Rna binding protein immunoprecipitation. Medical search. Frequent questions

The Imprint Ultra Chromatin IP Kit is Sigma′s second generation chromatin immunoprecipitation (ChIP) kit developed for maximum sensitivity and optimum next-generation sequencing results. (sigmaaldrich.com)
It provides a complete solution for Chromatin Immunoprecipitation, including columns and reagents for DNA purification. (sigmaaldrich.com)
It is optimized for ChIP reactions with chromatin from 10 6 cells (up to ~50 μg DNA), and can also be scaled up (or several preparations pooled) to accommodate 10 8 cells for genome-wide binding studies in ChIP-chip and ChIP-Seq applications. (sigmaaldrich.com)
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)
Using RNA chromatin immunoprecipitation assays (ChIPs), in which specific pieces of RNA are isolated from bound proteins, the team discovered that TERRA is bound by telomeric proteins indicating that TERRA was a component of the Shelterin complex. (news-medical.net)
instead, they combined RNA-DNA proximity ligation ( Red-C ) with chromatin immunoprecipitation (ChIP) to create RedChIP, which identifies RNAs associated with a DNA-bound protein of interest. (epigenie.com)
Recently, an international team of scientists from the United States, China, and Canada collaborated on an ENCODE project to survey RNA-binding proteins on the chromatin regions of the human genome. (abclonal.com)
The researchers used chromatin immunoprecipitation and RNA-sequencing methods to identify binding regions and to quantify the effects of RBPs on transcription output. (abclonal.com)
With ChiP sequencing, the scientists found that RNA-binding proteins were in fact predominantly (~60%) localized on active chromatin regions. (abclonal.com)
In particular, all chromatin-associated RBPs had preference for binding to active gene promot ers, hinting at their potential involvement in transcription as previously hypothesized. (abclonal.com)

CLIP can be used either with antibodies against endogenous proteins, or with common peptide tags (including FLAG, V5, HA, and others) or affinity purification, which enables the possibility of profiling model organisms or RBPs otherwise lacking suitable antibodies. (wikipedia.org)
PAR-CLIP (photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation) is also used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). (wikipedia.org)
Irradiation of the cells by UV light of 365 nm induces efficient cross-linking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. (wikipedia.org)
PAR-CLIP has been employed to determine the transcriptome-wide binding sites of several known RBPs and microRNA-containing ribonucleoprotein complexes at high resolution. (wikipedia.org)
Mutations in many genes encoding RNA-binding proteins (RBPs) cause neurologic diseases, and especially the amyotrophic lateral sclerosis (ALS). (canal-u.tv)
Since RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression precise knowledge of their binding sites is critical for determining their molecular function and for understanding their roles in cell development and disease. (biosyn.com)
LINC01305 interacts with KHSRP in CC. ( A ) Prediction of RNA-binding proteins (RBPs) of LINC01305. (aging-us.com)
To identify novel ITSN1 and ITSN2 partners among RNA-binding proteins (RBPs) involved in regulation of mRNA processing. (nbuv.gov.ua)
Throughout Drosophila oogenesis, the localization and translational regulation of maternal transcripts depends on RNA-binding proteins (RBPs). (fondamental.org)
Utilizing immunoprecipitation from entire Drosophila ovaries coupled to mass spectrometry, we examined protein-protein associations of 6 GFP-tagged RBPs. (fondamental.org)
Lately, RNA-binding proteins have garnered renewed attention from scientists as recent proteome-wide studies revealed that there is over double the amount of RBPs than previously thought. (abclonal.com)
In light of these findings, researchers have become curious about other functions RBPs might have besides their roles in RNA metabolism. (abclonal.com)
To narrow down the list of RBPs, the team started with proteins localized in the nuclei of two human cell lines, HepG2 and K562. (abclonal.com)
Knowckdown of individual RBPs showed that six RBPs (RBM22, XRCC5, RBM25, HNRNPK, HNRNPLL, and U2AF1) had considerable direct impacts on output, as measured by RNA-seq. (abclonal.com)

