Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA191095 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR766743.fastq.gz | Fastqsanger.gz | |||
| SRR766744.fastq.gz | Fastqsanger.gz | |||
| SRR766745.fastq.gz | Fastqsanger.gz | |||
| SRR766746.fastq.gz | Fastqsanger.gz | |||
| SRR766747.fastq.gz | Fastqsanger.gz |
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Project description:Alternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms leading to transcripts with distinct localization, stability and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESC) and neural progenitor cells (NPC) derived from the same ESC. We performed de novo transcriptome assembly from high-confidence long reads from cytosolic, monosomal, light and heavy polyribosomal fractions and quantified their abundance using short reads from their respective subcellular fractions. Thousands of transcripts in each cell type exhibited association with particular subcellular fractions relative to the cytosol. Of the multi-isoform genes, 27% and 19% exhibited significant differential isoform sedimentation in ESC and NPC respectively. Alternative promoter usage and internal exon skipping accounted for the majority of differences between isoforms from the same gene. Random forest classifiers implicated coding sequence (CDS) and UTR lengths as important determinants of isoform-specific sedimentation profiles, and motif analyses reveal potential cell type-specific and subcellular fraction-associated RNA-binding protein signatures. Taken together our data demonstrate that alternative mRNA processing within the CDS and UTRs impacts the translational control of mRNA isoforms during stem cell differentiation, and highlights the utility of using a novel long-read sequencing-based method to study translational control.
2024-03-11 | GSE244655 | GEO
Project description:T cell activation is a well-established model for studying cellular responses to exogenous stimulation. In this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells, and applied computational modeling to investigate the impact of IR on the kinetics of mRNA degradation. As expected, intron retained transcripts are considerably less stable than spliced transcripts. In addition, the decrease in the steady-state IR level in activated CD4+ T cells are in part due to increased splicing efficiency and further stabilization of spliced transcripts. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to achieve spatiotemporal control of gene expression during T cell activation. We also found the mRNA stability change is not due to the 3’UTR-isoform choice but may be regulated by the RBP for example the LARP4 is the most significant binding protein in 3’ UTR of the β1-decreased genes. Furthermore, the mRNAs of the activated CD4+ T cells in LARP4 Knock-out (KO) mice showed the decreased stability and comparable transcriptional level for some genes including the NFkB1 and PSMD7 when comparing to the wild-type (WT) mice, resulting in the down-regulation of these genes. Finally, the LARP4 KO down-regulated NFkB1 target genes such as IL2 and IFNG upon CD4+ T cell activation, which is critical for the T cell proliferation and function.
2020-07-21 | GSE113730 | GEO
Project description:Gene expression regulation in eukaryotes is a multi-level process, including transcription, mRNA translation, and protein turnover. Many studies have reported the sophisticated transcriptional regulations during neural development, but the global translational dynamics is still ambiguous. Here, we differentiated human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and performed ribosome sequencing and RNA sequencing on both ESCs and NPCs. Data analysis revealed that translational controls engaged in many critical pathways and contributed significantly to neural fate determination regulation. Furthermore, we showed that the sequence characteristics in the untranslated region (UTR) might regulate translation efficiency. Specifically, genes with short 5UTR and intense Kozak sequence are associated with high translation efficiency in human ESCs, while genes with long 3'UTR are related to high translation efficiency in NPCs. In addition, we identified four biasedly-used codons (GAC, GAT, AGA, and AGG) and dozens of short open reading frames during neural progenitor differentiation. Thus, our study reveals the translational landscape during early human neural differentiation and provides insights into the regulation of cell fate determination at the translational level.
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Project description:Alternative polyadenylation generates numerous 3' mRNA isoforms per gene; regulation of this process is critical in development and impaired in cancer. Individual isoforms from the same gene can vary greatly in biological properties such as translational efficiency, localization, and half-life. Even closely related isoforms - including those differing by a single nt - can have different biological properties, but the underlying mechanisms are unknown. Here we show that many highly similar yeast isoforms unexpectedly exhibit extensive structural variation and differential Pab1 binding, and that these physical properties serve as a good predictor of relative isoform stability. We developed DREADS, a dimethyl sulphate (DMS)-based technique, to obtain the first transcriptome-scale structural description of individual 3' mRNA isoforms in vivo. Strikingly, near-identical yeast mRNA isoforms arising from the same gene can possess dramatically different DMS modification profiles over hundreds of nt upstream of the poly(A) tail. DREADS analyses of the same mRNAs refolded in vitro or in different species indicate that structural differences in vivo are often due to trans- acting factors. CLIP-READS, a technique we developed to measure isoform-specific binding, reveals that differences in Poly(A) binding protein (Pab1) binding to 3' ends correlate with the extent of structural variation for closely-spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-stranded character of the poly(A) tail, and low Pab1 binding is significantly associated with mRNA stability. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, and are indicative of biological function.
