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Nat Commun
2020 Nov 20;111:5913. doi: 10.1038/s41467-020-19700-1.
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Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation.
Bhardwaj SK
,
Hailu SG
,
Olufemi L
,
Brahma S
,
Kundu S
,
Hota SK
,
Persinger J
,
Bartholomew B
.
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Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.
Albert,
GeneTrack--a genomic data processing and visualization framework.
2008, Pubmed
Albert,
GeneTrack--a genomic data processing and visualization framework.
2008,
Pubmed
Altaf,
NuA4-dependent acetylation of nucleosomal histones H4 and H2A directly stimulates incorporation of H2A.Z by the SWR1 complex.
2010,
Pubmed
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015,
Pubmed
Blankenberg,
Galaxy: a web-based genome analysis tool for experimentalists.
2010,
Pubmed
Chatterjee,
Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms.
2011,
Pubmed
,
Xenbase
Chatterjee,
Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF.
2015,
Pubmed
,
Xenbase
Chittuluru,
Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes.
2011,
Pubmed
Collart,
Preparation of yeast RNA.
2001,
Pubmed
Dann,
ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference.
2017,
Pubmed
Dao,
A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing.
2020,
Pubmed
Dechassa,
Architecture of the SWI/SNF-nucleosome complex.
2008,
Pubmed
,
Xenbase
Dechassa,
SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes.
2010,
Pubmed
Doyon,
Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans.
2004,
Pubmed
Eden,
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
2009,
Pubmed
Eden,
Discovering motifs in ranked lists of DNA sequences.
2007,
Pubmed
Fyodorov,
Chromatin assembly in vitro with purified recombinant ACF and NAP-1.
2003,
Pubmed
Gamarra,
The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h.
2018,
Pubmed
Gangaraju,
Dependency of ISW1a chromatin remodeling on extranucleosomal DNA.
2007,
Pubmed
Giardine,
Galaxy: a platform for interactive large-scale genome analysis.
2005,
Pubmed
Goecks,
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
2010,
Pubmed
Goldman,
Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z.
2010,
Pubmed
Gossett,
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.
2012,
Pubmed
Hada,
Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling.
2019,
Pubmed
Hota,
Mapping protein-DNA and protein-protein interactions of ATP-dependent chromatin remodelers.
2012,
Pubmed
Hota,
Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains.
2013,
Pubmed
Hulsen,
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.
2008,
Pubmed
Kassabov,
Site-directed histone-DNA contact mapping for analysis of nucleosome dynamics.
2004,
Pubmed
Kassabov,
High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2.
2002,
Pubmed
Keogh,
The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.
2006,
Pubmed
Kim,
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
2013,
Pubmed
Krietenstein,
Genomic Nucleosome Organization Reconstituted with Pure Proteins.
2016,
Pubmed
Kusch,
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions.
2004,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Leonard,
A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler.
2015,
Pubmed
Lindstrom,
Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress-induced gene repression.
2006,
Pubmed
Lu,
NuA4 and SWR1-C: two chromatin-modifying complexes with overlapping functions and components.
2009,
Pubmed
Maltby,
Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin.
2012,
Pubmed
McCarthy,
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
2012,
Pubmed
Millar,
Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast.
2006,
Pubmed
Mizuguchi,
ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex.
2004,
Pubmed
Morillon,
Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II.
2003,
Pubmed
Nagalakshmi,
The transcriptional landscape of the yeast genome defined by RNA sequencing.
2008,
Pubmed
Persinger,
Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.
2009,
Pubmed
Racki,
The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.
2009,
Pubmed
Ramírez,
deepTools2: a next generation web server for deep-sequencing data analysis.
2016,
Pubmed
Ranjan,
Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.
2013,
Pubmed
Ritchie,
limma powers differential expression analyses for RNA-sequencing and microarray studies.
2015,
Pubmed
Robinson,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
2010,
Pubmed
Saldanha,
Java Treeview--extensible visualization of microarray data.
2004,
Pubmed
Santisteban,
Histone variant H2A.Z and RNA polymerase II transcription elongation.
2011,
Pubmed
Skene,
A simple method for generating high-resolution maps of genome-wide protein binding.
2015,
Pubmed
Smolle,
Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange.
2012,
Pubmed
Suto,
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
2000,
Pubmed
,
Xenbase
Tirosh,
Widespread remodeling of mid-coding sequence nucleosomes by Isw1.
2010,
Pubmed
Tullius,
Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts.
1987,
Pubmed
Vary,
Assembly of yeast chromatin using ISWI complexes.
2004,
Pubmed
Yamada,
Structure and mechanism of the chromatin remodelling factor ISW1a.
2011,
Pubmed
,
Xenbase
Yan,
Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling.
2019,
Pubmed
Yen,
Genome-wide nucleosome specificity and directionality of chromatin remodelers.
2012,
Pubmed
Zentner,
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.
2013,
Pubmed
Zhang,
Model-based analysis of ChIP-Seq (MACS).
2008,
Pubmed
Zhang,
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss.
2005,
Pubmed
