Binds rna untranslated. Medical search. Frequent questions

As a means to identify cellular RNA targets for these proteins, we devised combinatorial shape libraries representing naturally derived 3' untranslated regions and were able to select a structurally related subset of transcripts that bound to Hel-N1. (duke.edu)
This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins. (duke.edu)
The method enables a comprehensive evaluation of significantly mutated areas in both coding and noncoding regions of DNA that affect the sites for RNA-binding proteins. (aacr.org)
RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. (nih.gov)
Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. (nih.gov)
By transporting "cargos" such as proteins, RNAs, DNAs, and lipids [ 26 ], exosomes regulate the eventual fate of recipient cells. (hindawi.com)
Several skeletal dysplasias in specific dog breeds have been associated with mutations in members of the collagen gene family or its binding proteins ( 8 - 10 ), fibrilin related protein ( 11 ), as well as an altered sulfate transporter protein ( 12 ). (frontiersin.org)
MicroRNAs (miRNAs) are short (21-24 nucleotides) sequences of RNA that reduce gene expression by promoting the breakdown of messenger RNAs (mRNAs) and by repressing translation of mRNAs into proteins. (freethoughtblogs.com)
Using ribosome profiling, I wanted to see how the binding of ribosomes to RNA related to the timing of when those proteins actually got made. (eurekalert.org)
In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. (embl.de)
Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)
Quantitative comparisons of RNA-binding sites showed that NXF1 and SR proteins bind mRNA targets at adjacent sites, indicative of cobinding. (uni-frankfurt.de)
Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5'- or 3'- untranslated regions of genes involved in iron metabolism (e.g. (uni-wuerzburg.de)
Surprisingly, Loc1p was found to be strictly nuclear, unlike other known RNA-binding proteins involved in mRNA localization which shuttle between the nucleus and the cytoplasm. (elsevierpure.com)
Professor Jin and her lab propose that structured 5'UTRs can facilitate translation initiation via sequential remodeling: the 5'UTR undergoes sequential conformational changes that are facilitated by RNA binding proteins and translational factors, which ultimately leads to recruitment of the ribosome for translation of the mRNA. (illinois.edu)
Several proteins attach (bind) to this RNA molecule, forming an enzyme called mitochondrial RNA-processing endoribonuclease, or RNase MRP. (medlineplus.gov)
The RNase MRP enzyme also processes ribosomal RNA, which is required for assembling protein building blocks (amino acids) into functioning proteins. (medlineplus.gov)
Mutations in the RMRP gene likely result in the production of a noncoding RNA that cannot bind to some of the proteins that are normally part of the RNase MRP enzyme complex. (medlineplus.gov)