Cross-linking and immunoprecipitation (CLIP, or CLIP-seq) is a method used in molecular biology that combines UV crosslinking with immunoprecipitation in order to identify RNA binding sites of proteins on a transcriptome-wide scale, thereby increasing our understanding of post-transcriptional regulatory networks. (wikipedia.org)
HITS-CLIP combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. (wikipedia.org)
Our detailed protocol and tips for carrying out UV cross-linking and immunoprecipitation (CLIP). (abcam.com)

CLIP was originally undertaken to study interactions between the neuron-specific RNA-binding protein and splicing factors NOVA1 and NOVA2 in the mouse brain, identifying RNA binding sites that contained the expected Nova-binding motifs. (wikipedia.org)
RNA-protein interactions are central to biological regulation. (nih.gov)
Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
To understand how these mutations act, we developed crosslinking and Immunoprecipitation (CLIP) to obtain transcriptome-wide maps of in vivo protein-RNA interactions. (canal-u.tv)
The Wistar team demonstrated how TERRA mediates and partially stabilizes interactions between telomeric proteins that play essential roles in DNA replication. (news-medical.net)
Now, "RedChIP" has us stampeding in anticipation towards the exploration of the complex interactions taking place between RNA, DNA, and proteins in the nucleus. (epigenie.com)
While RNA-DNA proximity ligation techniques map genome-wide ncRNA interactions , they don´t describe the proteins involved. (epigenie.com)
As a parallel to HiChIP , which takes a protein-centric view of mapping DNA-DNA interactions , RedChIP evaluates RNA-DNA interactions occurring with a given protein. (epigenie.com)
Finally, RNA-DNA sequencing reports on RNA-DNA interactions mediated by the protein and protein-DNA interactions mediated by RNAs. (epigenie.com)
Indeed, the identification of Kcnq1ot1, which targets Polycomb complexes to repressed genomic domains, and the significant overlap of ncRNAs isolated via a conventional technique suggest that RedChIP represents the way forward for studies of RNA-protein-DNA interactions in live cells. (epigenie.com)
The characterization of RNA and RNA interactions is closely related to transcription, for example, gene expression levels are investigated within a biological context. (biosyn.com)
Over the last decades, a variety of RNA methods have been developed for the study of RNA-DNA, RNA-RNA, and RNA-protein interactions including RNA complexes with ligand molecules. (biosyn.com)
The mapping of RNA-protein or RNA-RNA interactions by protein pull-down or affinity pull-down methods allow studying RNA structures, as well as RNA-protein, and RNA-RNA interactions. (biosyn.com)
However, the task of predicting these interactions given a protein structure is difficult. (edu.sa)
Our data show that the distinct protein interactions of these highly homologous translation factor paralogs shape protein synthesis during mTORC1 inhibition and provide a unique example of the repressive role of a universal translation activator. (biorxiv.org)
A luciferase reporter assay, RNA immunoprecipitation (RIP), RNA pulldown assays and fluorescence in situ hybridization were performed to identify the interactions among circIGF2BP3, miR-328-3p, miR-3173-5p and plakophilin 3 (PKP3). (biomedcentral.com)
Interest in RNA-protein interactions is booming as we begin to appreciate the role of RNA, not just in well-established processes such as transcription, splicing, and translation, but also in newer fields such as RNA interference and gene regulation by non-coding RNAs. (abcam.com)
CLIP is an antibody-based technique used to study RNA-protein interactions related to RNA immunoprecipitation (RIP) but differs from RIP in the use of UV radiation to cross-link RNA-binding proteins to the RNA that they are bound to. (abcam.com)
2011. "iCLIP -Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution. (abcam.com)
2014. "iCLIP: Protein-RNA interactions at nucleotide resolution. (abcam.com)

The effects of PTX-induced exosomal circBACH1 on BC cell function were assessed using RNA Binding Protein Immunoprecipitation (RIP), dual luciferase reporter gene, tube formation, CCK-8, and Western Blot assays. (biomedcentral.com)
Protein translation assays using both N2A and ALS patient fibroblasts demonstrated suppression of protein biosynthesis in mutant FUS expressing cells. (uky.edu)
The molecular mechanism of PKP3-induced PD-L1 upregulation was explored by immunoprecipitation, RIP, and ubiquitination assays. (biomedcentral.com)

