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The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

ABSTRACT: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

PROVIDER: PRJNA633796 | ENA |

REPOSITORIES: ENA

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The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [RNA-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 | GSE150828 | GEO

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

2020-07-31 | GSE150827 | GEO

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

2020-07-31 | GSE150826 | GEO

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

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

| PRJNA633798 | ENA

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

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

| PRJNA633799 | ENA

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

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

| PRJNA633800 | ENA

The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-07-31 | GSE150829 | GEO

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

| PRJNA657070 | ENA

The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells

Project description:Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.

2023-03-14 | GSE216057 | GEO

Genetic regulation of the ATP synthase in neurons modulates cognition

Project description:The goal of this analysis was to profile the gene expression signatures associated to different neuronal doses of IF1. The mitochondrial ATP synthase produces ATP by oxidative phosphorylation and integrates different signals to regulate cellular functions and fate. The ATPase inhibitory factor 1 (IF1) is a structurally-disordered protein that inhibits the ATP synthase, contributing to metabolic reprogramming and signalling through mitochondrial reactive oxygen species (mtROS). mtROS regulate kinases and transcription factors in mitohormetic responses that favour adaptation to toxic insults. IF1 is tissue-specifically expressed and in human and mouse brain is in molar excess over the ATP synthase. Herein, we have used genetic approaches to ablate or overexpress IF1 in neurons to investigate its role in brain functions. IF1 inhibits a fraction of the ATP synthase under physiological conditions and regulates respiration, mtROS production and mitochondrial structure. Transcriptomic, proteomic and metabolomic analyses indicate that IF1 regulates synaptic transmission and cognition. Ablation of IF1 impairs short-term memory whereas IF1 overexpression increases basal synaptic transmission and learning by mtROS-dependent activation of the extracellular signal-regulated kinases 1/2 (ERK 1/2). Overall, we show that IF1 dose plays a fundamental role in the regulation of neuronal function by controlling the fraction of inhibited ATP synthase that acts as source of mitohormetic mtROS, further emphasizing the ATP synthase/IF1 as promising targets to treat cognitive disorders.

2021-05-24 | GSE154064 | GEO

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