Scholars@Duke publication: Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1. (duke.edu)
Hel-N1, a human RNA-binding protein, shares significant homology with Drosophila protein ELAV, which is essential for fly neuronal development. (duke.edu)
RNA-protein interactions are central to biological regulation. (nih.gov)
Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and nonhuman RNAs. (nih.gov)
FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2-bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. (nih.gov)
These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs. (nih.gov)
In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. (nih.gov)
The vimentin 3′ UTR protein-binding region is an RNA element that contains a Y shaped structure which has been shown to have protein binding activity. (wikipedia.org)
When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
The binding of miRNA- protein complexes to mRNA causes translation inhibition or destabilisation of target transcripts. (ukessays.com)
CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. (nih.gov)
Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. (nih.gov)
CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. (nih.gov)
CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. (nih.gov)
Many different principles of thermoregulation have been identified in bacteria, which can be assigned to the class of protein-, DNA- or RNA-thermosensors. (springer.com)
It can directly bind to the 3'-untranslated region of the target mRNA through its seed sequence and inhibit the expression of the encoded protein at the post-transcriptional level [3]. (scirp.org)
Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green alga Chlamydomonas reinhardtii to quantify the effects of miRNA on protein synthesis and RNA abundance. (freethoughtblogs.com)
By using ribosome profiling, the research team examined the timing of ribosome binding in relation to peak protein and RNA levels. (eurekalert.org)
The researchers found many upstream open reading frames (uORFs) in the 5' untranslated region of circadian mRNAs, which is the part of RNA before the so-called "coding sequence" that gets translated by ribosomes into protein. (eurekalert.org)
These uORFs were associated with reduced ribosome binding in the main coding sequence and reduced reporter expression in a variety of circadian assays tested by the researchers suggesting a role for uORFs in shaping circadian protein expression. (eurekalert.org)
Genetic systems often behave unpredictably due to structural interactions between DNA, RNA and protein components as well as functional interactions with host factors and metabolites. (universityofcalifornia.edu)
Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)
Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein-protein and protein-RNA interactions. (uni-frankfurt.de)
The basal transcriptional apparatus (RNA Polymerase II, TATA-box binding protein and other components) in Pf is similar to that in free-living eukaryotes. (biomedcentral.com)
In addition, PVT1 binds to the UPF1 protein, thereby inducing epithelial-mesenchymal transition, proliferation and metastasis in breast cancer cells. (biomedcentral.com)
Using this element in the three-hybrid in vivo RNA-binding assay, we identified a protein, Loc1p, that binds in vitro directly to the wild-type ASH1 3′-UTR RNA, but not to a mutant RNA incapable of localizing to the bud nor to several other mRNAs. (elsevierpure.com)
LOC1 codes for a novel protein that recognizes double-stranded RNA structures and is required for efficient localization of ASH1 mRNA. (elsevierpure.com)
The p38 pathway is required for the induction of TNF-alpha RNA-binding activity and for the expression of TTP protein and mRNA. (ed.ac.uk)
Our findings demonstrate a direct link between a specific signal transduction pathway and a specific RNA-binding protein, both of which are known to regulate TNF-alpha gene expression at a posttranscriptional level. (ed.ac.uk)
In all organisms, translation is catalyzed in the ribosome, an extraordinary RNA-protein molecular machine in every living cell. (illinois.edu)
Although more and animals and plants and regulate gene/protein expression more progressions have been made about the through direct complementarity between their 5' region pathogenesis of asthma in recent years, the increasing and the 3' untranslated region of target mRNAs. (cdc.gov)
As binding of miRNAs to a target mRNA may result in an airway inflammatory disease closely correlates with either mRNA degradation or inhibition of protein immune regulation, more and more evidences suggest translation.1 More than 2000 miRNAs have been discovered in humans. (cdc.gov)
The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. (lu.se)

MicroRNAs (miRNAs) are a group of endogenous non-coding RNAs, which are single-stranded and ~21 nucleotides (~21 nt) in length. (nature.com)
MicroRNAs (miRNAs) are endogenous noncoding RNAs that act as post-transcriptional regulators of gene expression by binding to the 3′-untranslated region (UTR) of target mRNAs. (nature.com)
MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs, which act as key post-transcriptional regulators of target-gene expression. (spandidos-publications.com)
MicroRNAs are ~22-25 nucleotide non-coding RNAs. (ukessays.com)
MicroRNAs (miRNAs/miRs) are endogenous, single-stranded, small (approximately 22 nucleotides in length) noncoding RNA molecules that play an important and ubiquitous role in regulating genes expression. (spandidos-publications.com)
In recent years, noncoding RNAs (ncRNAs), especially microRNAs, long noncoding RNAs and circular RNAs, have been found to be associated with abnormalities of the ASMCs. (ersjournals.com)
MicroRNAs (miRNAs) are the most altered subset of ncRNAs, followed by long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). (ersjournals.com)
MicroRNAs (miRNAs), single-stranded RNA molecules with 19~25 nucleotides in length, are recognized as key modulators governing multiple gene expression via binding to the 3' untranslated region (3'-UTR) of target mRNA at the posttranscriptional level [ 7 ]. (oncotarget.com)