The kit allows researchers to explore the genome-wide binding sites of low abundance transcription factors (TFs), as well as novel histone modifications. (sigmaaldrich.com)
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)
Further, we developed a pipeline to characterise novel genome-wide endogenous short interfering RNAs (endo-siRNAs). (uni-frankfurt.de)

CLIP analysis of the RNA-binding protein Argonaute led to identification of microRNA targets by decoding microRNA-mRNA and protein-RNA interaction maps in the mouse brain and subsequently in budding yeast (Saccharomyces cerevisiae), Caenorhabditis elegans, embryonic stem cells and tissue culture cells. (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 more mRNA copies it makes, the more protein it can produce. (elifesciences.org)
A simple way to control protein production is to raise or lower the number of these mRNA messages, and living cells have lots of ways to make this happen. (elifesciences.org)
Here we report a class of mRNA granules in human neuronal processes that are enriched in the nuclear cap-binding protein complex (CBC) and exon junction complex (EJC) core components, Y14 and eIF4AIII. (frontiersin.org)
Here we demonstrate that the epitope-tagged RNA binding protein, PABP, expressed separately in tumor cells and endothelial cells can be used to discriminate their respective mRNA targets from mixtures of these cells without significant mRNA reassortment or exchange. (biomedcentral.com)
RNA-binding proteins can be used as reporters to elucidate components of operational mRNA networks and operons involved in regulating cell-type specific gene expression in tissues and tumors. (biomedcentral.com)
Here we demonstrate that RNA-binding proteins can be used to isolate mRNA populations representing total cell mRNA from specific types of cells, as well as discrete mRNA subpopulations that represent post-transcriptionally regulated subsets of mRNAs that encode functionally related proteins. (biomedcentral.com)
Our lab has devised biochemical and immunological approaches to gene expression profiling by using RNA-binding proteins as reporters of discrete mRNA subsets in metazoan cells [ 8 - 10 ]. (biomedcentral.com)
While we and other labs have demonstrated the isolation of mRNA subsets that are potentially co-regulated using RNA binding proteins as reporters of gene expression, methods have not been described that provide information about coordinated posttranscriptional regulation within specific types of cells during tumorigenesis and development. (biomedcentral.com)
Moreover, because many different mRNA-binding proteins in specific cell types are known to interact with unique subpopulations of mRNAs encoding functionally related proteins [ 9 - 15 ] they can be informative of the dynamic effects of cells on one another. (biomedcentral.com)
UCK2 promoted cell cycle progression of HCC by preventing the degradation of mTOR protein and maintaining the stability of PDPK1 mRNA. (biomedcentral.com)
Its research objects include mRNA and non-coding RNA. (nkygroup.cn)
The biological system is complex with many regulatory features such as DNA, mRNA, proteins, metabolites, and epigenetic features such as DNA methylation and histone post-translational modifications (PTMs). (rsc.org)
Furthermore, PKP3 engages with the RNA-binding protein FXR1 to stabilize OTUB1 mRNA, and OTUB1 elevates PD-L1 abundance by facilitating its deubiquitination. (biomedcentral.com)

RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
Together these proteins shorten the end of the mRNAs, preparing the molecules for degradation. (elifesciences.org)
The test-tube system confirmed previous suggestions that a protein called Puf3 forms a bridge between Ccr4-Not and mRNAs. (elifesciences.org)
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)
During vesiculation, nucleic acids, including mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs or miRs) are encapsulated within EVs and when released, they are protected from degrading enzymes ( 8 - 10 ). (spandidos-publications.com)
In the glioma cells, EIF5B promotes cell survival by enhancing the translation of several IRES-containing mRNAs including those encoding anti-apoptotic proteins such as XIAP and Bcl-xL [ 4 ]. (techscience.com)
Heterogeneous population of RNA granules serve as motile units to translocate, store, translate, and degrade mRNAs in the dendrites contain cis -elements and trans -acting factors such as RNA-binding proteins and microRNAs to convey stimulus-, transcript-specific local translation. (frontiersin.org)
The existence of mRNAs retaining both nuclear cap binding protein and EJC in the distal sites of neuronal processes suggests that some localized mRNAs have not yet undergone the "very first translation," which contribute to the spatio-temporal regulation of gene expression. (frontiersin.org)
Through this interaction, mRNAs and their associative proteins form messenger ribonucleoprotein particles (mRNPs) that are actively transported along the cytoskeleton to intracellular destinations. (frontiersin.org)
For example, we identified subpopulations of mRNAs that are associated with ELAV/Hu RNA-binding proteins that are expressed in specific cell types [ 10 ]. (biomedcentral.com)
In this study, we define a model system for using poly (A) binding protein (PABP) to recover mRNAs from specific cell-types in mixed cell cultures. (biomedcentral.com)
RNA-immunoprecipitation sequencing (RIP-Seq) of the two eIF4A paralogs revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTOR inhibition. (biorxiv.org)

Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)

Their interaction with FUS varied greatly in their requirements for RNA. (uky.edu)
RNA molecules in solution may adopt secondary structures that are only partially determined by thermodynamics since RNA molecules can undergo conformational changes during interaction with other RNAs, RNA binding proteins or RNA binding peptides. (biosyn.com)
Protein-RNA interaction plays important roles in post-transcriptional regulation. (edu.sa)
On a diverse set of challenging RNA-binding proteins, including Fem-3-binding-factor 2, Argonaute 2 and Ribonuclease III, NucleicNet can accurately recover interaction modes discovered by structural biology experiments. (edu.sa)
This biased interaction depends on a La-related RNA-binding protein, LARP1. (biorxiv.org)
B ) RNA pull-down for interaction between LINC01305 and KHSRP. (aging-us.com)

it has been reported that 4-SU inhibits ribosomal RNA synthesis, induces a nucleolar stress response, and reduces cell proliferation. (wikipedia.org)
To understand how protein synthesis is suppressed by mutant FUS mediated defects in RNA metabolism, we examined changes in a well conserved RNA turnover pathway namely: nonsense mediated decay (NMD). (uky.edu)

Long noncoding RNAs (lncRNAs), due to their multifunction in various biological processes, have been indicated to play a crucial role in CSC renewal and stemness maintenance. (nature.com)
The RIP-seq result showed 14 lncRNAs that bound to the NF-κB p65 protein in RM. (biomedcentral.com)
Long non-coding RNAs (lncRNAs) are characterized as untranslated RNAs greater than 200 nt in length[ 10 ]. (biomedcentral.com)
In this study, we screened for lncRNAs directly binding to NF-κΒ p65 in microglia, and selected one lncRNA (Tug1) for in vitro validation. (biomedcentral.com)

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)
Furthermore, we show that, without seeing any in vitro or in vivo assay data, NucleicNet can still achieve consistency with experiments, including RNAcompete, Immunoprecipitation Assay, and siRNA Knockdown Benchmark. (edu.sa)
C ) RNA immunoprecipitation assay. (aging-us.com)

This process is carried out by the human spliceosome machinery, in which over 300 proteins sequentially assemble with uridine-rich small nuclear RNA molecules (U snRNAs) to form distinct small nuclear ribonucleoprotein complexes (snRNPs). (biomedcentral.com)
RNA molecules are functionally diverse and involved in many cellular processes such as catalysis, ligand binding, and protein recognition. (biosyn.com)
RNA molecules are structural flexible and can adopt different structures. (biosyn.com)
RNAs are single-stranded molecules and the unlinked monomer building blocks are known as nucleotides. (biosyn.com)
RNA molecules are generally folded into compact and defined tertiary structures. (biosyn.com)
In particular, CLIP has been used to identify targets of microRNAs, small non-coding RNA molecules that bind to a protein Ago2 and thus regulate gene expression post-transcriptionally. (princeton.edu)

In the majority of cases, Rf genes produce proteins that act directly on the CMS conferring mitochondrial transcripts by binding them specifically and promoting processing events. (frontiersin.org)
In the majority of cases, Rf genes produce proteins that bind specifically to the CMS conferring transcripts in the mitochondria and promote processing events leading to a strong reduction in the production of mitochondrial CMS-inducing proteins (reviewed in Chen and Liu, 2014 ). (frontiersin.org)
The transcriptomic and epigenomic regulatory landscape of the MAC genome, which has 80% protein-coding genes and short intergenic regions, is poorly understood. (uni-frankfurt.de)
The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. (rsc.org)
In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)

