Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3’ processing

ABSTRACT: Our study of CstF64 and CstF64τ revealed both functional overlap and specificity of these two important mRNA 3’ processing factors and provided new insights into the regulatory mechanisms of mRNA 3’ processing.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE51156 | GEO | 2013/09/30

SECONDARY ACCESSION(S): PRJNA221564

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3’ processing

Project description:Our study of CstF64 and CstF64τ revealed both functional overlap and specificity of these two important mRNA 3’ processing factors and provided new insights into the regulatory mechanisms of mRNA 3’ processing. CstF64tau iCLIP-seq in HeLa cells; direct RNA sequencing (DRS) of control HeLa cells, CstF64tau-RNAi cells and SELEX-seq for RNA control pool, CstF64 and CstF64tau.

2013-09-30 | E-GEOD-51156 | biostudies-arrayexpress

Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3’ processing

Project description:Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3’ processing

| PRJNA221564 | ENA

Overlapping and distinct functions of CstF64 and CstF64? in mammalian mRNA 3' processing.

Project description:mRNA 3' processing is dynamically regulated spatially and temporally. However, the underlying mechanisms remain poorly understood. CstF64? is a paralog of the general mRNA 3' processing factor, CstF64, and has been implicated in mediating testis-specific mRNA alternative polyadenylation (APA). However, the functions of CstF64? in mRNA 3' processing have not been systematically investigated. We carried out a comprehensive characterization of CstF64? and compared its properties to those of CstF64. In contrast to previous reports, we found that both CstF64 and CstF64? are widely expressed in mammalian tissues, and their protein levels display tissue-specific variations. We further demonstrated that CstF64 and CstF64? have highly similar RNA-binding specificities both in vitro and in vivo. CstF64 and CstF64? modulate one another's expression and play overlapping as well as distinct roles in regulating global APA profiles. Interestingly, protein interactome analyses revealed key differences between CstF64 and CstF64?, including their interactions with another mRNA 3' processing factor, symplekin. Together, our study of CstF64 and CstF64? revealed both functional overlap and specificity of these two important mRNA 3' processing factors and provided new insights into the regulatory mechanisms of mRNA 3' processing.

| S-EPMC3884657 | biostudies-literature

Global changes in processing of 3'-UTR characterize clinically distinct tumor types

Project description:We used a novel probe-level microarray analysis, revealing connections between mRNA processing and lymphoid neoplasia, in a mouse leukemia model. Characteristic differences in mRNA processing, primarily in the 3’-untranslated region, distinguished histologically similar tumor subtypes with different survival characteristics. Gene sets with specific processing in each tumor subtype defined signatures useful for tumor subclassification, as demonstrated by internal cross-validation with up to 80% discrimination accuracy. A combination of mRNA expression and sequence analysis suggested that differences in isoform abundance likely arose from both alternative polyadenylation and differential degradation.

2009-10-08 | GSE15808 | GEO

Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis

Project description:Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis

| PRJNA379118 | ENA

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

Project description:We mapped CstF64-RNA interactions at the transcriptome level and studied CstF64-mediated regulation of global mRNA alternative polyadenylation by using iCLIP-seq and direct RNA sequencing analyses. CstF64 iCLIP-seq in HeLa cells; direct RNA sequencing (DRS) of control HeLa cells, CstF64-RNAi cells and CstF64&CstF64tau-RNAi cells

2012-10-01 | E-GEOD-40859 | biostudies-arrayexpress

Distinct and overlapping functions of ptpn11 genes in Zebrafish development.

Project description:The PTPN11 (protein-tyrosine phosphatase, non-receptor type 11) gene encodes SHP2, a cytoplasmic PTP that is essential for vertebrate development. Mutations in PTPN11 are associated with Noonan and LEOPARD syndrome. Human patients with these autosomal dominant disorders display various symptoms, including short stature, craniofacial defects and heart abnormalities. We have used the zebrafish as a model to investigate the role of Shp2 in embryonic development. The zebrafish genome encodes two ptpn11 genes, ptpn11a and ptpn11b. Here, we report that ptpn11a is expressed constitutively and ptpn11b expression is strongly upregulated during development. In addition, the products of both ptpn11 genes, Shp2a and Shp2b, are functional. Target-selected inactivation of ptpn11a and ptpn11b revealed that double homozygous mutants are embryonic lethal at 5-6 days post fertilization (dpf). Ptpn11a-/-ptpn11b-/- embryos showed pleiotropic defects from 4 dpf onwards, including reduced body axis extension and craniofacial defects, which was accompanied by low levels of phosphorylated Erk at 5 dpf. Interestingly, defects in homozygous ptpn11a-/- mutants overlapped with defects in the double mutants albeit they were milder, whereas ptpn11b-/- single mutants did not show detectable developmental defects and were viable and fertile. Ptpn11a-/-ptpn11b-/- mutants were rescued by expression of exogenous ptpn11a and ptpn11b alike, indicating functional redundance of Shp2a and Shp2b. The ptpn11 mutants provide a good basis for further unravelling of the function of Shp2 in vertebrate development.

| S-EPMC3988099 | biostudies-literature

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

2012-10-01 | GSE40859 | GEO

The competition between splicing and 3′ processing shapes the human transcriptome

Project description:Eukaryotic pre-mRNA processing steps, including splicing and 3′ processing, are tightly coordinated, but the underlying mechanisms remain poorly understood. Previous studies proposed that the splicing factor U1 snRNP inhibits 3′ processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism, called telescripting. However, we found that global or gene-specific perturbation of splicing by targeting multiple splicing factors, including U1 snRNP, U2 snRNP, U2AF, and SF3b led to activation of 3′ processing at IPA sites. Inhibiting different splicing factors activated overlapping and distinct IPA sites and such specificity was determined, at least in part, by alterations in RNA polymerase II elongation and termination. Conversely, we showed that blocking pre-mRNA 3′ processing promoted splicing globally. These results strongly suggest that splicing and 3′ processing are competing processes that shape the transcriptome. Finally, as splicing inhibition-induced shifts to IPA site usage can lead to gene inactivation, including tumor suppressor genes, the use of general splicing inhibitors to treat human diseases may pose a significant risk.

2024-10-28 | GSE275154 | GEO

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

Project description:Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era. Here, we present a method, allele-specific alternative mRNA processing (ASARP), to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The method examines RNA-Seq data at both single nucleotide and whole-gene/isoform levels to identify allele-specific expression (ASE) and existence of allele-specific regulation of mRNA processing. We applied the methods to data obtained from the human glioblastoma cell line U87MG and primary breast cancer tissues and found that 26M-bM-^@M-^S45% of all genes with sufficient read coverage demonstrated ASE, with significant overlap between the two cell types. Our methods predicted potential mechanisms underlying ASE due to regulations affecting either whole-gene-level expression or alternative mRNA processing, including alternative splicing, alternative polyadenylation and alternative transcriptional initiation. Allele-specific alternative splicing and alternative polyadenylation may explain ASE in hundreds of genes in each cell type. Reporter studies following these predictions identified the causal single nucleotide variants (SNVs) for several allele-specific alternative splicing events. Finally, many genes identified in our study were also reported as disease/phenotype-associated genes in genome-wide association studies. Future applications of our approach may provide ample insights for a better understanding of the genetic basis of gene regulation underlying phenotypic diversity and disease mechanisms. Examine allele-specific gene expression and alternative RNA processing in U87MG cell line

2012-03-29 | E-GEOD-29738 | 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