Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Heat stress induced alternative splicing in a species-dependent manner

ABSTRACT: Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.

ORGANISM(S): Arabidopsis thaliana Boechera depauperata

PROVIDER: GSE107820 | GEO | 2018/03/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Heat stress induced alternative splicing in a species-dependent manner

Project description:Heat stress induced alternative splicing in a species-dependent manner

| PRJNA421490 | ENA

Alternative splicing in tomato pollen in response to heat stress

Project description:Alternative splicing caused by exposure of pollen to high temperatures leads to the generation of transcripts with pre-mature termination codon targeted for degradation or mRNAs putatively coding for truncated proteins with altered functions thereby controlling important cellular pathways including transport and localization, heat stress response, gene expression and various biosynthetic processes.

2016-11-04 | GSE80556 | GEO

Transformation of elongation factor 1Bdelta into heat shock response transcription factor by alternative splicing

Project description:Protein translation factors play crucial roles in a variety of stress responses. Here, we show that the eukaryotic elongation factor 1Bdelta (eEF1Bdelta) changes its structure and function from a translation factor into a heat shock response transcription factor by alternative splicing. While eEF1Bdelta is specifically localized in the cytoplasm, the long isoform of eEF1Bdelta (eEF1BdeltaL) is localized in the nucleus and induces heat shock element (HSE)-containing genes in cooperation with heat-shock transcription factor 1 (HSF1). Moreover, the N-terminal domain of eEF1BdeltaL binds with NF-E2-related factor 2 (Nrf2) and induces stress response heme oxygenase 1 (HO-1). Specific inhibition of eEF1BdeltaL with siRNA completely inhibits Nrf2-dependent HO-1 induction. In addition, eEF1BdeltaL directly binds to HSE oligo DNA in vitro and associates with HSE containing the HO-1-enhancer region in vivo. Thus, the transcriptional role of eEF1BdeltaL could provide new insights into the molecular mechanism of stress responses. We performed microarray analysis to compare the gene expression induced by eEF1Bdelta1 or eEF1BdeltaL overexpression. HEK293 cells transfected with expression plasmids encoding flag-tagged-eEF1Bdelta1 or eEF1BdeltaL protein

2011-04-12 | E-GEOD-28506 | biostudies-arrayexpress

Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

Project description:Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

| PRJNA566413 | ENA

Cohesin regulates alternative splicing alone or with BRD4

Project description:By targeted depletion of Cohesin (RAD21 subunit) or BRD4 alone or together, we have established that cohesin alone or with BRD4 regulates the alternative splicing of a large subset of genes under both physiological and heat shock conditions.

2022-08-31 | GSE182960 | GEO

Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

Project description:Regulation and functionality of species-specific alternative splicing has remained enigmatic for many years. Calcium/calmodulin-dependent protein kinase IIβ (CaMKIIβ) is expressed in several splice variants and plays a key role in learning and memory. Here, we identify and characterize several primate-specific CAMK2B splice isoforms, which show altered kinetic properties and changes in substrate specificity. Furthermore, we demonstrate that primate-specific Camk2β alternative splicing is achieved through branch point weakening during evolution. We show that reducing branch point and splice site strength during evolution globally renders constitutive exons alternative, thus providing a paradigm for cis-directed species-specific alternative splicing regulation. Using CRISPR/Cas9 we introduced the weaker human branch point into the mouse genome, resulting in human-like CAMK2B splicing in the brain of mutant mice. We observe a strong impairment of long-term potentiation in CA3-CA1 synapses of mutant mice, thus connecting branch point-controlled, species-specific alternative splicing with a fundamental function in learning and memory.

2022-12-19 | PXD035346 | Pride

The evolutionary landscape of alternative splicing in vertebrate species

Project description:How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species.

2012-12-22 | GSE41338 | GEO

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series

2010-09-01 | E-GEOD-23522 | biostudies-arrayexpress

Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

2022-12-02 | GSE208181 | GEO

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | 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