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Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [ISO-seq]

ABSTRACT: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [ISO-seq]

PROVIDER: PRJNA750100 | ENA |

REPOSITORIES: ENA

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Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes

Project description:Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes

| PRJNA750117 | ENA

Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [ISO-seq]

Project description:We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Iso-Seq (this data set).

2022-07-31 | GSE180918 | GEO

Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [total RNA-seq]

Project description:Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [total RNA-seq]

| PRJNA749777 | ENA

Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [total RNA-seq]

2022-07-31 | GSE180854 | GEO

Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-07-28 | GSE180930 | GEO

Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma

Project description:The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from 6 patients. A custom-built cDNA microarray platform was used, comprising 2,292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. Intronic transcription was detected in all normal and neoplastic renal tissues. A subset of 55 transcripts was significantly down-regulated in clear cell RCC relative to the matched non-tumor tissue as determined by a combination of two statistical tests and leave-one-out patient cross-validation. Among the down-regulated transcripts, 49 mapped to untranslated or coding exons and 6 were intronic relative to known exons of protein-coding genes. Lower levels of expression of SIN3B, TRIP3, SYNJ2BP and NDE1 (p < 0.02), and of intronic transcripts derived from SND1 and ACTN4 loci (p < 0.05), were confirmed in clear cell RCC by Real-time RT-PCR. A subset of 25 transcripts was deregulated in additional 6 non-clear cell RCC samples, pointing to common transcriptional alterations in RCC irrespective of the histological subtype or differentiation state of the tumor. Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells. Fluorescently labeled cDNA targets derived from tumor and non-tumor tissue from each patient were combined and hybridized to spotted cDNA microarrays. For each patient, a replicate hybridization with dye-swap of labeled targets was performed. For each tissue (tumor and adjacent non-tumor tissue), there are 4 replicate mesurements for each probe.

2010-06-25 | E-GEOD-7367 | biostudies-arrayexpress

Peptides encoded by 5’ untranslated regions mediate pain sensitization

Project description:Nociceptors are neurons responsible for the detection of pain producing stimuli. Persistent changes in their activity, termed plasticity, benefit survival through injury avoidance and are regulated on a translational basis. Yet, the mRNAs whose translation facilitates plasticity are unknown. Here, we apply ribosome profiling to dorsal root ganglion and identify a small number of transcripts that are selectively translated in response to plasticity mediators. Among them are Arc and Fos, genes implicated in episodic learning in the brain. We demonstrate that the ribosomal S6 kinase 1 is responsible for their production in nociceptors. Blocking S6 driven translation also reduces pain associated behavioral responses in vivo. In addition to translation of coding regions of mRNA, we detect pervasive ribosome occupancy in 5’ untranslated regions. We find that peptides encoded by open reading frames in the 5’ untranslated regions of Calca and Egr2 increase neuronal excitability in vitro and are sufficient to induce pain-like behaviors in vivo. Together, our findings uncover new targets of translational control that drive changes in plasticity and suggest new mechanisms for targeted pain therapeutics that disrupt pain signaling.

2020-02-01 | GSE117043 | GEO

One-shot analysis of translated mammalian lncRNAs with AHARIBO

Project description:A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

2021-02-28 | GSE167865 | GEO

Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma

2008-03-25 | GSE7367 | GEO

mRNAs translated at eIF4F

Project description:Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5' end-dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs have been shown to be translated by internal ribosome entry, a mechanism that can operate in the presence of low levels of functional eIF4F. To identify cellular mRNAs that can be translated when eIF4F is depleted or in low abundance and that, therefore, may contain internal ribosome entry sites, mRNAs that remained associated with polysomes were isolated from human cells after infection with poliovirus and were identified by using a cDNA microarray. Approximately 200 of the 7000 mRNAs analyzed remained associated with polysomes under these conditions. Among the gene products encoded by these polysome-associated mRNAs were immediate-early transcription factors, kinases, and phosphatases of the mitogen-activated protein kinase pathways and several protooncogenes, including c-myc and Pim-1. In addition, the mRNA encoding Cyr61, a secreted factor that can promote angiogenesis and tumor growth, was selectively mobilized into polysomes when eIF4F concentrations were reduced, although its overall abundance changed only slightly. Subsequent tests confirmed the presence of internal ribosome entry sites in the 5' noncoding regions of both Cyr61 and Pim-1 mRNAs. Overall, this study suggests that diverse mRNAs whose gene products have been implicated in a variety of stress responses, including inflammation, angiogenesis, and the response to serum, can use translational initiation mechanisms that require little or no intact cap binding protein complex eIF4F. This study is described more fully in Johannes G et al.(1999) Proc Natl Acad Sci U S A 96:13118-23.

2002-06-27 | E-GEOD-62 | biostudies-arrayexpress

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