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Virus modified paraspeckles are essential hubs for gene expression and their formation drives genomic instability

ABSTRACT: Virus modified paraspeckles are essential hubs for gene expression and their formation drives genomic instability

PROVIDER: PRJNA1160834 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30658515_1.fastq.gz	Fastqsanger.gz
	SRR30658515_2.fastq.gz	Fastqsanger.gz
	SRR30658516_1.fastq.gz	Fastqsanger.gz
	SRR30658516_2.fastq.gz	Fastqsanger.gz
	SRR30658517_1.fastq.gz	Fastqsanger.gz

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Virus modified paraspeckles are essential hubs for gene expression and their formation drives genomic instability

Project description:The nucleus is a highly organised yet dynamic environment containing distinct membrane nuclear bodies. This spatial separation enables a subset of components to be concentrated within bimolecular condensates, allowing efficient and discrete processes to occur which regulate cellular function. One such nuclear body, paraspeckles, are comprised of multiple paraspeckle proteins (PSPs) built around the architectural RNA, NEAT1_2. Paraspeckle function is yet to be fully elucidated but has been implicated in a variety of developmental and disease scenarios.  We demonstrate that Kaposi’s sarcoma-associated herpesvirus (KSHV) drives formation of structurally distinct paraspeckles with a dramatically increased size and altered protein composition that are essential for productive lytic replication. We highlight these virus-modified paraspeckles form adjacent to virus replication centres, functioning as RNA processing hubs for both viral and cellular transcripts during infection. Notably, we reveal that PSP sequestration into virus-modified paraspeckles results in increased genome instability during both KSHV and Epstein Barr virus (EBV) infection, implicating their formation in virus-mediated tumorigenesis.

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Project description:The nucleus is a highly structured environment containing multiple membrane-less bodies formed through liquid-liquid phase separation. These provide spatial separation and concentration of specific biomolecules enabling efficient and discrete processes to occur which regulate gene expression. One such nuclear body, paraspeckles, are comprised of multiple paraspeckle proteins (PSPs) built around the architectural RNA, NEAT1_2. Paraspeckle function is yet to be fully elucidated but has been implicated in a variety of developmental and disease scenarios. We demonstrate that Kaposi’s sarcoma-associated herpesvirus (KSHV) drives formation of structurally distinct paraspeckles with a dramatically increased size and altered protein composition that are essential for productive lytic replication. We highlight these virus-induced paraspeckle-like structures form adjacent to virus replication centres, functioning as RNA processing hubs for both viral and cellular transcripts during infection. Notably, we reveal that PSP sequestration into virus-induced paraspeckle-like structures results in increased genome instability during both KSHV and Epstein Barr virus (EBV) infection, implicating their formation in virus-mediated tumorigenesis.

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AATF/Che-1 localizes to paraspeckles and suppresses R-loops accumulation and interferon activation in Multiple Myeloma

Project description:We investigated the interactions of AATF/Che1 with paraspeckles complex in Multiple Myeloma(MM) cells by looking at its relationship with lncRNA NEAT1_1(NEAT1) and the essential paraspeckles proteins. By analyzing ChIP- and ChIRP-sequencing of MM cells, we assessed that the interaction between AATF/Che1 and NEAT1 occurs also onto DNA and detected the sites where they co-localize. To better characterize the interaction, we studied the effects of interfering AATF/Che1 or NEAT1 on co-localizing sites through ChIP-seq with NEAT1 interfered (GapmerNEAT1) and ChIRP-seq with AATF/Che1 interfered (siChe). We found that NEAT1 is essential in maintaining the paraspeckles complex onto those sites. Moreover, by exploring DRIP-seq data with siChe, we also detected that AATF/Che1 and NEAT1 localize on R-loops, RNA:DNA hybrid structure involved in DNA transcription and repair. A depletion of AATF/Che1 causes a further increase of those hybrid structures and the activation of the immune response in MM, in particular the interferon (IFN) activation. To further explore these findings, we performed RNA-seq with siChe and GapmerNEAT1 which confirm that AATF/Che-1 down-regulation induces a strong up-regulation of genes involved in IFN response.

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