Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Virtual northern on human brain samples using DNA microarrays for systematic genome wide analysis of mRNA lengths

ABSTRACT: Background We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale. Methodology/Principal Findings We used separation by gel electrophoresis followed by hybridization to cDNA microarrays to measure 8,774 mRNA transcript lengths representing at least 6,238 genes at high (>90%) confidence. By comparing these transcript lengths to the Refseq and H-Invitational full-length cDNA databases, we found that nearly half of our measurements appeared to represent novel transcript variants. Comparison of length measurements determined by hybridization to different cDNAs derived from the same gene identified clones that potentially correspond to alternative transcript variants. We observed a close linear relationship between ORF and mRNA lengths in human mRNAs, identical in form to the relationship we had previously identified in yeast. Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and yeast. Conclusions/Significance Human transcript diversity is extensive and largely unannotated. Our length dataset can be used as a new criterion for judging the completeness of cDNAs and annotating mRNA sequences. Similar relationships between the lengths of the UTRs in human and yeast mRNAs and the functions of the proteins they encode suggest that UTR sequences serve an important regulatory role among eukaryotes.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-4088 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing of S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A strains

Project description:The goal of our study was to perform RNA sequencing of whole transcripts to determine and compare the real length of 3’UTRs among closely-related staphylococcal species. We found that most of the mRNAs encoding orthologous genes in staphylococcal species have 3’UTRs with different lengths in addition to sequence variation.

2020-01-15 | GSE143600 | GEO

Pombe_polyA_mapping_NGS_v3

Project description:Regulatory elements in the 3M-^R untranslated regions (UTRs) of eukaryotic mRNAs influence mRNA localization, translation, and stability. The length of these regions is determined by the location at which mRNAs are cleaved and polyadenylated. The use of alternative polyadenylation sites is common, and can be regulated in different situations. I present here a new method to identify cleavage and polyadenylation sites (CSs) at the genome-wide level. The approach is strand-specific, avoids RNA enzymatic modification steps that can introduce sequence-specific biases, and uses molecular barcodes to ensure that every identified CS originates from an individual RNA molecule. I applied to create the first comprehensive genome-wide map of polyadenylation sites in the fission yeast Schizosaccharomyces pombe, comprising the analysis of over two million individual mRNAs that defined 10,422 major CSs. CSs were identified for 90% of coding genes and 15% of non-coding RNAs. Alternative polyadenylation was prevalent in both groups, with 61% and 49% of all detected genes, respectively, displaying more than one CS. The specificity of the cleavage reaction was gene-specific, resulting in highly variable levels of heterogeneity in the length of the 3' UTRs. Finally, I show that for both coding and non-coding genes the most common regulatory motif associated with CSs in fission yeast is the canonical human AAUAAA sequence.

2013-11-19 | E-MTAB-1642 | biostudies-arrayexpress

Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability

Project description:The half-life of mRNAs, as well as their translation, increases proportionally to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the coupling in yeast displays a dichotomous behavior regarding the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs even though they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality-dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell-cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.

2023-09-28 | GSE235627 | GEO

Codon and amino acid identity are major determinants of mRNA stability in humans

Project description:To investigate the effects of the coding sequence on mRNA decay, we globally analyzed the stability of endogenous mRNAs as well as those derived from the human ORFeome collection, which contains full-length coding sequences in the context of invariant UTRs.

