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SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (RIP-seq)

ABSTRACT: SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (RIP-seq)

PROVIDER: PRJNA471291 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7161100.fastq.gz	Fastqsanger.gz
	SRR7161110.fastq.gz	Fastqsanger.gz
	SRR7161101.fastq.gz	Fastqsanger.gz
	SRR7161111.fastq.gz	Fastqsanger.gz
	SRR7161102.fastq.gz	Fastqsanger.gz

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SWI/SNF remains localized to chromatin in the presence of SCHLAP1

Project description:SWI/SNF remains localized to chromatin in the presence of SCHLAP1

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SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ChIP-seq)

Project description:SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ChIP-seq)

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SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ATAC-seq)

Project description:SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ATAC-seq)

| PRJNA471289 | ENA

SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (RIP-seq)

Project description:RNA immunoprecipitation of SWI/SNF in prostate cacner

2018-05-14 | GSE114393 | GEO

SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ChIP-seq)

Project description:ChIP-seq of SWI/SNF subunits and histone modifications in RWPE1 cells

2018-05-14 | GSE114392 | GEO

SWI/SNF remains localized to chromatin in the presence of SCHLAP1 (ATAC-seq)

Project description:Changes to chromatin openness were measured by ATAC seq in RWPE1 cells expression SCHLAP1 or a control cell line infected with a LACZ lentivirus.

2018-05-14 | GSE114391 | GEO

Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion

Project description:The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or SChLAP1:protein complexes. Herein, we report the first secondary structure model of SChLAP1 using SHAPE-MaP in vitro, in cellulo, and ex cellulo (protein-free). Comparison of the ex cellulo and in cellulo data via ΔSHAPE identified putative protein binding sites within SChLAP1. In addition, we identified primate conserved exons of SChLAP1 as well as regions that appear to have been incorporated through retroviral insertion. In particular, we characterized a complex structural landscape in a protein binding region at the 3′-end of SChLAP1 derived from a THE1B-type retroviral insertion, suggesting a role for an exapted RNA structure in SChLAP1:protein recognition and prostate cancer progression. This work lays the foundation for future efforts to selectively target and disrupt the SChLAP1:protein interface and to develop new therapeutic avenues in prostate cancer treatment.

2024-01-12 | GSE243328 | GEO

SWI/SNF remains localized to chromatin in the presence of SCHLAP1.

Project description:SCHLAP1 is a long noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays, we found that SWI/SNF is not depleted from the genome by SCHLAP1 and that SWI/SNF is associated with many coding and noncoding RNAs, suggesting that SCHLAP1 may function in a SWI/SNF-independent manner.

| S-EPMC6339527 | biostudies-literature

SWI/SNF remains localized to chromatin in the presence of SCHLAP1

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

2018-05-14 | GSE114394 | GEO

LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [RIP-seq]

Project description:The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. However, the precise mechanisms determining how SWI/SNF is targeted to specific genomic sites remain elusive. In this study we demonstrate that long non-coding RNAs (lncRNAs) are pivotal in the binding of the SWI/SNF complex to specific genomic targets. The interaction between SWI/SNF and lncRNAs is essential for the recruitment of the complex to gene regulatory elements, where it plays a critical role. We show that trans-acting lncRNAs direct the SWI/SNF complex to cell-specific enhancers, with lncRNA knockdowns leading to a genome-wide redistribution of SWI/SNF away from these enhancers. This redistribution impacts the expression of genes connected to these enhancers, underscoring the critical role of lncRNAs in the specific targeting of SWI/SNF to DNA. This insight into the targeting mechanisms of SWI/SNF by lncRNAs has broad implications, from understanding the processes of gene expression control to identifying therapeutic targets in diseases associated with SWI/SNF dysfunction, such as cancer.

2024-11-27 | GSE262063 | GEO

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