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Project description:Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5′ and 3′ untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5′UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identical coding sequences and demonstrate that the underlying transcription start site heterogeneity frequently results in 5′ terminal oligopyrimidine (TOP) and pyrimidine-rich translational element (PRTE) motif switches to drive mTORC1-dependent translation of the mRNA. Genome-wide, we show that highly translated squamous cell carcinoma transcripts switch towards increased use of 5′TOP and PRTE motifs, have generally shorter 5′UTRs and expose decreased RNA secondary structures. Notably, we found that the two 5′TOP motif-containing, but not the TOP-less, RPL21 transcript isoforms strongly correlated with overall survival in human head and neck squamous cell carcinoma patients. Our findings warrant isoform-specific analyses in human cancer datasets and suggest that switching between 5′UTR isoforms is an elegant and simple way to alter protein synthesis rates, set their sensitivity to the mTORC1-dependent nutrient-sensing pathway and direct the translational potential of an mRNA by the precise 5′UTR sequence.
2022-12-08 | GSE201308 | GEO
Project description:Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5′ and 3′ untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5′UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identical coding sequences and demonstrate that the underlying transcription start site heterogeneity frequently results in 5′ terminal oligopyrimidine (TOP) and pyrimidine-rich translational element (PRTE) motif switches to drive mTORC1-dependent translation of the mRNA. Genome-wide, we show that highly translated squamous cell carcinoma transcripts switch towards increased use of 5′TOP and PRTE motifs, have generally shorter 5′UTRs and expose decreased RNA secondary structures. Notably, we found that the two 5′TOP motif-containing, but not the TOP-less, RPL21 transcript isoforms strongly correlated with overall survival in human head and neck squamous cell carcinoma patients. Our findings warrant isoform-specific analyses in human cancer datasets and suggest that switching between 5′UTR isoforms is an elegant and simple way to alter protein synthesis rates, set their sensitivity to the mTORC1-dependent nutrient-sensing pathway and direct the translational potential of an mRNA by the precise 5′UTR sequence.
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Project description:Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and mRNA turnover in the cytoplasm. On a global basis, same-gene 3’ mRNA isoforms with > two-fold differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of two. In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3’ mRNA isoform. This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested. These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability.
2022-02-02 | GSE191091 | GEO
Project description:Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. Here, we characterized the RNA-binding landscape of three broadly expressed PABs in Arabidopsis thaliana. We observed substantial variation in the AtPAB-binding efficiency among mRNAs, which can be partly explained by the guanosine (G) content of poly(A) tails. AtPAB-binding efficiency of a gene was positively associated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibited a greater reduction in translational efficiency when AtPAB is depleted. Our study provides a new mechanism that translational efficiency of a gene can be regulated through G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
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Project description:A cell synchronization protocol was established in which global and individual mRNA translational efficiencies could be examined. While global translational efficiency was reduced in mitotic cells, approximately 3% of mRNAs remained predominantly associated with large polysomes during mitosis, as determined by cDNA microarray analyses. The 5 noncoding regions of six mRNAs were shown to contain internal ribosome entry sites (IRES). However, not all known mRNAs that contain IRES elements were actively translated during mitosis, arguing that specific IRES sequences are differentially regulated during mitosis.
2005-10-31 | E-SMDB-2546 | biostudies-arrayexpress
Project description:The contributions of phosphorylation-mediated signaling networks to colon cancer metastasis are poorly defined. To better understand the role of constitutive signaling alterations in cancer progression, the global phosphoproteomes of the SW480 and SW620 cell lines were compared by LC-MS/MS. These patient-matched cell lines were derived from a primary colon tumor and a lymph node metastasis, respectively. Network analysis of the significantly altered phosphosites revealed differential regulation in cellular adhesion, mitosis, and mRNA translational machinery. Among the latter group were sites on phosphoproteins with known roles in mRNA biogenesis and splicing, transport through the nuclear pores, initiating translation, as well as mRNA stability and degradation. Though alterations in these processes have been associated with oncogenic transformation, control of mRNA stability has typically not been associated with cancer progression. Notably, the single phosphosite with the greatest relative change in SW620 was Ser2 on eIF2S2, suggesting that SW620 cells translate faster or with greater efficiency than SW480 cells. These broad changes in the regulation of translation also occur without over-expression of eIF4E. Altogether, this work shows that metastatic cells exhibit constitutive changes to the phosphoproteome, and that mRNA stability and translational efficiency may be important targets of deregulation during cancer progression.
2017-04-01 | MSV000080864 | MassIVE