3.3 in transcriptional regulation and the recent discoveries and molecular mechanisms of H3.3 mutations in human cancer.

show abstract

EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation

Cited by 106 publications

References 59 publications

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

The Histone Variant H3.3 in Transcriptional Regulation and Human Disease

Contact Info

Product

Resources

About