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SWI/SNF-dependent genes are defined by their chromatin landscape [MNase-seq]

ABSTRACT: SWI/SNF-dependent genes are defined by their chromatin landscape [MNase-seq]

PROVIDER: PRJNA942307 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23750138_1.fastq.gz	Fastqsanger.gz
	SRR23750138_2.fastq.gz	Fastqsanger.gz
	SRR23750139_1.fastq.gz	Fastqsanger.gz
	SRR23750139_2.fastq.gz	Fastqsanger.gz
	SRR23750140_1.fastq.gz	Fastqsanger.gz

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SWI/SNF-dependent genes are defined by their chromatin landscape

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape

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SWI/SNF-dependent genes are defined by their chromatin landscape [MNase-seq]

Project description:The SWI/SNF complex was the first chromatin remodeling machinery discovered. Although it has been extensively investigated, numerous aspects of its regulation and activity are still poorly understood, especially in higher eukaryotes. In mammals, there is not a single SWI/SNF complex (also called BRM or BRG1 associated factors, BAF, complex) but rather a polymorphic family of complexes, with three main subtypes called canonical BAF (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF), with relatively different specificities. The enzymatic motors of the complexes are two mutually exclusive ATPases of the SNF2 family called BRAHMA (BRM, also called SMARCA2) and BRAHMA RELATED GENE 1 (BRG1, also called SMARCA4). Recently, an specific inhibitor of BRM and BRG1 ATPase activity, called BRM014, has been developed. We have extensively investigated the effect of BRM014 on the transcriptome and the chromatin landscape of non-tumoral normal murine mammary (NMuMG) epithelial cells.

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SWI/SNF-dependent genes are defined by their chromatin landscape [ATAC-seq]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [ATAC-seq]

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SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2]

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SWI/SNF-dependent genes are defined by their chromatin landscape [ChRNA-seq]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [ChRNA-seq]

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SWI/SNF-dependent genes are defined by their chromatin landscape [Cut&Tag]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [Cut&Tag]

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SWI/SNF-dependent genes are defined by their chromatin landscape [RNA-seq]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [RNA-seq]

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SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq]

Project description:SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq]

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Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing (MNase-Seq)

Project description:RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long non-coding RNAs (lncRNAs)1, which in Arabidopsis thaliana are produced by a specialized RNA Polymerase V (Pol V)2. lncRNAs guide Argonaute-siRNA complexes to specific genomic loci and mediate the establishment of DNA methylation3,4. The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF nucleosome remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding IDN2 protein5,6. RNA-mediated DNA methylation and transcriptional silencing was compromised in the swi3 mutant. Moreover, targets of SWI/SNF significantly overlapped with genes controlled by Pol V, which shows that the physical interaction reflects a functional relationship. We further found that non-coding transcription by Pol V affects nucleosome positioning on silenced regions. We propose that lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin remodeling complexes may be a more general function of lncRNAs. Mnase-seq of 2 samples (Col-0 and nrpe1).

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SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2]

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