2019-09-22 | GSE123165 | GEO

Antibody crossreactivity with mRNA cap accounts for widespread appearance of m1A throughout the transcriptome

Project description:N1-methyladenosine (m1A) was recently identified as a new mRNA modification based on its mapping to the 5’UTRs of thousands of mRNAs with an m1A-binding antibody. More recent studies have questioned the prevalence of m1A. To address this discrepancy, we mapped m1A using ultra-deep RNA-Seq datasets based on m1A-induced misincorporations during reverse transcription. Using this approach, we find m1A only in the mitochondrial MT-ND5 transcript. In contrast, m1A mapping using an m1A-binding antibody showed binding to transcription start nucleotides in mRNA 5’UTRs. Biochemical measurements indicate that m1A is not present at these sites. Instead, we find that the m1A antibody exhibits m1A-independent binding to mRNA cap structures. Our data demonstrate that high-stoichiometry m1A sites are rare in the transcriptome and that previous mapping of m1A to mRNA 5’UTRs reflect an unintended binding to mRNA caps.

2019-06-23 | GSE97909 | GEO

Virtual northern using DNA microarrays for genome wide systematic analysis of mRNA lengths, used to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the yeast genome

Project description:We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors 1 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. Analysis of genes deviating from that relationship identified ORFs with annotation errors, ORFs that appear not to be bona fide genes, and potentially novel genes. Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.

2005-10-27 | E-SMDB-2508 | biostudies-arrayexpress

Transcriptome-wide profiling of poly(A)-tail length, translation efficiency and mRNA stability using TED-seq, mRNA-seq, Ribo-seq and PRO-seq in ER stress conditions

Project description:We report systematical profiling of translation efficiency and mRNA stability dependent on the dynamics of poly(A)-tail length in stress conditions of human cells. In this study, we developed a new feasible method measuring poly(A)-tail length called TED-seq and applied it to investigate the change of mRNA's poly(A)-tail lengths in ER stress pharmacologically induced by thapsigargin (THAP). Combined with other global RNA analyses such as RNA-seq, Ribo-seq and PRO-seq, we observed that ER stress induced lenthening poly(A)-tail length, in particular of ER-stress-regulators, upon ER stress. More specifically, these mRNAs are translationally de-repressed and more stabilized based on increase in poly(A)-tail length. We also identified that insoluble fractions which include stress-induced RNA-granules have overall shorter length of poly(A) tail. Taken together, our data suggest that poly(A)-tail lengths are dynamically regulated and influence both translation efficiency and mRNA stability in ER stress.

2018-01-01 | GSE103719 | GEO

Cellular stress alters 3’UTR landscape through alternative polyadenylation and isoform-specific degradation

Project description:Most eukaryotic genes express alternative polyadenylation (APA) isoforms with different lengths of 3’ untranslated region (3’UTR). Here we show arsenic stress elicits global shortening of 3’UTRs through two mechanisms. First, stress leads to immediate shortening of 3’UTR due to preferential usage of proximal cleavage and polyadenylation sites (PASs), as revealed by 3’ end sequencing of newly made RNAs that are metabolically labeled with 4-thiouridine. Second, long 3’UTR isoforms are more rapidly degraded during recovery from stress as compared to short 3’UTR isoforms, further shortening 3’UTR lengths in the cell. Using ribonucleoprotein immunoprecipitation coupled with 3’ end sequencing (3’READS+RIP), we show that the RNA-binding protein T cell-restricted intracellular antigen-1 (Tia1) preferentially interacts with long 3’UTR isoforms via U-rich elements in alternative 3’UTR sequences, and the interaction correlates with stress granule (SG) association during stress and with mRNA decay during recovery from stress, indicating SG-mediated RNA clearance mechanism post stress. Importantly, genes whose 3’UTRs are shortened by APA during stress can evade stress-induced 3’UTR size-based mRNA degradation, leading to higher transcript abundance post stress. Moreover, proliferating and differentiated cells display different extents of 3’UTR shortening after stress, indicating cell type-specific of impact of stress on the 3’UTR landscape. Together, our data indicate that 3’UTR length plays important roles in gene expression in stressed cells, and APA functions as an adaptive stress response mechanism to preserve mRNAs.

2018-06-13 | GSE101851 | GEO

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

2005-12-29 | E-GEOD-3932 | biostudies-arrayexpress

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

2005-12-30 | GSE3932 | GEO