Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380824 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5388393.fastq.gz | Fastqsanger.gz |
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Project description:Translation is a tightly regulated and is predominantly controlled at the level of its initiation. Initiation occurs in a cap-dependent manner. Under stress conditions when cap-dependent translation is hampered, internal ribosome entry sites (IRESes) allow for cap-independent translation of certain mRNAs. IRES-dependent translation is commonly regulated by RNA-interacting proteins, known as IRES trans-acting factors (ITAFs). In the present study, we searched for new IRESes by identifying 5’ untranslated regions (UTRs) bound by the ITAF hnRNPA1. Using a PAR-iCLIP approach, we found the mRNA of thioredoxin interacting protein (TXNIP) bound by hnRNPA1. Upon verification of an IRES element within the 5’UTR of TXNIP, we determined additional interacting proteins, which predominantly appeared to interact with the IRES-regulatory second half of the 5’UTR. Amongst these PTB, FBP3, and GEMIN5 emerged as functional ITAFs. Finally, we found that the TXNIP IRES-inhibitory effect of PTB was dominant over the activating effect of FBP3, while it succumbed to the stimulatory function of GEMIN5. In summary, we identified and characterized a novel IRES within the 5’UTR of TXNIP, which is regulated by the ITAFs PTB, FBP3, and GEMIN5.
2018-01-23 | GSE97159 | GEO
Project description:Gene regulation occurs through trans-acting factors (e.g. transcription factors) acting on cis-regulatory elements (e.g. enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of cis-regulatory elements for regulatory potential, but do not identify the trans-acting factors that mediate any observed effects. Here we include preliminary data from a pilot transMPRA experiment — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identify trans-acting factors that modulate the regulatory activity of specific enhancers.
2020-09-30 | GSE157430 | GEO
Project description:Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and Rps2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as the site of IRESome assembly in the nucleus. Polysome PCR array showed that the Neat1_2 isoform widely affects translation of mRNAs containing IRESs, involved in stress response, angiogenesis or cardioprotection.
2023-01-03 | PXD024067 | Pride
Project description:Identification of cis- and trans-acting factors involved in the localization of MALAT-1 to nuclear speckles
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Project description:Trans-acting regulatory variation in Saccharomyces cerevisiae
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Project description:SINEUPs are antisense long non-coding RNAs (lncRNAs) that increase translation of overlapping mRNAs through the activity of two domains: an embedded SINEB2 sequence UP-regulates translation (Effector Domain) while the antisense region provides target specificity (Binding Domain). In this study, we show that the invSINEB2 sequence from the natural SINEUP AS Uchl1 RNA exhibits the functions of an Internal Ribosomal Entry Site (IRES), while viral and cellular IRES sequences act as Effector Domains, promoting protein expression in trans. We demonstrate that the Stem Loop1 of AS Uchl1 SINEB2 is functionally equivalent to the IIId loop of Hepatitis C Virus IRES. The natural circ5533, a circular RNA at the c-myc locus, up-regulates the protein expression in trans of specific target mRNAs through an IRES sequence serving as Effector Domain and antisense regions as Binding Domains. This work shows a new function for embedded transposable elements in lncRNAs, proves that an IRES sequence can work in trans enhancing the translation of a target mRNA and identify a new class of regulatory circRNAs.
2025-08-25 | PXD028571 | Pride
Project description:Background: Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results: A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8’-hydroxylase pseudogene.
2011-06-22 | GSE29964 | GEO
Project description:Circular RNAs (circRNAs) are a class of abundant RNAs with ambiguous function. Although some circRNAs can be translated through IRES driven mechanisms, the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we developed a cell-based system to screen random sequences and identified 97 overrepresented AU-rich hexamers (>2% of all hexamers) that drive cap-independent translation of circRNAs. These IRES-like short elements are significantly enriched in circRNAs and sufficient to drive circRNA translation. We further identified multiple trans-acting factors that bind these IRES-like short elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides were identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which were experimentally validated by western blotting. Consistently, the mutation of the IRES-like short element in one circRNA reduced its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in circRNA function.
2022-06-03 | GSE152560 | GEO
Project description:Introducing a clinical-practical, alternative splicing activity-based proteogenomic method that identifies, in their oncogenically active states, biomarker genes bearing patient-specific GE or copy-number alterations of prognostic significance. This integrated multi-omics method uses intronic splicing enhancers (ISEs) probes to sort in situ ISE-interacting trans-acting protein factors (trans-interactome) directly from a heterogeneous tumor for subsequent mass spectrometry (MS) characterization.
2018-03-20 | PXD008642 | Pride
Project description:Effects of genetic modification of trans-acting transcription factors and a chromatin remodeler on noncoding RNA transcription and trans-acting factor binding at loci in yeast.
2010-03-29 | E-MEXP-2269 | biostudies-arrayexpress