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MRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription [SLAM-seq]

ABSTRACT: mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription [SLAM-seq]

PROVIDER: PRJNA1197500 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31699600_1.fastq.gz	Fastqsanger.gz
	SRR31699600_2.fastq.gz	Fastqsanger.gz
	SRR31699601_1.fastq.gz	Fastqsanger.gz
	SRR31699601_2.fastq.gz	Fastqsanger.gz
	SRR31699602_1.fastq.gz	Fastqsanger.gz

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mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription [SLAM-seq]

Project description:Several transcription inhibitors have been developed as cancer therapies. However, they show modest clinical activity highlighting that our understanding of the cellular response to transcriptional inhibition remains incomplete. Here we report that potent inhibitors of transcription not only impact mRNA output, but also markedly impair mRNA transcript localisation and nuclear export. We demonstrate that retention of newly transcribed mRNA in nuclear speckles is an adaptive response to chemically distinct transcriptional inhibitors. Retained transcripts are fully processed and accumulate in proportion to the expression level of the genes from which they emanate. The TREX mRNA export complex plays an integral role in directing nascent transcripts to nuclear speckles where they are bound to NXF1, protected from degradation, and poised for rapid export following re-initiation of transcription. Our findings provide new insights into the crosstalk between transcription and mRNA export, with important implications for drugs aiming to inhibit transcription for therapeutic gain.

2025-02-13 | GSE284174 | GEO

mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

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mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

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mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

Project description:mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

| PRJNA761338 | ENA

mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

Project description:mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

| PRJNA761339 | ENA

mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

Project description:mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

| PRJNA761329 | ENA

mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

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

2025-02-12 | GSE183571 | GEO

Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag

Project description:Nuclear compartments are membrane-less nuclear regions that are enriched in functionally related molecules. RNA is a major component of many nuclear compartments, but the identity and dynamics of transcripts within nuclear compartments are poorly understood. Here, we applied Reverse Transcribe & Tagment (RT&Tag) to identify the transcript populations of Polycomb domains and of nuclear speckles within the nucleus. We also developed SLAM-RT&Tag, which combines RNA metabolic labeling with RT&Tag, to quantify transcript dynamics within nuclear compartments. Intriguingly, exceptionally long genes are transcribed adjacent to Polycomb domains, and are transiently associated with chromatin. In contrast, diverse incompletely spliced mature transcripts migrate to nuclear speckles, and are generally transient within speckles. Speckle transcripts are retained longer when splicing is inhibited, suggesting post-transcriptional processing is coupled to speckle dynamics. Our findings argue that nuclear speckles act as quality control checkpoints that transiently confine incompletely spliced transcripts and facilitate their post-transcriptional splicing.

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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [SLAM-seq]

Project description:Using SLAM-seq to capture de novo synthesized polyadenylated RNAs, we quantitated changes in nascent RNA expression, as well as in total RNA expression.

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