In order to allow for priming of reverse transcription, RNA adapters are ligated to the 3' ends, and RNA fragments are labelled to enable the analysis of the RNA-protein complexes after they have been separated from free RNA using gel electrophoresis and membrane transfer. (wikipedia.org)
Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
A wide variety of interacting proteins were identified and they are involved in a multitude of pathways including: chromosomal organization, transcription, RNA splicing, RNA transport, localized translation, and stress response. (uky.edu)
In the ENCODE study published in Cell , the team of scientists wanted to explore the potential for RBP involvement in transcriptional activities due to the fact that many RNA-processing events are tightly coupled with transcription. (abclonal.com)
A sample of the patient's deep throat saliva tested positive for SARS-CoV-2 RNA by reverse transcription PCR (RT-PCR). (cdc.gov)

Head-to-head comparison of available commercial antibodies against RNA-binding protein TIA1 by immunoblot (Western blot), immunoprecipitation and immunofluorescence. (openaire.eu)
Within 30 days after infection, most persons with SARS-CoV-2 begin producing antibodies against the spike and N proteins of the virus ( 3 , 4 ). (cdc.gov)

A team of researchers from The Wistar Institute have shown that a large non-coding RNA in mammals and yeast plays a central role in helping maintain telomeres, the tips of chromosomes that contain important genetic information and help regulate cell division. (news-medical.net)
circRNAs can interact with miRNAs and thereby regulate miRNA-targeted gene expression by competitively binding to miRNA response elements [ 12 ]. (biomedcentral.com)

FUS performs a diverse set of cellular functions, including being a major regulator of RNA metabolism. (uky.edu)

It has been previously shown that rbf1 pro-apoptotic activity depends on its ability to decrease the level of anti-apoptotic proteins such as the Bcl-2 family protein Buffy. (sdbonline.org)

Polyclonal antibody raised in rabbit against the Cas9 nuclease (CRISPR-associated protein 9) using a recombinant protein. (diagenode.com)
Monoclonal antibody raised in mouse against the N-terminus of the Cas9 nuclease (CRISPR-associated protein 9) using a recombinant protein. (diagenode.com)
Alternative name: Csn1 Monoclonal antibody raised in mouse against the N-terminus of the Cas9 nuclease (CRISPR-associated protein 9) using a recom. (diagenode.com)
Polyclonal antibody raised in rabbit against Lachnospiraceae bacterium (Lb) Cpf1 (CRISPR from Prevotella and Francisella 1) using a recombinant protein. (diagenode.com)
Polyclonal antibody raised in rabbit against the C-terminus of the S. aureus Cas9 nuclease (CRISPR-associated protein 9) using a recombinant protein. (diagenode.com)
Polyclonal antibody raised in rabbit against CEBP Alpha (CCAAT/enhancer binding protein (C/EBP), alpha), using a KLH-conjugated synthetic peptide. (diagenode.com)
Polyclonal antibody raised in rabbit against human CHD1 (Chromodomain Helicase DNA Binding Protein 1), using a synthetic peptide containing a sequence from t. (diagenode.com)
then, a specific antibody immunoprecipitates protein-associated RNA-DNA complexes. (epigenie.com)

Non-coding RNAs (ncRNAs) are enriched in exosomes, which participated in generation, progression, and resistance of BC. (biomedcentral.com)

What pathways are this gene/protein implicaed in? (cancerindex.org)
Further pathway and disease association analysis suggested that proteins associated with translation and RNA quality control pathways may be the most significant. (uky.edu)
We found that NMD is hyperactivated in cells expressing mutant FUS, likely due to chronic suppression of protein translation shifting the pathways autoregulatory circuit to allow for hyperactivation. (uky.edu)
Recent multi-omics studies have revealed the heterogeneity and complexity of tumor features such as their genetic mutations, transcriptome, proteins, and signaling pathways. (rsc.org)
We previously showed that Musashi-2 (MSI2) RNA-binding protein is associated with NSCLC progression by regulating several signaling pathways relevant to NSCLC. (researchgate.net)

Employs DNA-Blocked 'Staph-Seq' for IP (immunoprecipitation), minimizing contaminating Staph A DNA in downstream ChIP-Seq applications. (sigmaaldrich.com)

