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Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [ARTR-seq]

ABSTRACT: Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [ARTR-seq]

PROVIDER: PRJNA1073947 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27892600.fastq.gz	Fastqsanger.gz
	SRR27892601.fastq.gz	Fastqsanger.gz
	SRR27892602.fastq.gz	Fastqsanger.gz
	SRR27892603.fastq.gz	Fastqsanger.gz
	SRR27892604.fastq.gz	Fastqsanger.gz

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Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency

Project description:Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency

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Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [RNA-Seq]

Project description:Nuclear speckles, a type of membraneless nuclear organelle in higher eukaryotic cells, play a vital role in gene expression regulation. Using the reverse transcription-based RBP binding sites sequencing (ARTR-seq) method, we study human transcripts associated with nuclear speckles. We identify three gene groups whose transcripts demonstrate different speckle localization properties and dynamics – stably enriched in nuclear speckle post-transcriptionally, transiently enriched in speckles at the pre-mRNA stage co-transcriptionally, and not enriched in speckles. We show that nuclear speckles specifically facilitate splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, underscoring a tight interplay between genome organization, RNA cis-elements, and transcript speckle enrichment, and connecting transcript speckle localization with splicing logic. Finally, we show that speckles can act as hubs for the regulated retention of introns during cellular stress. Collectively, our data highlight a role of nuclear speckles in both co- and post-transcriptional splicing regulation.

2024-09-05 | GSE255207 | GEO

Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [ARTR-seq]

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Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [RNA-Seq]

Project description:Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency [RNA-Seq]

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Genome organization around nuclear speckles drives mRNA splicing efficiency

Project description:The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One example is the nuclear speckle, which is defined by high concentrations of protein and non-coding RNA regulators of pre-mRNA splicing. What functional role, if any, speckles might play in the process of mRNA splicing remains unknown. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs, and higher co-transcriptional splicing levels relative to genes that are located farther from nuclear speckles. We show that directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Finally, we show that gene organization around nuclear speckles is highly dynamic with differential localization between cell types corresponding to differences in splicing efficiency. Together, our results integrate the longstanding observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a critical role for dynamic 3D spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.

2024-03-22 | GSE247833 | GEO

Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-09-05 | GSE255208 | GEO

Genome organization around nuclear speckles drives mRNA splicing efficiency

Project description:Genome organization around nuclear speckles drives mRNA splicing efficiency

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Identification of cis- and trans-acting factors involved in the localization of MALAT-1 to nuclear speckles

Project description:MALAT-1 is a long mammalian non-coding transcript of approximately 8500 nucleotides. It is localized to nuclear speckles despite its mRNA-like characteristics, which usually result in the export of transcripts to the cytoplasm. In the present study, we report the identification of several factors that influence the nuclear speckle localization of MALAT-1, and we provide evidence that MALAT-1 is involved in the regulation of gene expression. Heterokaryon assays revealed that MALAT-1 does not shuttle between the nucleus and cytoplasm, but is stably retained within the nucleus. Analysis of MALAT-1 fragments showed that MALAT-1 contains two distinct nuclear speckle-directing elements (between nucleotides 1961 to 3040 and 6008 to 7011 of the MALAT-1 sequence). The knockdown of the nuclear speckle proteins, RNPS1, SRm160 or IBP160, resulted in the diffusion of MALAT-1 to the nucleoplasm. In addition, we have demonstrated that depletion of MALAT-1 represses the expression of several genes. This repression of gene expression also occurs in response to the delocalization of MALAT-1 from the nuclear speckles. These results suggest that RNPS1, SRm160 and IBP160 contribute to the localization of MALAT-1 to nuclear speckles where it is involved in regulating gene expression

2010-06-02 | GSE20506 | GEO

Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program [Chipmentation]

Project description:Senescence —the end-point of the replicative life span of normal cells— is characterized by a complex sequence of molecular and biochemical events. One of these is the dramatic reorganization of CTCF into large senescence-induced CTCF clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine super-resolution imaging, 3D genomics, and functional assays with computational modelling to address all aspects of SICC emergence. First, we used modelling and data from the overexpression of nuclear factors lost upon senescence entry to explain how changes in the nuclear environment allow for CTCF clustering. Second, we discovered that cells entering senescence repurpose SRRM2 —a key component of nuclear speckles— and BANF1 —a protein known to act as ‘molecular glue’ for chromosomes during mitosis— to cluster CTCF on the surface of speckles, while rewiring higher-order genome architecture. Last, we could show that SICCs are required for the faithful execution of the senescence splicing program as their disruption by SRRM2 or BANF1 depletion reverts splicing choices. Together, the senescence-specific clustering of CTCF on nuclear speckles is a new paradigm of a change in the biochemical environment of the nucleus being translated into its architectural reorganization to allow for the deployment of a splicing program driving homeostatic deregulation.

2024-06-17 | GSE269858 | GEO

RIP-seq analysis for RNAs associated with hTERT in nuclear speckles.

Project description:To investigate the function of p-hTERT in nuclear speckles, we isolated hTERT complex by immunoprecipitation with an anti-hTERT mAb from nuclear speckles purified biochemically and conducted RIP-seq analysis for RNAs associated with hTERT in nuclear speckles.

2024-04-08 | GSE226964 | GEO

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