Hel-N1 has been shown to bind in vitro to 3' untranslated regions of mRNAs encoding c-myc, c-fos, granulocyte/macrophage colony-stimulating factor, and transcriptional repressor, Id. (duke.edu)
They bind primarily to 3′-untranslated regions (3′-UTRs) of target gene mRNAs. (spandidos-publications.com)
MiRNAs bind the 3' untranslated region (3'UTR) of target mRNAs. (ukessays.com)
It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. (nih.gov)

MiRNAs typically bind to the 3′ untranslated region (UTR) of their mRNA targets and downregulate gene expression via mRNA degradation or translational inhibition ( 8 - 10 ). (spandidos-publications.com)
MiRNAs are approximately 19- to 25-nucleotide estimated about 250,000 and mortality does not appear single-stranded, noncoding RNAs that exist in both to correlate well with prevalence. (cdc.gov)
miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. (lu.se)

Enteroviruses (EVs) are common human pathogens that are small, naked, single-stranded, positive-sense RNA viruses of ≈7,400 nt. (cdc.gov)
HCV is a small (50 nm) single-stranded RNA member of the flaviviridae family. (biomedcentral.com)

3' Untranslated regions (3' UTRs) length is regulated in relation to cellular state. (nih.gov)
This analysis revealed previously unidentified alterations in untranslated regions, long noncoding RNAs, and introns that may guide the interpretation of noncoding variants in cancer genomes. (aacr.org)
For example, the transcription, translation, and degradation of an mRNA is crucial to any gene expression event, and all three processes are controlled by a combination of elements including promoters, ribosome binding sites (RBSs), and cis -regulatory signals encoded in untranslated regions (UTRs). (universityofcalifornia.edu)
They are likely to have conserved DNA sequence elements, called transcription factor binding motifs (TFBMs), in their promoter regions. (biomedcentral.com)
TFBMs act as binding sites for transcription factors and coordinate the expression of the genes in whose promoter regions they appear. (biomedcentral.com)
Furthermore, 5'-untranslated regions (5'UTRs) of mRNA are essential for translation. (illinois.edu)

We show via an in vitro binding assay that miR-9a binds to sNPFR1 mRNA in insect cells and to the mammalian orthologue NPY2R in rat insulinoma cells. (nature.com)
it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. (nih.gov)

We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. (embl.de)
SRSF3 emerged as the most potent NXF1 adaptor, conferring sequence specificity to RNA binding by NXF1 in last exons. (uni-frankfurt.de)

miRNA is a non-coded RNA with a length of 19 - 25 bases. (scirp.org)
MiRNA usually binds directly to the 3′-untranslated region (3′-UTR) of target gene mRNA through the RNA-induced silencing complex (RISC) [ 15 , 16 ]. (ersjournals.com)
Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species. (lu.se)
The student will create a pipeline for identifying conserved miRNA binding sites across several sparrow species using TargetScan as a framework. (lu.se)
Following TargetScan's approach, students will evaluate conservation of miRNA binding sites across annotations. (lu.se)

Selection of RNA targets from randomized combinatorial libraries yielded (A+U)-rich consensus sequences for both Hel-N1 and Hel-N2. (duke.edu)
The third class of thermosensing is based on the temperature-dependent conformation of specific RNA sequences, which are termed RNA-thermometer (RNAT). (springer.com)
These sequences typically include the 5′-untranslated region in mRNA including the ribosome binding site (Shine-Dalgarno sequence) and in some cases the start codon (Klinkert and Narberhaus 2009 ). (springer.com)
Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
The HCV RNA polymerase is highly error prone, and the sequences of HCV genomes display enormous amounts of variation. (biomedcentral.com)

To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. (nih.gov)
Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. (nih.gov)
They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. (nih.gov)
Results IRE-like motifs were identified from genomic nucleic acid databases by an algorithm combining primary nucleic acid sequence and RNA structural criteria. (uni-wuerzburg.de)