CLIP begins with the in-vivo cross-linking of RNA-protein complexes using ultraviolet light (UV). (wikipedia.org)
2021). I'll also discuss how insights into the specificity of RBP condensation open new doors for understanding of protein-RNA complexes as mediators of signalling, disease and evolution. (canal-u.tv)

The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. (wikipedia.org)
Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.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)

Upon UV exposure, covalent bonds are formed between proteins and nucleic acids that are in close proximity (on the order of Angstroms apart). (wikipedia.org)
Exosomes are extracellular micro-vesicles containing various proteins and nucleic acids, which play roles in transporting information and substance among cells [ 16 , 17 ]. (biomedcentral.com)

In cell cultures, through RNA affinity purification, a process that isolates a single type of protein from a complex mixture, the team identified telomeric proteins (Shelterin components TRF1 and TRF2, and origin recognition complex subunits ORC1, ORC2, and ORC4) that bound to a TERRA oligonucleotide sequence but not to control oligonucleotides. (news-medical.net)
In this first study, we utilized immunoprecipitation of wild-type and mutant FUS in the presence and absence of RNase, followed by LC MS/MS. The identified proteins represent those that directly or indirectly interact with FUS, with relatively high affinity that can be pulled down with immunoprecipitation. (uky.edu)

In a study published on-line on August 27 in Molecular Cell, the Wistar scientists, led by Lieberman, describe how they discovered the telomere proteins that interact with TERRA and the processes by which they do so. (news-medical.net)
The protein has been shown to interact with retinoid and thyroid hormone receptors, inhibiting their ligand-dependent transcriptional activation. (cancerindex.org)

EVs released from HLSCs were enriched with miRNAs and expressed Alix and several RNA-binding proteins, including Argonaute 2 (Ago2), a member of the Argonaute family known to be involved in the transport and the processing of miRNAs. (spandidos-publications.com)

We developed a generic automated eukaryotic short interfering RNA (siRNA) analysis tool, called RAPID. (uni-frankfurt.de)
Eukaryotic translation initiation factor (eIF) 4A - a DEAD-box RNA-binding protein - plays an essential role in translation initiation. (biorxiv.org)

Aliotta et al ( 15 ) demonstrated that lung-derived vesicles carried RNA to marrow cells and altered the phenotype of these cells both genetically and functionally. (spandidos-publications.com)

Since this RNA also facilitates the formation of DNA at telomeres-a process that can protect aging cells and destabilize tumor cells-manipulating its expression may be useful in treating cancer and other diseases. (news-medical.net)
Vascular endothelial growth factor receptor-2 (VEGFR2) is a member of the VEGF family of receptor tyrosine kinase proteins, which are expressed on both endothelial and tumor cells, are one of the key proteins contributing to cancer development, and are involved in drug resistance. (researchgate.net)

Bioinformatic algorithms allowing predicting of biomolecular folding for proteins, peptides, and RNAs, even though sometimes successful, have all their limitations. (biosyn.com)

Circular RNAs (circRNAs) have been implicated in cancer progression. (biomedcentral.com)

Studies suggest that the protein represses nuclear hormone receptor-mediated transactivation via two separate steps: competition with coactivators and the direct effects of its transcriptional repressor function. (cancerindex.org)
Specific tertiary structure types are observed for transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), certain introns, and ribozymes. (biosyn.com)

CLIP enabled us to disentangle the principles driving the condensation of TDP-43 on cellular RNAs, which showed that the IDR selectively fine-tunes the RNA binding properties and functions of the protein (Hallegger et al. (canal-u.tv)
Neurons are cells with a complex morphology, which maintain their cellular structure through the compartmentalized expression of proteins essential for growth and plasticity. (canal-u.tv)
Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5′ splice sites. (biomedcentral.com)
Mitochondrial porin , also known as the voltage-dependent anion channel (VDAC), is a multi-functional channel protein that shuttles metabolites between the mitochondria and the cytosol and implicated in cellular life and death decisions. (sdbonline.org)

These models are being used to systematically elucidate proteins required for cutaneous carcinogenesis and to test their potential role as therapeutic targets. (stanford.edu)

