Computational messenger rna localization of specific rnas. Medical search. Frequent questions

At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)
RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. (biomed.news)
Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. (biomed.news)
Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins. (biomed.news)

Cutting-edge RNA technologies and computational methods fuel new discoveries, advancing the field of RNA biology across disciplines. (cuanschutz.edu)
This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. (frontiersin.org)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
With the rapid development of computational biology and deep sequencing technology, more and more studies have shown that a large number of non-classical open reading frames that have not been annotated and hidden in non-coding RNA can encode functional micropeptide. (biomed.news)

miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. (cancerindex.org)
It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. (lookformedical.com)
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. (lookformedical.com)
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. (lookformedical.com)

Does a transcript get translated, stored, decayed or transported to a specific subcellular location? (biomedcentral.com)
Additionally, the 5′ and 3′ UTRs flanking the coding region regulate mRNA translation, half-life, and subcellular localization [2]. (researchgate.net)

N 6 -Methyladenosine (m 6 A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. (nature.com)
Puf3 allows Ccr4-Not to select specific mRNAs from a mixture of molecules. (elifesciences.org)
Researchers at the Children's Hospital of Philadelphia (CHOP) have created a flexible and affordable approach for targeted sequencing of full-length RNA molecules, which might hasten the development of novel diagnostics and therapies. (azolifesciences.com)

The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. (cancerindex.org)

microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. (cancerindex.org)

The RNA Technology and Bioinformatics Group within the RNA Bioscience Initiative develops new molecular and bioinformatic methods to analyze RNA sequence, diversity, nascent transcription, structure, and localization. (cuanschutz.edu)

This class of noncoding RNAs is small, single stranded, and 19-25 nucleotide long that act as negative regulators involved in posttranscriptional silencing of the gene expression [ 5 ]. (hindawi.com)

However, the bacterial extracellular RNA complement has so far not been comprehensively characterized. (uni.lu)
Here, we have analyzed, using a combination of physical characterization and high-throughput sequencing, the extracellular RNA complement of both outer membrane vesicle (OMV)-associated and OMV-free RNA of the enteric Gram-negative model bacterium Escherichia coli K-12 substrain MG1655 and have compared it to its intracellular RNA comple- ment. (uni.lu)
Our results demonstrate that a large part of the extracellular RNA com- plement is in the size range between 15 and 40 nucleotides and is derived from specific intracellular RNAs. (uni.lu)
Apart from rRNA fragments, a significant portion of the extracellular RNA complement is composed of specific cleavage products of functionally important structural noncoding RNAs, including tRNAs, 4.5S RNA, 6S RNA, and tmRNA. (uni.lu)
In addition, the extracellular RNA pool includes RNA biotypes from cryptic prophages, intergenic, and coding regions, of which some are so far uncharacterised, for example, transcripts mapping to the fimA- fimL and ves-spy intergenic regions. (uni.lu)
Our study provides the first detailed char- acterization of the extracellular RNA complement of the enteric model bacte- rium E. coli. (uni.lu)
Analogous to findings in eukaryotes, our results suggest the selective export of specific RNA biotypes by E. coli, which in turn indicates a potential role for extracellular bacterial RNAs in intercellular communication. (uni.lu)

ABSTRACT {Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. (giwebb.com)
Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. (salk.edu)
Little quantitative information exists as to either how many transcript copies of particular genes are m 6 A modified ('m 6 A levels') or the relationship of m 6 A modification(s) to alternative RNA isoforms. (nature.com)
New secondary mesenchyme specific genes, expressed exclusively in pigment cells, were isolated from sea urchin embryos using a differential screening of a macroarray cDNA library. (silverchair.com)
A better understanding of how these species cause disease and spread antibiotic resistance requires a knowledge of how its genes are controlled, on both the DNA and the RNA level. (frontiersin.org)

Furthermore, RNA is associated with OMVs and the relative abundances of RNA biotypes in the intracellular, OMV and OMV- free fractions are distinct. (uni.lu)

Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. (azolifesciences.com)

We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. (biomedcentral.com)

More importantly, we summarize the potential of various RNA-based therapeutics clinically available for cancer treatment. (biomedcentral.com)
RNA-dependent targeting of the TIME, as monotherapy or combined with other evolving therapeutics, might be beneficial for cancer patients' treatment in the near future. (biomedcentral.com)

TIME-related RNA or RNA regulators could be promising targets for anticancer immunotherapy. (biomedcentral.com)

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

In bacteria, promoters are recognized by RNA polymerases and associated sigma factors. (giwebb.com)
Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. (frontiersin.org)
As seen with many other bacteria, RNA-seq technology has now become the method of choice for transcriptome analysis in the enterococcus. (frontiersin.org)

Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. (salk.edu)
We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer's disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders. (salk.edu)
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. (lookformedical.com)

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)

To date, only a few predictors are available for identifying general bacterial promoters with limited predictive performance.In this study, we developed TIMER, a Siamese neural network-based approach for identifying both general and species-specific bacterial promoters. (giwebb.com)
Specifically, TIMER uses DNA sequences as the input and employs three Siamese neural networks with the attention layers to train and optimize the models for a total of 13 species-specific and general bacterial promoters. (giwebb.com)

Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. (mdpi.com)

Extensive 10-fold cross-validation and independent tests demonstrated that TIMER achieves a competitive performance and outperforms several existing methods on both general and species-specific promoter prediction. (giwebb.com)

have developed a new method to detect RNA viruses based on the triplex-forming probe technology. (azolifesciences.com)

Sequences of DNA or RNA that occur in multiple copies. (lookformedical.com)

Pan, T. N 6 -methyl-Adenosine modification in messenger and long non-coding RNA. (nature.com)

Advancements in RNA-based technology have improved understanding of the complexity and diversity of the TIME and its effects on therapy. (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)

N 6 -methyladenosine modulates messenger RNA translation efficiency. (nature.com)

This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains. (salk.edu)

Messenger RNA (mRNA) vaccines represent a relatively new vaccine class showing great promise for the future. (researchgate.net)

The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. (lookformedical.com)
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. (lookformedical.com)

Using CrossHub software, we analyzed RNA-Seq expression profile data of CRC derived from The Cancer Genome Atlas (TCGA) project. (biomedcentral.com)

Find support for a specific problem in the support section of our website. (mdpi.com)

In this review, we discuss the available RNA-based cancer immunotherapies targeting the TIME. (biomedcentral.com)

His work primarily focuses on a step in gene expression referred to as RNA splicing. (unibas.ch)

Anatomy29

Organisms20

Diseases1

Chemicals and Drugs95

Analytical, Diagnostic and Therapeutic Techniques and Equipment36

Psychiatry and Psychology1

Phenomena and Processes76

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science4

Proteins5

Biology4

Polymerase4

Subcellular2

Molecules3

MiRNA1

MRNAs1

Bioinformatics1

Single stranded1

Extracellular7

Genes5

Intracellular1

Nucleotides1

Motifs1

Therapeutics2

Targets1

Selective1

Bacteria3

Regulatory3

Protein1

Promoters2

Regulators1

Prediction1

Viruses1

Sequences1

Modification1

Technology1

Poly1

Translation1

Gene regulation1

Class1

Elements2

Software1

Support1

Review1

Expression1