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

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

PROVIDER: PRJNA471271 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7161070.fastq.gz	Fastqsanger.gz
	SRR7161070_1.fastq.gz	Fastqsanger.gz
	SRR7161070_2.fastq.gz	Fastqsanger.gz
	SRR7161080.fastq.gz	Fastqsanger.gz
	SRR7161090.fastq.gz	Fastqsanger.gz

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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)

| PRJNA471288 | ENA

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

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

| PRJNA471291 | ENA

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

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

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

siRNA Knockdown of SWI/SNF complex proteins in prostate cancer cell lines

Project description:Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus siRNAs targeting SWI/SNF complex proteins (SMARCA2, SMARCA4, and SMARCB1). Goal was to determine the effect of SWI/SNF knockdown on gene expression in prostate cancer. Two-condition experiment: non-targeting siRNA versus SWI/SNF-siRNA treated cells. Three SWI/SNF proteins were targeted: SMARCA2, SMARCA4, and SMARB1. Biological replicates: 1 control replicate, 2 treatment replicates per SWI/SNF protein. Technical replicates: 1 replicate per SWI/SNF protein. Cell lines: 22Rv1 and LNCaP.

2013-07-20 | E-GEOD-40384 | biostudies-arrayexpress

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