Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [RNA-Seq]

ABSTRACT: CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [RNA-Seq]

PROVIDER: PRJNA1217922 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [RNA-Seq]

Project description:Transcription and co-transcriptional pre-mRNA splicing are kinetically coupled as shown by the widespread effects of transcription speed on alternative splicing. The molecular basis for kinetic coupling is incompletely understood, but one potential mechanism is through elongation rate dependent alternative folding pathways of the nascent pre-mRNA. To search for RNA structures in nascent pre-mRNA, we modified SPLASH (1) (Sequencing of Psoralen Crosslinked, Ligated And Selected Hybrids) for use with Chromatin Associated RNA. We applied this new method called CAR-SPLASH to cells expressing WT and slow mutant pol II and identified >3000 intragenic RNA structures of which >400 are proximal to splice sites. ASO disruption of several structures identified by CAR-SPLASH that sequester splice sites changed alternative splicing outcomes in vivo. We identified three examples of novel regulatory elements we designate “RNA kinetic switches”. ASO disruption of these structures modified alternative splicing of NISCH Exon 18 GAK Exon 7 and MEGF8 Exon 24 in a way that depended on the rate of transcription elongation. These results demonstrate that individual RNA structures can mediate kinetic coupling between transcription and pre-mRNA splicing and that nascent RNA structures can serve as targets for splice modifying ASO’s.

2025-09-14 | GSE288524 | GEO

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [smallRNA-Seq]

2025-09-14 | GSE288523 | GEO

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [smallRNA-Seq]

Project description:CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing [smallRNA-Seq]

| PRJNA1217919 | ENA

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes

Project description:Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes

| PRJNA525152 | ENA

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [4sURDB-Seq]

Project description:The rate of RNA Polymerase II (RNAPII) elongation has an important role in the control of Alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked-in for a slow elongating form of RNAPII. We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice and impairs the differentiation of ESCs into the neural lineage. This is accompanied by changes in splicing and in gene expression in ESCs and along the pathway of neuronal differentiation. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is more predominant in ESC-differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.

2019-04-15 | GSE127740 | GEO

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [RNA-seq]

2019-04-15 | GSE125413 | GEO

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [RNA-seq]

Project description:Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [RNA-seq]

| PRJNA516337 | ENA

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [4sURDB-Seq]

Project description:Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes [4sURDB-Seq]

| PRJNA525151 | ENA

Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events

Project description:Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events

| PRJNA413480 | ENA

KINETIC AND COMPOSITIONAL ANALYSIS OF RNA POLYMERASE II IN TRYPANOSOMA BRUCEI

Project description:Genome-wide analysis of nascent RNA synthesis gives kinetic information on the transcriptional status of RNA polymerase II (Pol II). In parallel, immunoprecipitation of the largest subunit of Pol II (RPB1) provides the protein composition of the enzyme complex in the presence or absence of the transcriptional inhibitor Actinomycin D.

2023-05-23 | PXD039878 | Pride

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