Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA 5'end sequencing in polysome profiling fractions

ABSTRACT: It has been shown that in mammalian cells alternative transcription initiation is extensively regulated during development and across cell-types, which confers dynamic transcript 5’UTR repertoire. However it is underexplored how the heterogeneity of 5’UTR isoforms would affect the downstream steps for protein expression, such as translation. To this end, we globally compared the translational profile of distinct mRNA TSS isoforms in mouse fibroblast cells, by combining deep-sequencing based mRNA 5’ends profiling and polysome fractionation. We demonstrated the extensive translation regulation conferred by TSS heterogeneity.

ORGANISM(S): Mus musculus

PROVIDER: GSE78241 | GEO | 2016/07/20

SECONDARY ACCESSION(S): PRJNA313018

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA 5'end sequencing in polysome profiling fractions

Project description:It has been shown that in mammalian cells alternative transcription initiation is extensively regulated during development and across cell-types, which confers dynamic transcript 5âUTR repertoire. However it is underexplored how the heterogeneity of 5âUTR isoforms would affect the downstream steps for protein expression, such as translation. To this end, we globally compared the translational profile of distinct mRNA TSS isoforms in mouse fibroblast cells, by combining deep-sequencing based mRNA 5âends profiling and polysome fractionation. We demonstrated the extensive translation regulation conferred by TSS heterogeneity. 5'end sequencing in seven polysome fractions, in two replicates, using Illumina Hiseq2000

2016-07-20 | E-GEOD-78241 | biostudies-arrayexpress

Alternative 3’UTRs play a widespread role in translation-independent mRNA association with endoplasmic reticulum

Project description:Transcripts encoding membrane and secreted proteins are known to undergo translation on endoplasmic reticulum (ER). Translation-independent ER association (TiERA) has been reported for certain mRNAs, but the phenomenon is poorly understood. Here, using cell fractionation, polysome profiling, and 3’ end sequencing, we examine TiERA of poly(A)+ RNAs in mouse C2C12 myoblast cells. We identify transcript features that facilitate TiERA, including transcript size and GG and GC content. Consistent with the feature analysis, alternative polyadenylation (APA) isoforms differ substantially in TiERA, with long 3’UTR isoforms generally having a higher TiERA potential than short 3’UTR isoforms. Importantly, the widespread 3’UTR lengthening taking place in cell differentiation leads to greater transcript association with ER in differentiated myotubes, despite that the TiERA potential being generally maintained. In addition, we show that TiERA correlates negatively with mRNA stability, highlighting 3’UTR-mediated mRNA decay on ER. Together, our data indicate that sequence and size features impact ER association independent of translation, leading to distinct mRNA metabolism for different transcript groups, and APA can alter transcript stability and translation through isoform-specific ER association.

2021-07-20 | GSE162971 | GEO

Roles for Transcript Leaders in Translation and mRNA Decay Revealed by Transcript Leader Sequencing

Project description:Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-Sequencing (TL-Seq), a technique combining enzymatic capture of m7G-capped mRNA 5'-ends with high-throughput sequencing. TL-Seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Transcription initiation sites occur in at least 5% of protein-coding regions and are concentrated near the 5'ends of ORFs. These truncated mRNAs are translated, based on ribosome density analysis. Translation Associated TL-Seq (TATL-Seq), which combines TL-Seq with polysome fractionation, revealed substantial differences in translation of alternative TL isoforms. Globally, while some TL features are associated with poor translation and nonsense-mediated mRNA decay (uAUGs, very short length), others (secondary structure, long length) have much less impact than predicted from analyses of individual genes. TL-Seq and TATL-Seq can be applied to any eukaryote to investigate TL-mediated regulation of gene expression. TL-Seq (+/- pyrophosphatase), TATL-Seq (TL-Seq libraries from polysome gradient)

2013-04-03 | E-GEOD-39074 | biostudies-arrayexpress

Polysome-seq in zebrafish early embryonic development

Project description:We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development, prior to and after MBT. We isolated polysome-associated (bound) and non-polysome-associated (unbound) mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing (RNA-seq), we profiled the transcriptome in polysome-bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs.

2017-10-14 | GSE88776 | GEO

Membrane-polysome associated fractionation of HES2 embryonic stem cells

Project description:The membrane fraction and the cytosolic fraction of HES2 cells were collected and subjected to microarray. The experiment was performed in triplicate Keywords: membrane-polysome fractionation of RNA Three consecutive passages of HES2 cells were grown and subject to membrane-polysome fractionation. A total of 6 samples, (3 replicates of 2 fractions) were included in the experiment

2010-04-07 | E-GEOD-14037 | biostudies-arrayexpress

Membrane-polysome associated fractionation of HES2 embryonic stem cells

2009-10-01 | GSE14037 | GEO

eif3h/WT polysome loading

Project description:Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant Goal: To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5’ leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5’ leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Keywords: mutant, polysome, non-polysome

2007-05-01 | GSE6024 | GEO

RNA bisulfite sequencing for polysome fractions

Project description:RNA bisulfite sequencing for polysome fractions

| PRJNA625655 | ENA

Changes in polysome loading as a consequence of RHA downregulation

Project description:RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5’ untranslated region (UTR). This interaction represents an “RNA switch” that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays. Changes in cytoplasmic RNA steady state abundance was monitored as well. Sixty nine genes exhibit decreased transcript polysome association when subjected to RHA downregulation. A majority of the transcripts that experienced a reduction in the polysome fraction had no significant change in their cytoplasmic abundance (45 genes). Keywords: gene expression array-based

2008-12-20 | GSE14055 | GEO

PSN1 Polysome and INK128

Project description:Polysome-bound mRNA was analyzed to determine the effects of INK128 and radiation on mRNA translation

2014-02-03 | GSE48098 | GEO