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Investigation into SATB2 DNA-binding sites and the effect of SATB2 removal on the transcriptome of skeletal muscle satellite cells

ABSTRACT: Investigation into SATB2 DNA-binding sites and the effect of SATB2 removal on the transcriptome of skeletal muscle satellite cells

PROVIDER: PRJNA623414 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11492161_1.fastq.gz	Fastqsanger.gz
	SRR11492161_2.fastq.gz	Fastqsanger.gz
	SRR11492162_1.fastq.gz	Fastqsanger.gz
	SRR11492162_2.fastq.gz	Fastqsanger.gz
	SRR11492163_1.fastq.gz	Fastqsanger.gz

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Investigation into SATB2 DNA-binding sites and the effect of SATB2 removal on the transcriptome of skeletal muscle satellite cells

Project description:Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. In our associated paper, we found that the removal of special AT-rich binding protein 2 (SATB2), a nuclear protein that binds matrix attachment regions, is a key event in initiating myogenic differentiation. This study included ChIP-seq analyses to assess the genetic binding sites of SATB2 prior to differentiation and categorize their respective roles within the cell. Furthermore, transcriptome analyses using RNA-seq was conducted on C2C12 cells treated with control siRNA and siRNA against SATB2 prior to differentiation. This was done to assess the changes in transcript expression following the loss of SATB2.

2023-04-06 | GSE148193 | GEO

Mass Spectra of a caspase 7 cleavage fragment of SATB2

Project description:This data identifies the cleavage fragment of an in vitro reaction between recombinant, active caspase 7 and recombinant SATB2. The data confirms that this fragment is indeed a part of SATB2 and this information was used to further our investigation into the role SATB2 in mammalian skeletal muscle satellite cells.

2020-04-08 | MSV000085254 | MassIVE

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [RNA-seq]

Project description:Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that removal of special AT-rich binding protein 2 (SATB2), a nuclear protein known to bind matrix attachment regions, is a key event in initiating myogenic differentiation. Deletion of myoblast SATB2 in vitro initiates chromatin remodeling and accelerates differentiation, while in vivo ablation depletes the muscle progenitor pool. Genome wide analysis indicates that SATB2 binding influences both chromatin loop and sub-TAD domain formation. These chromatin changes are both repressive and inductive, as loss of SATB2 leads to expression of differentiation regulatory factors and inhibition of genes that impair this process. Finally, we noted that the differentiation-specific decline in SATB2 protein is dependent on a caspase 7-mediated cleavage event. Taken together, this study demonstrates that temporal control of SATB2 protein is critical for shaping the chromatin environment and coordinating the myogenic differentiation program

2022-03-31 | GSE185436 | GEO

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

Project description:Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that removal of special AT-rich binding protein 2 (SATB2), a nuclear protein known to bind matrix attachment regions, is a key event in initiating myogenic differentiation. Deletion of myoblast SATB2 in vitro initiates chromatin remodeling and accelerates differentiation, while in vivo ablation depletes the muscle progenitor pool. Genome wide analysis indicates that SATB2 binding influences both chromatin loop and sub-TAD domain formation. These chromatin changes are both repressive and inductive, as loss of SATB2 leads to expression of differentiation regulatory factors and inhibition of genes that impair this process. Finally, we noted that the differentiation-specific decline in SATB2 protein is dependent on a caspase 7-mediated cleavage event. Taken together, this study demonstrates that temporal control of SATB2 protein is critical for shaping the chromatin environment and coordinating the myogenic differentiation program

2022-03-31 | GSE185435 | GEO

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [Hi-C]

Project description:Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that removal of special AT-rich binding protein 2 (SATB2), a nuclear protein known to bind matrix attachment regions, is a key event in initiating myogenic differentiation. Deletion of myoblast SATB2 in vitro initiates chromatin remodeling and accelerates differentiation, while in vivo ablation depletes the muscle progenitor pool. Genome wide analysis indicates that SATB2 binding influences both chromatin loop and sub-TAD domain formation. These chromatin changes are both repressive and inductive, as loss of SATB2 leads to expression of differentiation regulatory factors and inhibition of genes that impair this process. Finally, we noted that the differentiation-specific decline in SATB2 protein is dependent on a caspase 7-mediated cleavage event. Taken together, this study demonstrates that temporal control of SATB2 protein is critical for shaping the chromatin environment and coordinating the myogenic differentiation program

2022-03-31 | GSE185434 | GEO

ChIP-seq for Satb2 in E15 cortex

Project description:The goal of the study was to identify the binding site of SATB2 in wild-ype cortex by performing ChIP-seq using SATB2 antibody. E15 cortical tissues were dissected, lysed and fixed. Chromatin was prepared by sonication. Sequences bound by SATB2 protein was precipitated using a SATB2 antibody. Sequencing was performed on Illumina Genome Analyzer II. SATB2 binding peaks were called using MACS. ChIP for Satb2, followed by sequencing on Illumina Genome Analyzer II platform

2015-09-08 | E-GEOD-68910 | biostudies-arrayexpress

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2

| PRJNA769098 | ENA

Transcription profiling of mouse satellite cells isolated from skeletal muscle

Project description:(Abstract of publication submitted currently) To clarify molecular regulation of satellite cells, we performed genome-wide gene expression analysis of quiescent satellite cells isolated from mouse skeletal muscle by flow cytometry. We identified 53 novel quiescent satellite cell-specific genes whose expressions are sharply down-regulated upon activation. The gene list contains a number of cell surface molecules, transcriptional factors, and cytokines and other signal transduction molecules. We further confirmed that Odz4 and calcitonin receptor proteins were expressed by quiescent but not by activated satellite cells in vivo. Importantly, we found that Pax7+/calcitonin receptor+ satellite cells reappear in close association with regenerating myofibers 7 days after muscle damage, often outside the basal lamina. Moreover, an agonist of calcitonin receptor suppressed the activation of quiescent satellite cells on myofibers in in vitro culture, suggesting that calcitonin receptor signaling plays an important role in renewal and maintenance of satellite cells. Our results show the gene expression profile of quiescent satellite cells for the first time and reveal the temporal and spatial reappearance of a satellite cell pool. Experiment Overall Design: Satellite cells and non-satellite cells were examined. Totally three types of cells (groups), the satellite cells in quiescent and activated states and the non-satellite cells, were compared. Each has 4 replicates.

2008-06-12 | E-GEOD-3483 | biostudies-arrayexpress

Role of Satb1 and Satb2 in embryonic stem cells

Project description:Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells. This SuperSeries is composed of the following subset Series: GSE17487: Expression data in WT and Satb1-/- ES cells GSE17488: Expression data in WT and ES cells overexpressing Satb1 GSE17489: Expression data in WT and ES cells overexpressing Satb2 Refer to individual Series

2009-09-01 | E-GEOD-17490 | biostudies-arrayexpress

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

| PRJNA769207 | ENA