Comment on “A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme”

Wang, Feng; Ranjan, Anand; Wei, Debbie; Wu, Carl

doi:10.1126/science.aad5921

Cited by 35 publications

(28 citation statements)

References 12 publications

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“…Part of the SWR-C captures chaperone-bound H2A.Z–H2B and delivers it to the now vacated H2A– H2B site. Much of this is further regulated through histone acetylation of H2A.Z and H3 and reversed by another remodeller INO80 ( 55 ), although this point has been controversial 56,57 . The replacement of the H2A histone with H2A.Z histone variants results in increased turnover of the full nucleosome octamer, possibly owing to increased exposure of the remaining core histones during replacement 26,56 .…”

Section: Nucleosome Occupancymentioning

confidence: 99%

Understanding nucleosome dynamics and their links to gene expression and DNA replication

Lai

Pugh

2017

Nat Rev Mol Cell Biol

418

381

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Advances in genomics technology have provided the means to probe myriad chromatin interactions at unprecedented spatial and temporal resolution. This has led to a profound understanding of nucleosome organization within the genome, revealing that nucleosomes are highly dynamic. Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general regulatory factors, chromatin remodellers, chaperones and polymerases. It is now known that these dynamics regulate diverse cellular processes ranging from gene transcription to DNA replication and repair.

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Section: Nucleosome Occupancymentioning

confidence: 99%

Understanding nucleosome dynamics and their links to gene expression and DNA replication

Lai

Pugh

2017

Nat Rev Mol Cell Biol

418

381

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“…The histone H2A variant H2A.Z (termed H2AFV in zebrafish) is similar to canonical H2A, but differs along its amino terminal ''tail'' and at key residues in the globular domain and C terminus. Precise genomic incorporation of H2A.Z occurs by the nucleosome remodeler SRCAP (Snf2-related CREBBP activator protein) complex (Kobor et al, 2004;Krogan et al, 2003;Wang et al, 2016). H2A.Z installation is antagonized by its chaperone Anp32e, which promotes H2A.Z removal (Mao et al, 2014;Obri et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

Murphy

James

et al. 2018

Cell

146

140

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The fate and function of epigenetic marks during the germline-to-embryo transition is a key issue in developmental biology, with relevance to stem cell programming and transgenerational inheritance. In zebrafish, DNA methylation patterns are programmed in transcriptionally quiescent cleavage embryos; paternally inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal. Here, we provide the mechanism by demonstrating that "Placeholder" nucleosomes, containing histone H2A variant H2A.Z(FV) and H3K4me1, virtually occupy all regions lacking DNA methylation in both sperm and cleavage embryos and reside at promoters encoding housekeeping and early embryonic transcription factors. Upon genome-wide transcriptional onset, genes with Placeholder become either active (H3K4me3) or silent (H3K4me3/K27me3). Notably, perturbations causing Placeholder loss confer DNA methylation accumulation, whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus, during transcriptionally quiescent gametic and embryonic stages, an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNA methylation, poising parental genes for either gene-specific activation or facultative repression.

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“…Curiously, despite acting mostly within gene bodies, binding by these CRs is detected predominantly at gene promoters (Zentner et al, 2013). Finally, members of the INO80 family, SWR-C and INO80, are implicated in deposition and removal of histone H2A.Z, respectively (Kobor et al, 2004;Krogan et al, 2003;Mizuguchi et al, 2004;Papamichos-Chronakis et al, 2011), although the latter function is currently controversial (Wang et al, 2016;Watanabe and Peterson, 2016). In vitro, INO80 but not SWR-C can slide nucleosomes similarly to ISWI (Udugama et al, 2011) and recently was also shown to be able to move a significant number of +1 nucleosomes to in vivo-like positions on a reconstituted yeast chromatin template (Krietenstein et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Kubik¹,

Challal

Bruzzone³

et al. 2019

Preprint

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Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome displacement activity following rapid remodeler depletion, we investigate the interplay between these enzymes and their impact on transcription in budding yeast. We show that many promoters are acted upon by multiple CRs that operate either cooperatively or in opposition to position the key transcription start site-associated +1 nucleosome. Functional assays suggest that +1 nucleosome positioning often reflects a trade-off between maximizing RNA Polymerase II recruitment and minimizing transcription initiation at incorrect sites.Finally, we show that nucleosome movement following CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity +1 nucleosomes maintain their positions. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.

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Comment on “A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme”

Cited by 35 publications

References 12 publications

Understanding nucleosome dynamics and their links to gene expression and DNA replication

Understanding nucleosome dynamics and their links to gene expression and DNA replication

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

Opposing chromatin remodelers control transcription initiation frequency and start site selection

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