Interestingly, SRSF3 and SRSF7 were shown to bind different sites in last exons and regulate 3' untranslated region length in an opposing manner. (uni-frankfurt.de)

In addition to classical gene regulatory networks noted above, we have recently identified a central role for additional biologic mechanisms, namely gene regulation by chromatin regulators and by noncoding RNAs. (stanford.edu)
This review highlights findings concerning noncoding RNAs (ncRNAs) in asthmatic ASMCs so far and proposes a schematic diagram that helps us to better understand how ncRNAs are involved in pathophysiological behavioural changes in asthmatic ASMCs. (ersjournals.com)
Many noncoding RNAs (ncRNAs) have been identified in asthmatic ASMCs in recent years [ 5 ]. (ersjournals.com)
Mounting evidence supports that long noncoding RNAs (lncRNAs) have critical roles during cancer initiation and progression. (biomedcentral.com)

Furthermore, single or double substitutions of the dinucleotides targeted for cleavage as well as mutations altering the predicted RNA secondary structure encompassing both cleavage sites also prevent mRNA degradation, confirming that these dinucleotides are the bona fide cleavage sites. (uni-frankfurt.de)

The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. (embl.de)
The RNA has one open reading frame, preceded by a ribosome-binding site within a UTR (untranslated region). (biomedcentral.com)
A localization element that is predominantly in the 3′-untranslated region (UTR) can direct this mRNA to the bud. (elsevierpure.com)
We show that stimulation of RAW264.7 mouse macrophages with LPS induces the binding of TTP to the TNF-alpha 3' untranslated region. (ed.ac.uk)

The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)

We performed ribosome profiling on the Per2 uORF mutant mice, and although ribosome binding was enhanced in the mutant mice, it was the increase in Per2 mRNA levels that was the most surprising," continues Arthur Millius. (eurekalert.org)

By modeling these associations between mutational signature and gene expression, mutational signatures can be potentially inferred in future RNA-seq studies. (hep.com.cn)
The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)

Using a two-color assay to simultaneously monitor poly(A) tail removal from different RNAs, we demonstrate that Puf3 can distinguish between RNAs of very similar sequence. (elifesciences.org)
Dual-luciferase reporter assay and RNA pull-down experiments were used to examine the mechanisms interaction between molecules. (biomedcentral.com)

Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. (embl.de)
Here, we used site-directed mutagenesis and in silico RNA structural studies to delineate the cis-acting requirements within 79-nt SII for cleavage and mRNA degradation. (uni-frankfurt.de)

To address the mechanism, transcriptome-wide RNA-binding profiles of NXF1 and SRSF1-7 were determined in parallel by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP). (uni-frankfurt.de)

RNA editing is a molecular process through which cells can make specific alterations in the chemical structure of RNA molecules after transcription. (biomedcentral.com)

We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)
We have isolated a SARS-associ- the complete genome of SARS-CoV has shown an RNA ated CoV (SARS-CoV) strain by injecting Vero cells with a molecule of about 29,750 bases in length, with a genome sputum specimen from an Italian patient affected by a organization similar to that of other coronaviruses (9-11). (cdc.gov)

However, regulatory elements can unpredictably interact with each other through the formation of RNA structures and the recruitment of factors that affect global transcript accessibility and stability. (universityofcalifornia.edu)
Prediction of RNARNA interaction is a key to elucidating possible functions of small non-coding RNAs, and a number of computational methods have been proposed to analyze interacting RNA secondary structures. (elsevierpure.com)
bistaRNA employs binding profiles that represent scores for hybridized structures, leading to reducing the computational cost for interaction prediction. (elsevierpure.com)

