Insights into promoter chromatin remodeling from the structure of ISW1a complex bound to the dinucleosome
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ABSTRACT:
PROVIDER: PRJNA838483 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19217313_1.fastq.gz | Fastqsanger.gz | |||
| SRR19217313_2.fastq.gz | Fastqsanger.gz | |||
| SRR19217314_1.fastq.gz | Fastqsanger.gz | |||
| SRR19217314_2.fastq.gz | Fastqsanger.gz | |||
| SRR19217315_1.fastq.gz | Fastqsanger.gz |
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Project description:Nucleosomes, the basic repeating units of chromatin, form evenly spaced arrays inside the cell. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression. Here we report the cryoEM structure of the chromatin remodeler ISW1a complex bound to the dinucleosome. Both subunits of the complex recognize one nucleosome. The motor subunit binds at the canonical position of the nucleosome, with two arginine anchors recognizing the acidic patch. The DNA-binding module interacts with the entry linker DNA at the nucleosome edge, consistent with the protein ruler model in nucleosome spacing. The Ioc3 subunit recognizes the disk face of the adjacent nucleosome, being important for the spacing activity in vitro, and for chromatin organization in vivo. Together, our findings illustrate a new mode of chromatin remodeling in the context of higher-order chromatin
2023-05-15 | GSE203073 | GEO
Project description:Nucleosomes are basic repeating units of chromatin, and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression. Here we report the cryoEM structure of chromatin remodeler ISW1a complex bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, and the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro, and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a, and add a new mode of nucleosome remodeling in the context of a chromatin environment.
2023-08-09 | GSE240192 | GEO
Project description:Structure of the ISW1a complex bound to the dinucleosome
| PRJNA1002781 | ENA
Project description:The large family of ATP-dependent chromatin remodelers that regulate chromatin organization and composition are thought to act only on individual mononucleosomes. We discovered however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes, not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome specificity by mutating Ioc3 interferes with its localization immediately downstream of the early transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone exchanger, are required together to slow early passage of RNA polymerase II. These findings provide new insights into the unusual specificity of a chromatin remodeler regulating the transition from transcription initiation to elongation and its functional interplay with other chromatin modifiers.
2020-07-31 | GSE150828 | GEO
Project description:The large family of ATP-dependent chromatin remodelers that regulate chromatin organization and composition are thought to act only on individual mononucleosomes. We discovered however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes, not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome specificity by mutating Ioc3 interferes with its localization immediately downstream of the early transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone exchanger, are required together to slow early passage of RNA polymerase II. These findings provide new insights into the unusual specificity of a chromatin remodeler regulating the transition from transcription initiation to elongation and its functional interplay with other chromatin modifiers.
2020-07-31 | GSE150827 | GEO
Project description:The large family of ATP-dependent chromatin remodelers that regulate chromatin organization and composition are thought to act only on individual mononucleosomes. We discovered however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes, not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome specificity by mutating Ioc3 interferes with its localization immediately downstream of the early transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone exchanger, are required together to slow early passage of RNA polymerase II. These findings provide new insights into the unusual specificity of a chromatin remodeler regulating the transition from transcription initiation to elongation and its functional interplay with other chromatin modifiers.
2020-07-31 | GSE150826 | GEO
Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures. Genomic localization of RSC, ISW1a, and SWI/SNF complexes were measured by chromatin immunoprecipitation followed by Illumina paired-end sequencing. Four strains were analyzed, including Rsc8-9xMyc (YBC2882), Sth1-2xFlag (YBC601 p3018), Ioc3-13xMyc (YBC2883), and Snf2-13xMyc (YBC3010). Each sample consists of one chromatin immunoprecipitate and one input chromatin control.
2015-04-01 | E-GEOD-65592 | biostudies-arrayexpress
Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures.
2015-04-01 | GSE65593 | GEO
Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures.
2015-04-01 | GSE65592 | GEO
Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures.
2015-04-01 | GSE65591 | GEO