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Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

ABSTRACT: Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

PROVIDER: PRJNA736259 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14765800.fastq.gz	Fastqsanger.gz
	SRR14765801.fastq.gz	Fastqsanger.gz
	SRR14765802.fastq.gz	Fastqsanger.gz
	SRR14765803.fastq.gz	Fastqsanger.gz
	SRR14765804.fastq.gz	Fastqsanger.gz

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Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

Project description:The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains, yet the composition and function of many of these structures is not well understood. Using APEX2-mediated proximity labelling and RNA sequencing, we surveyed transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Our study thus provides a resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.

2022-02-18 | GSE176439 | GEO

Genome-wide analysis of PTBP1-regulated retained introns in mESCs

Project description:Intron retention (IR) is an alternative splicing event where mRNAs containing unspliced introns are exported to the cytoplasm and then either translated, giving rise to new protein isoforms, or degraded via the nonsense-mediated decay pathway. However, unspliced introns are also seen in nuclear RNA. Some of these are spliced at a low rate but do eventually become fully spliced and their respective mRNAs exported, while others stay retained and are recognized by nuclear decay machineries. IR has been shown to be regulated during granulocyte and neuronal differentiation and in some cancers, and a subset of the nuclear retained introns, called detained introns, have been implicated in growth control pathways. Despite many findings on IR and its biological significance, it is still not clear whether an incompletely spliced intron observed is a true retained intron that is exported as an mRNA or is a product of slow splicing that remains in the nucleus. A better understanding is needed of the molecular events that reduce intron excision rate and determine the release of an RNA for export. We have found that some genes in mouse embryonic stem cells (mESCs) produce RNAs that are highly associated with the high molecular-weight nuclear pellet (chromatin), rather than the soluble nucleoplasm or cytoplasm. This chromatin-associated RNA is polyadenylated, usually contains one or more incompletely spliced introns, and is often extensively bound by polypyrimidine tract-binding protein 1 (PTBP1). We hypothesize that PTBP1 inhibits splicing of these introns, and this causes sequestration of the transcript on chromatin. We are studying the role of PTBP1 in inhibiting intron excision and anchoring RNAs in the nuclear and chromatin compartments of mESCs.

2020-11-18 | GSE159993 | GEO

Genome-wide analysis of PTBP1-regulated retained introns in mESCs

Project description:Genome-wide analysis of PTBP1-regulated retained introns in mESCs

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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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Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

Project description:Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

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Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

Project description:Coordinated intron retention and poison exon inclusion define a subset of kidney tumors by introducing premature stop codons that typically trigger nonsense-mediated decay (NMD). In this study we investigate how mTOR activity modulates these NMD targets, revealing that mTOR inhibition increases the expression of transcripts bearing retained introns and poison exons in certain patient-derived tumors. Our findings show that tumors with low NMD and mTOR activities are more aggressive and have worse outcomes yet display pronounced immune infiltration, highlighting a potential role for these RNA isoforms in shaping tumor progression and immune responses.

2025-05-08 | GSE289050 | GEO

Widespread transcriptional readthrough caused by Nab2 depletion leads to chimeric transcripts with retained introns

Project description:Widespread transcriptional readthrough caused by Nab2 depletion leads to chimeric transcripts with retained introns

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RasimBarutcu_MingkunWu_et_al_APEX_2021

Project description:This dataset consists of 26 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Rasim Barutcu and Mingkun Wu (some clones also generated by Boris Dyakov). Streptavidin affinity purification and mass spectrometric acquisition was performed by Zhen-Yuan Lin. Mass Spectrometry data analysis was performed by Boris Dyakov. The files are associated with a manuscript submitted for publication by Barutcu et al. that identifies functionally distinct proteins and retained intron RNAs associated with nuclear domains (speckles and lamina) using APEX2-mediated proximity labeling. ("Systematic mapping of nuclear domain associated transcripts reveals speckles and lamina as hubs of functionally distinct populations of retained introns") Benjamin Blencowe is the corresponding author of the manuscript (b.blencowe@utoronto.ca). Anne-Claude Gingras should be contacted for questions about this dataset (gingras@lunenfeld.ca).

2021-06-17 | MSV000087649 | MassIVE

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

Project description:Control of metazoan embryogenesis shifts from maternal to zygotic gene products as the zygotic genome becomes transcriptionally activated. In Drosophila, zygotic genome activation (ZGA) begins with a minor wave, but technical challenges have hampered the identification of early transcripts or obscured the onset of their transcription. Here, we develop an approach to isolate transcribed mRNAs and apply it over the course of the minor wave and the start of the major wave of Drosophila ZGA. Our results increase known genes of the minor wave by 10 fold and show that this wave is continuous and gradual. Transposable-element mRNAs are also produced, but discontinuously. Genes in the early and middle part of the minor wave are short with few if any introns, and their transcripts are frequently aborted and tend to have retained introns, suggesting that inefficient splicing as well as rapid cell divisions constrain the lengths of early transcripts.

2019-05-06 | GSE125575 | GEO

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