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Integrated HPV18 acts as enhancer-like RNA and form phase-separated condensates to promote oncogenic genes expression.

ABSTRACT: Integrated HPV18 acts as enhancer-like RNA and form phase-separated condensates to promote oncogenic genes expression.

PROVIDER: PRJNA1051147 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27180601_1.fastq.gz	Fastqsanger.gz
	SRR27180601_2.fastq.gz	Fastqsanger.gz
	SRR27180602_1.fastq.gz	Fastqsanger.gz
	SRR27180602_2.fastq.gz	Fastqsanger.gz
	SRR27180603_1.fastq.gz	Fastqsanger.gz

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Integrated HPV18 acts as enhancer-like RNA and form phase-separated condensates to promote oncogenic genes expression.

Project description:Most of the cervical cancers are caused by human papillomavirus (HPV) infection. It has been known that, in HeLa cells, HPV18 viral genome is integrated at chromosome 8q24.21 and activates transcription of proto-oncogene c-Myc. However, the mechanism of how the integrated HPV fragment exhibits transcription activation function has not been fully elucidated. In this study, we found that HPV18 transcripts themselves have an enhancer RNA-like function to activate their proximal genes including CCAT1-5L and c-Myc. We showed that the human genome-integrated HPV18 genes are activated by transcription coregulators BRD4, Mediator. The transcribed HPV18 RNAs form a liquid-like condensate at chromosome 8q24.21 locus, which in turn accumulates RNA polymerase II. Moreover, we identified uncharacterized transcript from Upstream Region of CCAT1-5L, named URC. The URC RNA is transcribed as a chimera RNA with HPV18 and is composed of 3'-untranslated region of HPV18 transcript. We found that the URC contributes to stabilization of HPV18 RNAs by supplying a poly-adenylation site for HPV18 transcript. Our findings suggest that HPV18 integration at 8q24.21 locus causes HPV18-URC chimera RNA and promotes tumorigenesis through RNA-based liquid droplet formation.

2024-12-31 | GSE249929 | GEO

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

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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 [RIP-seq]

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

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The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators

Project description:Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remainspoorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the FG-repeat region of NUP98 and the H3K4me3-binding PHD finger of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD finger targets condensates to H3K4me3-demarcated developmental genes and the FG repeats determine condensate composition and gene activation. The FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the MLL family of H3K4 methylation-writing enzymes and BRD4. The FG repeats are sufficient, when tethered to the genome, to partition these transcriptional regulators and activate genes. NUP98-PHF23 assembles chromatin-bound condensates that partition multiple positive regulators, initiating a feed-forward loop of reading-and-writing active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.

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Treacle’s ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair

Project description:We investigated the role of the nucleolar protein Treacle in organizing and regulating the nucleolus in human cells. Our results support Treacle’s ability to form liquid-like phase condensates through electrostatic interactions among molecules. The formation of these biomolecular condensates is crucial for segregating nucleolar fibrillar centers from the dense fibrillar component and ensuring high levels of rRNA gene transcription and accurate rRNA processing. Both the central and C-terminal domains of Treacle are required to form liquid-like condensates. The initiation of phase separation is attributed to the C-terminal domain. The central domain is characterized by repeated stretches of alternatively charged amino-acid residues and is vital for condensate stability. Overexpression of mutant forms of Treacle that cannot form liquid-like phase condensates compromises the assembly of fibrillar centers, suppressing rRNA gene transcription and disrupting rRNA processing. These mutant forms also fail to recruit DNA topoisomerase II binding protein 1 (TOPBP1), suppressing the DNA damage response in the nucleolus.

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Biomolecular condensates create phospholipid-enriched microenvironments (Part 1)

Project description:Proteins and RNA are able to phase separate from the aqueous cellular environment to form sub-cellular compartments called condensates. This process results in a protein-RNA mixture that is chemically distinct from the surrounding aqueous phase. Here we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and cellular metabolites and identified metabolites enriched in the condensate phase. These proteins included SARS-CoV-2 nucleocapsid, as well as low complexity domains of MED1 and HNRNPA1.

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Biomolecular condensates create phospholipid-enriched microenvironments (Part 3)

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