Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset1]

ABSTRACT: Here, we set out to understand if and how splicing kinetics are coordinated beyond individual intron removal and if this potential coordination could regulate alternative splicing outcomes. By measuring rates of transcription and splicing genome-wide, we found that the rate of splicing is coordinated across introns within individual genes. Furthermore, we found that elongation rates and splicing rates are coordinated within TADs, as are alternative splicing changes that result from cell type differences, differentiation programs, and alterations in splicing factor levels. Overall, our work establishes that the kinetics of transcription and splicing are coordinated within the spatial organization of the genome, which could be a control point for alternative splicing regulation that can modulate the function of a cell.

ORGANISM(S): Homo sapiens Drosophila melanogaster

PROVIDER: GSE146161 | GEO | 2021/05/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset1]

Project description:Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset1]

| PRJNA609632 | ENA

Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains

Project description:Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains

| PRJNA609986 | ENA

Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset2]

Project description:Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset2]

| PRJNA609643 | ENA

Transcription and splicing kinetics are coordinated within both genes and higher-order chromatin domains [dataset2]

Project description:In this study, we performed mRNA sequencing on IMR90 and A549 cells in order to understand the differences in gene expression patterns and alternative splicing patterns between the two cell lines.

2021-05-23 | GSE146164 | GEO

Human co-transcriptional splicing kinetics and coordination revealed by direct nascent RNA sequencing

Project description:Human genes have numerous exons that are differentially spliced within pre-mRNA. Understanding how multiple splicing events are coordinated across nascent transcripts requires quantitative analyses of transient RNA processing events in living cells. We developed nanopore analysis of CO-transcriptional Processing (nano-COP), in which nascent RNAs are directly sequenced through nanopores, exposing the dynamics and patterns of RNA splicing without biases introduced by amplification. nano-COP showed that in both human and Drosophila cells, co-transcriptional splicing occurs after RNA polymerase II transcribes several kilobases of pre-mRNA, suggesting that metazoan splicing transpires distally from the transcription machinery. Inhibition of the branch site recognition complex SF3B globally abolished co-transcriptional splicing in both species. Our findings revealed that splicing order does not strictly follow the order of transcription and is influenced by cis-regulatory elements. In human cells, introns with delayed splicing frequently neighbor alternative exons and are associated with RNA-binding factors. Moreover, neighboring introns in human cells tend to be spliced concurrently, implying that splicing occurs cooperatively. Thus, nano-COP unveils the organizational complexity of metazoan RNA processing.

2019-12-12 | GSE123191 | GEO

Global analysis of protein degradation rates in primary rodent skin fibroblasts

Project description:Within individual species and cell types, the range of protein turnover rates can span multiple orders of magnitude. However, it is not known if turnover kinetics of individual proteins are highly conserved or if they have evolved to meet the physiological demands of individual species. We have conducted systematic analyses of proteome turnover kinetics in primary dermal fibroblasts isolated from eight different rodent species. Our results demonstrate that protein turnover rates are generally well conserved across species but gradually deviate as a function of evolutionary distance.

2018-02-07 | PXD007598 | Pride

Kinetics and fidelity of the repair of Cas9-induced double-strand DNA breaks

Project description:The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ~10 h. Furthermore, repair of the DSBs tends to be error-prone. Both classical and microhomology-mediated end-joining pathways contribute to the erroneous repair. Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation. Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci, and indicates that Cas9-induced DSBs are repaired in an unusual manner.

2018-05-01 | GSE113129 | GEO

Global donor and acceptor splicing site kinetics in human cells

Project description:Transient transcriptome sequencing and kinetic modeling suggest how the kinetics and yield of RNA splicing are encoded in the human genome.

2019-04-12 | GSE129635 | GEO

PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Project description:Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., nascent transcriptome, whole transcriptome, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens, we were able to decipher the complexity of RNA dynamics (e.g., synthesis, splicing, and degradation) at both global and gene-specific levels. Our technique opens up the possibility to perform genome-wide perturbations across millions of single cells cost-effectively.

2023-08-10 | GSE218566 | GEO

Genomic encoding of transcriptional burst kinetics

Project description:We sequenced allele-resolution single-cell transcriptomes from mouse primary fibroblasts and embryonic stem cells with the overall aim to infer transcriptional kinetics for each gene and allele. Inferred transcriptional burst kinetics revealed the genomic encoding of transcriptional burst frequencies and sizes within the genome. Core promoter elements were found to specify burst sizes, whereas burst frequencies were regulated by enhancers. In particular burst frequencies were found to account for cell-type differences in gene expression levels and were also mostly correlating with absolute expression levels in cells. Importantly, the patterns identified were not detectable at the level of mean expression demonstrating the need to investigate transcriptional dynamics at the level of burst kinetics.

2018-11-30 | E-MTAB-7098 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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