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The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

ABSTRACT: We addressed the roles of primarily two remodeling complexes, ISW1a and ISW1b, in affecting the chromatin organization in the yeast Saccharomyces cerevisiae.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE156224 | GEO | 2021/02/02

REPOSITORIES: GEO

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The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution.

Project description:Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.

| S-EPMC7892562 | biostudies-literature

The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

Project description:The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

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The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

Project description:We addressed the roles of three nucleosome spacing enzymes (ISW1, ISW2 and CHD1) in specifying chromatin organization in S. cerevisiae.

2016-02-17 | GSE69400 | GEO

Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

Project description:Role of Itc1 subnit in ISW2 remodeler in nucleosome positioning and spacing in Saccharomyces cerevisiae

2024-04-07 | GSE205956 | GEO

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

Project description:We addressed the roles of three nucleosome spacing enzymes (ISW1, ISW2 and CHD1) in specifying chromatin organization in S. cerevisiae. Comparison of budding yeast nucleosome positions obtained using micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq). We sequenced nucleosomes from isogenic strains with the isw1Î, isw2Î or chd1Î mutations in all combinations. We measured gene activity by ChIP-seq for the Rpb3 subunit of RNA polymerase II for some of these mutants.

2016-02-17 | E-GEOD-69400 | biostudies-arrayexpress

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq]

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

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-seq]

2020-07-31 | GSE150828 | GEO

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [ChIP-seq]

2020-07-31 | GSE150826 | GEO

The SWI/SNF ATP-dependent nucleosome remodeler promotes resection initiation at a DNA double-strand break in yeast.

Project description:DNA double-strand breaks (DSBs) are repaired by either the non-homologous end joining (NHEJ) or homologous recombination (HR) pathway. Pathway choice is determined by the generation of 3? single-strand DNA overhangs at the break that are initiated by the action of the Mre11-Rad50-Xrs2 (MRX) complex to direct repair toward HR. DSB repair occurs in the context of chromatin, and multiple chromatin regulators have been shown to play important roles in the repair process. We have investigated the role of the SWI/SNF ATP-dependent nucleosome-remodeling complex in the repair of a defined DNA DSB. SWI/SNF was previously shown to regulate presynaptic events in HR, but its function in these events is unknown. We find that in the absence of functional SWI/SNF, the initiation of DNA end resection is significantly delayed. The delay in resection initiation is accompanied by impaired recruitment of MRX to the DSB, and other functions of MRX in HR including the recruitment of long-range resection factors and activation of the DNA damage response are also diminished. These phenotypes are correlated with a delay in the eviction of nucleosomes surrounding the DSB. We propose that SWI/SNF orchestrates the recruitment of a pool of MRX that is specifically dedicated to HR.

| S-EPMC5449591 | biostudies-literature

The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor.

Project description:The mobilization of nucleosomes by the ATP-dependent remodeler INO80 is quite different from another remodeler (SWI/SNF) that is also involved in gene activation. Unlike that recently shown for SWI/SNF, INO80 is unable to disassemble nucleosomes when remodeling short nucleosomal arrays. Instead, INO80 more closely resembles, although with notable exceptions, the nucleosome spacing activity of ISW2 and ISW1a, which are generally involved in transcription repression. INO80 required a minimum of 33 to 43 bp of extranucleosomal DNA for mobilizing nucleosomes, with 70 bp being optimal. INO80 prefers to move mononucleosomes to the center of DNA, like ISW2 and ISW1a, but does so with higher precision. Unlike ISW2/1a, INO80 does not require the H4 tail for nucleosome mobilization; instead, the H2A histone tail negatively regulates nucleosome movement by INO80. INO80 moved arrays of two or three nucleosomes with 50 or 79 bp of linker DNA closer together, with a final length of ?30 bp of linker DNA or a repeat length of ?177 bp. A minimum length of >30 bp of linker DNA was required for nucleosome movement and spacing by INO80 in arrays.

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