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Effect of DNA bindng small molecules on SSRP1 genomic distribution

ABSTRACT: Effect of DNA bindng small molecules on SSRP1 genomic distribution

PROVIDER: PRJNA420688 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6337550_1.fastq.gz	Fastqsanger.gz
	SRR6337550_2.fastq.gz	Fastqsanger.gz
	SRR6337551_1.fastq.gz	Fastqsanger.gz
	SRR6337551_2.fastq.gz	Fastqsanger.gz
	SRR6337545_1.fastq.gz	Fastqsanger.gz

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Effect of DNA bindng small molecules on SSRP1 genomic distribution

Project description:Small molecules directly binding DNA in cells destabilized chromatin what is "sensed" by histone chaperone FACT. FACT binds regions with destabilized chromatin via "c-trapping". DNA-targeting small molecules are widely used for anticancer therapy based on their ability to induce cell death, presumably via DNA damage. DNA in the eukaryotic cell is packed into chromatin, a highly-ordered complex of DNA, histones, and non-histone proteins. These agents perturb chromatin organization. However, the mechanisms, consequences, and impact of the alterations of chromatin structure in relation to their anti-cancer activity is unclear because it is difficult to separate DNA damage and chromatin damage in cells. We recently demonstrated that curaxins, small molecules with broad anticancer activity, bind DNA without causing detectable DNA damage by interfering with histone/DNA interactions and destabilizing the nucleosome. Chromatin unfolding caused by curaxins is sensed by histone chaperone FACT. FACT binds unfolded nucleosomes, which leads to chromatin trapping or c-trapping. In this study, we investigated whether other DNA-targeting small molecules disturb chromatin and cause c-trapping. We found that only compounds directly binding DNA induce chromatin damage and c-trapping. Chromatin damage may occur in the absence of DNA damage and is dependent on the mechanism of compound binding to DNA and its ability to bind chromatinized DNA in cells. We show that FACT is sensitive to a plethora of nucleosomes perturbations induced by DNA-binding small molecules, including displacement of the linker histone, eviction of core histones, and accumulation of negative supercoiling. Most importantly, the cytotoxicity of DNA-binding small molecules correlates with their ability to cause chromatin damage, but not DNA damage.

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Effect of DNA binding small molecules on the genomic distribution of nucleosomes with H3K27Ac

Project description:Effect of DNA binding small molecules on the genomic distribution of nucleosomes with H3K27Ac

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Effect of DNA binding small molecules on the genomic distribution of nucleosomes with H3K27Ac

Project description:Small molecule CBL0137 destabilizes nucleosome directly via binding to DNA. Effect of CBL0137 on nucleosomes with mark specific for more open chromatin characteristic for promoters and enhancers versus all nucleosomes H3 was measured.

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Ssrp1 co-immunoprecipitation and mass spectrometry

Project description:Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.

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ChIP-seq for SSRP1

Project description:SSRP1 ChIP-seq was performed in E14 cells

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Gene Specific Activation Driven by Small Molecules

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