With maximum values of 0.23 g/(g h) at 37 °C, this constitutes a more than 60% increase compared to the production rate of 0.14 g/(g h) at the growth optimum of 30 °C. Interestingly however, control experiments unveiled that besides the regulatory effect of the RNA-thermometer, multiple metabolic effects may contribute equally to the observed increase in production rate. (springer.com)
Methods and/or tools to facilitate the combination of various regulatory elements originating from various different sources to predictably control the activity of any desired RNA would be beneficial for numerous biotechnology applications. (universityofcalifornia.edu)
The invention allows for the combination of multiple regulatory elements in a fashion that predictably affects RNA activity. (universityofcalifornia.edu)
In this article, we focus on predicting binding sites of target RNAs that are expected to interact with regulatory antisense RNAs in a general form of interaction. (elsevierpure.com)

Moreover, we aim to find new targets given specific antisense RNAs, which provides interesting insights into antisense RNA regulation. (elsevierpure.com)

MELOE-1 and MELOE-2, two highly specific melanoma antigens involved in T cell immunosurveillance are produced by IRES-dependent translation of the long « non coding » and polycistronic RNA, meloe . (oncotarget.com)

FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. (nih.gov)
Results displayed a mix of deleted and full-length coxsackievirus B3, characterized by a low viral RNA load (8.10 2 copies/μg of nucleic acids) and a low viral RNA positive-sense to RNA negative-sense ratio of 4.8. (cdc.gov)
Generic EV-genus real-time quantitative reverse transcription PCR protocols showed the presence of EV total RNA detection with a low viral load of 8.10 2 /μg of total extracted nucleic acids and a low viral RNA positive-sense (RNA+) to RNA negative-sense (RNA-) ratio value of 4.8 ( 7 ). (cdc.gov)

The putative cleavage site(s) and other nucleotides predicted to alter the RNA secondary structure of 79-nt SII were either deleted or mutated and their effect on mRNA turnover was monitored using a gene reporter system. (uni-frankfurt.de)

Instead, a molecule called a noncoding RNA, a chemical cousin of DNA, is produced from the RMRP gene. (medlineplus.gov)

To improve our understanding of the biological and clinical significance of somatic mutations on RNA processing in cancer, the authors developed a new method, known as MIRA (mutation identification for RNA alterations). (aacr.org)
In conjunction with RNA sequencing data, the researchers used MIRA to identify mutations in binding sites that altered RNA expression and splicing. (aacr.org)
The RMRP gene mutations that cause anauxetic dysplasia alter the noncoding RNA produced from the gene, and the RNase MRP enzyme containing the altered noncoding RNA is impaired in its ribosomal RNA processing function. (medlineplus.gov)

Here we demonstrate that the sterile-alpha motif (SAM) domain of Smaug functions as an RNA-recognition domain. (embl.de)
RNA recognition via the SAM domain of Smaug. (embl.de)

It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. (nih.gov)

In this study, the temperature-induced regulation of this native RNA-thermometer for heterologous rhamnolipid production was evaluated and its potential application for process control is discussed. (springer.com)

The function of histone modifying epigenetic regulators and noncoding RNA as central mediators of epithelial stem cell renewal and differentiation represent major emerging areas of study in the lab. (stanford.edu)

It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. (nih.gov)

Adenosine-to-inosine RNA editing (ATIRE) is characterized as non-mutational epigenetic reprogramming hallmark of cancer, while little is known about its predictive role in cancer survival. (biomedcentral.com)

PVT1 may act as an oncogene in breast cancer through binding miR-128-3p and UPF1 and represents a potential target for BC therapeutic development. (biomedcentral.com)
For this purpose, we propose bistaRNA, a novel method for predicting multiple binding sites of target RNAs. (elsevierpure.com)

Here, we reconstitute accelerated and selective deadenylation of RNAs containing AU-rich elements (AREs) and Pumilio-response elements (PREs). (elifesciences.org)

Several studies demonstrate important associations between differential expression of micro-RNAs (miRs) and the prognosis of CRC. (biorxiv.org)

Because these flies are so small, we also extracted DNA and RNA of whatever organisms were living inside of sampled individuals. (lu.se)

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