The combination of different biochemical methods with computational modelling allows scientists to gain insight into molecular processes in which RNA is involved. (biosyn.com)
In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. (rsc.org)
Cross-linking immunoprecipitation followed by sequencing (CLIP-seq) is a family of methods for profiling sites of protein binding to RNA. (princeton.edu)

Bioinformatics analysis demonstrated that the EIF5B transcript and protein levels as well as the EIF5Bcopy number were significantly higher in the HCC tissues compared with the non-cancerous liver tissues. (techscience.com)

We concluded that mutant FUS suppresses protein biosynthesis and disrupts NMD regulation. (uky.edu)

Here, we review the literature that highlights those characteristics and help explain why PPR proteins are ideal for the roles they play as restorers of fertility. (frontiersin.org)
RNA transport and regulated local translation play critically important roles in spatially restricting gene expression in neurons. (frontiersin.org)

NucleicNet can thus serve to provide quantitative fitness of RNA sequences for given binding pockets or to predict potential binding pockets and binding RNAs for previously unknown RNA binding proteins. (edu.sa)

Overall, the authors see RedChIP as a straightforward and accurate means of identifying RNAs associated with genomic regions occupied by a protein of interest. (epigenie.com)

Evidence indicates that Alix, an accessory protein of the endosomal sorting complex required for transport (ESCRT), is involved in the biogenesis of extracellular vesicles (EVs). (spandidos-publications.com)
The horizontal transfer of extracellular RNAs carried by EVs has been shown to be able to reprogram hematopoietic progenitors ( 11 ) and to activate endothelial cells ( 12 ). (spandidos-publications.com)

Co-immunoprecipitation experiments revealed an association between Alix and Ago2. (spandidos-publications.com)

Recently, immune checkpoint blockade therapies (ICBs) blocking programmed cell death protein 1 (PD-1) and its ligand (PD-L1) have shown tremendous benefit for the treatment of advanced NSCLC [ 4 ]. (biomedcentral.com)

Our tool captures diverse siRNA characteristics from small RNA sequencing data and provides easily navigable visualisations. (uni-frankfurt.de)

The isolated RNA is converted into a cDNA library and deep sequenced using high-throughput sequencing technology. (wikipedia.org)

FUS undergoes liquid- liquid phase transition in vitro , allowing for its participation in stress granules and RNA transport granules. (uky.edu)

These results provide a mechanism by which Drosophila Bcl-2 family proteins can control apoptosis and shed light on a link between Rbf1 and mitochondrial dynamics, in vivo. (sdbonline.org)

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)

Our findings indicate that Alix binds to Ago2 and miRNAs, suggesting that it plays a key role in miRNA enrichment during EV biogenesis. (spandidos-publications.com)

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)

Proteinase K digestion is then performed in order to remove protein from the crosslinked RNA, which leaves a few amino acids at the crosslink site. (wikipedia.org)

The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. (abclonal.com)

Both proteins can localize at the mitochondrion , but the way they control apoptosis still remains unclear. (sdbonline.org)

Anatomy18

Organisms18

Chemicals and Drugs116

Analytical, Diagnostic and Therapeutic Techniques and Equipment31

Phenomena and Processes75

Disciplines and Occupations1

Information Science4

Health Care1

Chromatin10

RBPs14

Cross-linking and immunopreci3

Interactions20

Assays3

Genome-wide3

MRNA15

MRNAs12

Motifs1

Interaction6

Synthesis2

LncRNAs4

Assay3

Molecules6

Genes5

Transcription5

Antibodies2

Regulate2

Metabolism1

Anti-apoptotic proteins1

Antibody8

NcRNAs1

Pathways5

ChIP1

Complexes2

Transcripts2

Mediators1

Nucleic2

Affinity2

Interact2

Argonaute1

Eukaryotic2

Functionally1

Tumor cells2

Peptides1

Progression1

Nuclear2

Cellular4

Targets1

Methods3

Bioinformatics1

Regulation1

Roles2

Sequences1

Genomic1

Extracellular2

Experiments1

NSCLC1

SiRNA1

CDNA library1

Granules1

Vivo1

Viral1

MiRNAs1

Mechanisms1

Amino acids1

Encode1

Localize1