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LncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

ABSTRACT: lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

PROVIDER: PRJNA627192 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11581883_1.fastq.gz	Fastqsanger.gz
	SRR11581883_2.fastq.gz	Fastqsanger.gz
	SRR11581884_1.fastq.gz	Fastqsanger.gz
	SRR11581884_2.fastq.gz	Fastqsanger.gz
	SRR11581885_1.fastq.gz	Fastqsanger.gz

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lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

Project description:lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

2020-07-08 | GSE149032 | GEO

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Project description:Gene programs that control differentiation are regulated through the interplay between DNA, RNA, and protein. Cooperation among these fundamental cellular components can occur through highly structured interactions connecting domains formed by specific sequences of nucleotides, ribonucleotides, and/or amino acids and also through the assembly of biomolecular condensates. Here, we show that endoderm differentiation is regulated through the interaction of the long noncoding (lnc) RNA DIGITand the bromodomain and extra-terminal (BET) domain family protein BRD3. BRD3 forms phase-separated condensates that contain DIGIT, occupies enhancers of endoderm transcription factors, and is required for endoderm differentiation. Purified BRD3 binds to acetylated histone H3 lysine 18 (H3K18ac) in vitro and occupies regions of the genome enriched in H3K18ac during endoderm differentiation, including the key transcription factors that regulate endoderm differentiation. DIGIT is also enriched in regions of H3K18ac, and depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings support a model where cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest a broader role for protein-lncRNA phase-separated condensates as regulators of transcription in development.

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lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Project description:lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

| PRJNA522865 | ENA

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation.

Project description:Cooperation between DNA, RNA and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. Here, we report that endoderm differentiation is regulated by the interaction between the long non-coding RNA (lncRNA) DIGIT and the bromodomain and extraterminal domain protein BRD3. BRD3 forms phase-separated condensates of which the formation is promoted by DIGIT, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. BRD3 binds to histone H3 acetylated at lysine 18 (H3K18ac) in vitro and co-occupies the genome with H3K18ac. DIGIT is also enriched in regions of H3K18ac, and the depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings show that cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncRNA phase-separated condensates have a broader role as regulators of transcription.

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Project description:Endoderm differentiation is a critical step leading to development of the gastrointestinal system. We found that DIGIT is a lncRNA that is required for endoderm differentiation. We used directional RNA sequencing (RNA-seq) to globally evaluate the effects of loss of DIGIT expression during endoderm differentiation and chromatin immunoprecipitation and sequencing (ChIP-seq) to define the sites occupied by SMAD3 during endoderm diferentiation.

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Project description:Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin [TT-Seq]