Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Splicing transcriptome analysis reveals retained introns in retinal genes of the 5xFAD mouse, suggesting early diagnosis of Alzheimer’s disease through vision impairment

ABSTRACT: Splicing transcriptome analysis reveals retained introns in retinal genes of the 5xFAD mouse, suggesting early diagnosis of Alzheimer’s disease through vision impairment

PROVIDER: PRJNA1145411 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Splicing transcriptome analysis reveals retained introns in retinal genes of the 5xFAD mouse, suggesting early diagnosis of Alzheimer’s disease through vision impairment

Project description:Alzheimer’s disease (AD) is an age-related neurodegenerative disorder in which neuronal and synaptic loss of the brain leads to cognitive impairment and dementia. Therefore, the early diagnosis of AD with various biomarkers is important for the prevention and treatment. Although retina pathology is emerging biomarker that associated with AD, detailed molecular mechanisms of retinal impairments remain unclear. Here, we identify the genome-wide dysfunction of alternative splicing in the early stage of 5xFAD transgenic mouse retina by the RNA-seq analysis. Especially, retained intron (RI) highly enriched in phototransduction and retinal genes of 1.5-month-old 5xFAD mouse retina that significantly associated with retinal physiological impairment of rod photoreceptors by electroretinogram (ERG) analysis. These results indicate that the abnormal scotopic ERG associated with global splicing impairment may be useful early detection biomarker for AD.

2025-07-06 | GSE274214 | 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

| PRJNA671499 | ENA

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

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

| PRJNA1220709 | ENA

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

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

| PRJNA656824 | ENA

Transcriptome wide identification of retained introns upon depletion of the splicing factors WBP11 or SNW1

Project description:Transcriptome wide identification of retained introns upon depletion of the splicing factors WBP11 or SNW1

| PRJNA530564 | ENA

Limited effects of an eIF2αS51A allele on neurological impairments in the 5xFAD mouse model of Alzheimer’s disease

Project description:Transcriptome analysis of hippocampal RNA samples from wild-type, 5xFAD, 5xFAD;eIF2α+/S51A and eIF2α+/S51A mice Our transcriptome analyses showed clear transcriptional alterations in hippocampi of 5xFAD compared to wild type mice that were not corrected by the eIF2αS51A allele. Hemizygous 5xFAD mice, which were on a genetic background of B6/SJL, were crossed with eIF2α+/S51A mice (C57BL/6J background), to generate the offspring that was analyzed in the microarray. Hippocampal samples of 12 mice (4 groups: wild-type, 5xFAD, 5xFAD;eIF2α+/S51A and eIF2α+/S51A) were processed using Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No technical replicates were performed.

2013-09-10 | E-GEOD-50521 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data