The Chp1 chromodomain binds the H3K9me tail and the nucleosome core to assemble heterochromatin

Zocco, M.A.; Marasovic, Mirela; Pisacane, Paola; Bilokapić, Silvija; Halić, Mario

doi:10.1038/celldisc.2016.4

Cited by 19 publications

(18 citation statements)

References 50 publications

(89 reference statements)

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“…More recently, a number of subnanometre-resolution structures of NCP-chromatin-binding protein complexes have been determined (Maskell et al, 2015;Zocco et al, 2016;Wilson et al, 2016;Fig. 2).…”

Section: Using Single-particle Em To Study Ncp Interactorsmentioning

confidence: 99%

“…Left inset: magnified view of the UDR-ubiquitin-NCP interaction with ubiquitin fitted into density (PDB entry 1ubi). (d) Chp1 chromodomain-NCP-me structure (EMD entry 8063; Zocco et al, 2016). (e) 12-mer chromatin fibre (EMD entry 2600; Song et al, 2014).…”

Section: Visualizing Nucleosomes Under the Electron Microscopementioning

confidence: 99%

“…Cryo-EM was used to determine how a chromodomain from fission yeast Chp1 reads the heterochromatic H3K9me3 mark (Zocco et al, 2016;Fig. 2d).…”

Section: Studying Histone Modifications Using Cryo-emmentioning

confidence: 99%

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Cryo-electron microscopy of chromatin biology

Wilson

Costa

2017

Acta Cryst Sect D Struct Biol

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The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. Since its discovery, biochemists have sought to understand how this protein-DNA complex can help to control so many diverse tasks. Recent electron-microscopy (EM) studies on NCP-containing assemblies have helped to describe important chromatin transactions at a molecular level. With the implementation of recent technical advances in single-particle EM, our understanding of how nucleosomes are recognized and read looks to take a leap forward. In this review, the authors highlight recent advances in the architectural understanding of chromatin biology elucidated by EM.

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Section: Using Single-particle Em To Study Ncp Interactorsmentioning

confidence: 99%

Section: Visualizing Nucleosomes Under the Electron Microscopementioning

confidence: 99%

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Cryo-electron microscopy of chromatin biology

Wilson

Costa

2017

Acta Cryst Sect D Struct Biol

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“…To amplify small RNAs, RITS recruits the RNA-dependent RNA Polymerase complex (RDRC), which synthesizes doublestranded RNA that is processed by Dicer into siRNAs. In addition, RITS recruits the H3K9 methyltransferase complex CLRC to chromatin, which leads to repressive histone 3 lysine 9 methylation (H3K9me), recruitment of HP1 proteins, and heterochromatin formation (Volpe et al 2002;Verdel et al 2004;Allshire and Ekwall 2015;Holoch and Moazed 2015;Martienssen and Moazed 2015;Zocco et al 2016).…”

mentioning

confidence: 99%

Accumulation of RNA on chromatin disrupts heterochromatic silencing

Brönner¹,

Salvi²,

Zocco³

et al. 2017

Genome Res.

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Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochromatin is lost at transcribed regions in the absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA: RNA hybrids, and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing. The Ccr4-Not complex is localized to chromatin independently of H3K9me and degrades chromatin-associated transcripts, which is required for transcriptional silencing. Overexpression of heterochromatic RNA, but not euchromatic RNA, leads to chromatin localization and loss of silencing of a distant ade6 reporter in wild-type cells. Our results demonstrate that chromatin-bound RNAs disrupt heterochromatin organization and need to be degraded in a process of heterochromatin formation.

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“…Fluorescent nucleosomes have been constructed using Cy5-labeled DNA [14], or AlexaFluor647-labeled histone H3 [15]. Furthermore, MST has been used to derive insights in protein-binding mechanisms, e.g., demonstration of cooperative binding [16] or determination of binding sites from a comparison of different deletion mutants [17].…”

Section: Mst Of Chromatin Systemsmentioning

confidence: 99%

Microscale Thermophoresis Analysis of Chromatin Interactions

Corbeski

Horn

Valk

et al. 2018

Methods in Molecular Biology

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Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique that has seen increasing application in the study of biomolecular interactions thanks to its solution-based nature, its rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events. Here, we describe the use of MST in the study of chromatin interactions, with emphasis on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB; the sequential binding of core histone complexes to histone chaperone APLF; the impact of the nucleosomal context on the recognition of histone modifications; and the binding of a LANA-derived peptide to nucleosome core. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.

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The Chp1 chromodomain binds the H3K9me tail and the nucleosome core to assemble heterochromatin

Cited by 19 publications

References 50 publications

Cryo-electron microscopy of chromatin biology

Cryo-electron microscopy of chromatin biology

Accumulation of RNA on chromatin disrupts heterochromatic silencing

Microscale Thermophoresis Analysis of Chromatin Interactions

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