GenePolymeraseRibosomalSingle-strandedMoleculesMRNAChromatinGenesMessenger RNAPost-transcriptionalBiologyTranscriptsRRNADecayBiogenesisNascent transcriptionEukaryotesSequencesProteinsRibozymeLocalizationStrandsMoleculeCatalyticMaturationMechanismTranscriptionSmallTranscriptionalAbundanceSynthesisMammalsBiochemicalExonsPopulationsViralResearchersTranscriptomeSiRNAStableHumanHumansEssentialPresent
Gene22
- Here we present a computational approach called exon-intron split analysis (EISA) that measures changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. (nature.com)
- A recently discovered dimension of post-transcriptional gene regulation involves co-regulatory crosstalk between RNA transcripts, which compete for common pools of microRNA (miRNA) molecules. (biomedcentral.com)
- lncRNA HOX transcript antisense RNA (HOTAIR) represses gene expression through recruitment of chromatin modifiers. (biomedcentral.com)
- In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. (wikipedia.org)
- mRNA is created during the process of transcription, where an enzyme (RNA polymerase) converts the gene into primary transcript mRNA (also known as pre-mRNA). (wikipedia.org)
- During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. (wikipedia.org)
- Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
- Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
- Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. (mdpi.com)
- Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression. (scilifelab.se)
- Here, we explore the role of RNA stability in achieving balanced gene expression and present genome-wide RNA stabilities in Drosophila melanogaster male and female cells as well as male cells depleted of proteins essential for dosage compensation. (scilifelab.se)
- We identify two distinct RNA-stability mediated responses involved in regulation of gene expression. (scilifelab.se)
- The first of these responds to acute and global changes in transcription and thus counteracts potentially harmful gene mis-expression by shifting the RNA stability in the direction opposite to the transcriptional change. (scilifelab.se)
- The second response enhances inter-individual differential gene expression by adjusting the RNA stability in the same direction as a transcriptional change. (scilifelab.se)
- Mechanically, m6A can be recognized by "reader" proteins or can directly modify RNA conformation, and it widely affects gene expression by mediating RNA stability, translation, splicing and export. (scienceopen.com)
- Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression. (scienceopen.com)
- Nanowerk News ) A team of researchers and clinicians from UCLA's Jonsson Comprehensive Cancer Center and the California Institute of Technology (Caltech) has published the first proof that a targeted nanoparticle-used as an experimental therapeutic and injected directly into a patient's bloodstream-can navigate into tumors, deliver double-stranded small interfering RNAs (siRNAs) and turn off an important cancer gene. (nanowerk.com)
- This includes, 1) how small RNAs regulate gene expression in the male germline to support spermatogenesis and fertility, 2) how small RNAs are packaged into mature sperm, 3) how RNAs transmitted during fertilization are able to regulate early embryonic gene expression and development, and 4) how this regulation can alter developmental programs to produce a non-genetically inherited phenotype. (upenn.edu)
- In the Yildirim lab, we study how epigenetic mechanisms, particularly those that are mediated by long noncoding RNAs (ncRNAs), complement gene expression, impact genome stability and define cell fate decisions. (duke.edu)
- Our laboratory uses primarily XCI as a model to understand how long ncRNAs 1) regulate gene dosage and maintain epigenetic state, 2) impact genome stability, and 3) participate in cell fate decisions. (duke.edu)
- Gene silencing induced by small RNAs (sRNAs) is an important mechanism responsible for many crucial physiological responses in plants, such as genome integrity, defense against virus, adaptation to biotic and abiotic stresses and regulation of development. (edu.au)
- Using a small noncoding RNA, microRNA 211, and tools that track the stability and decay of the protein-coding and noncoding RNAs in lab-grown melanoma cells, a team led by a Johns Hopkins Kimmel Cancer Center researcher identified highly unstable RNA molecules in human melanomas , including a novel miR-211 target gene DUSP3. (news-medical.net)
Polymerase6
- One notable difference is that prokaryotic RNA polymerase associates with DNA-processing enzymes during transcription so that processing can proceed during transcription. (wikipedia.org)
- Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. (wikipedia.org)
- Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. (nature.com)
- 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
- After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)
- We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. (elifesciences.org)
Ribosomal4
- In general, these protocols aim to enrich for mature mRNA by selection of polyadenylated RNA or by depletion of ribosomal RNA. (nature.com)
- The translation of codons into amino acids requires two other types of RNA: transfer RNA, which recognizes the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), the central component of the ribosome's protein-manufacturing machinery. (wikipedia.org)
- Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. (nature.com)
- DEAD-box helicase DDX27 regulates 3' end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex. (nih.gov)
Single-stranded3
- PIWI-interacting RNAs (piRNAs) are a large family of small, single-stranded, non-coding RNAs present throughout the animal kingdom. (biomedcentral.com)
- 2004. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. (invivogen.com)
- 2004. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. (invivogen.com)
Molecules3
- RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
- More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
- Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. (mdpi.com)
MRNA8
- RNA-seq experiments generate reads derived not only from mature RNA transcripts but also from pre-mRNA. (nature.com)
- Mature mRNA is then read by the ribosome, and, utilising amino acids carried by transfer RNA (tRNA), the ribosome creates the protein. (wikipedia.org)
- The extensive processing of eukaryotic pre-mRNA that leads to the mature mRNA is the RNA splicing, a mechanism by which introns or outrons (non-coding regions) are removed and exons (coding regions) are joined. (wikipedia.org)
- RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
- A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
- The C-terminal domain of YTHDF2 selectively binds to m6A-containing mRNA whereas the N-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. (scienceopen.com)
- In contrast, RNA interference targets the messenger RNA (mRNA), which encodes the information needed to make a protein. (nanowerk.com)
- It's the first time anyone has found an RNA fragment from a patient's cells showing the mRNA was cut at exactly the right base via the RNAi mechanism," Davis said. (nanowerk.com)
Chromatin1
- Noncoding RNAs (ncRNAs) are noncoding transcripts that take part in epigenetic mechanisms by providing RNA-directed silencing, aiding recruitment of chromatin modifying complexes and in some instances, presenting enhancer-like functions to boost transcription. (duke.edu)
Genes4
- Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
- We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
- The discovery of RNA interference, the mechanism by which double strands of RNA silence genes, won researchers Andrew Fire and Craig Mello the 2006 Nobel Prize in Physiology or Medicine. (nanowerk.com)
- Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. (mpg.de)
Messenger RNA3
- A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m7G cap) is a modified guanine nucleotide that has been added to the "front" or 5' end of a eukaryotic messenger RNA shortly after the start of transcription. (wikipedia.org)
- Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. (wikipedia.org)
- Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. (scienceopen.com)
Post-transcriptional1
- EISA reveals both transcriptional and post-transcriptional contributions to expression changes, increasing the amount of information that can be gained from RNA-seq data sets. (nature.com)
Biology4
- They reported their findings June 16 in RNA Biology online. (news-medical.net)
- This sledgehammer method, however, is considered toxic, and can alter other aspects of a cell's biology in ways that may obscure transcript stability information. (news-medical.net)
- Cutting-edge RNA technologies and computational methods fuel new discoveries, advancing the field of RNA biology across disciplines. (cuanschutz.edu)
- RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. (elifesciences.org)
Transcripts2
- Other researchers, Perera notes, have attempted to profile genomewide transcript stability by using chemicals that block all transcription, and then observing the stability of the transcripts that existed before blocking. (news-medical.net)
- To address this, Perera and colleagues used BRIC-seq, a method that tags transcripts with 5-Bromouridine, which is incorporated into newly synthesized RNAs and then can be immunocytochemically analyzed over time without disturbing the rest of the cellular environment. (news-medical.net)
RRNA1
- The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. (nature.com)
Decay3
- The steady state levels of RNAs, often referred to as expression levels, result from a well-balanced combination of RNA transcription and decay. (scilifelab.se)
- Alterations in RNA levels will therefore result from tight regulation of transcription rates, decay rates or both. (scilifelab.se)
- So we decided to look at a completely new angle of genomewide RNA stability and decay during the first steps in the development of melanoma. (news-medical.net)
Biogenesis2
- We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. (nature.com)
- Traditionally, the nucleolar Pol I and nucleoplasmic Pol III are viewed as the sole mammalian RNA polymerases that directly mediate housekeeping ribosome biogenesis. (nature.com)
Nascent transcription1
- 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)
Eukaryotes1
- N6-methyladenosine (m6A) is the most abundant inner RNA modification in eukaryotes. (scienceopen.com)
Sequences2
- Although RNA-seq mostly generates reads that map to exons, it also captures less abundant intronic sequences 6 . (nature.com)
- H1 sequences with fewer than three base-pairs fail to support full activity in vitro or in vivo, arguing against any significant difference in the stability of short RNA helices under in vitro and intracellular conditions. (umassmed.edu)
Proteins3
- However, some scientists think that before life adopted DNA and proteins, it relied primarily on RNA. (elifesciences.org)
- Yet, some RNA strands can also fold to form ribozymes, 3D structures that could have guided life's chemical processes the way proteins do now. (elifesciences.org)
- All life on Earth today uses a triplet RNA code to make proteins from DNA, and these experiments showed how RNA triplets might have helped RNA sustain early life forms. (elifesciences.org)
Ribozyme9
- We developed a quantitative assay of hairpin ribozyme cleavage activity in yeast to learn how structure-function relationships defined for RNA enzymes in vitro relate to RNA-mediated reactions in cells. (umassmed.edu)
- H1 is the base-paired helix formed between ribozyme and 3' cleavage product RNAs. (umassmed.edu)
- Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit '+' and '-' strands in segments and assemble them into a new active ribozyme. (elifesciences.org)
- This duplication is a chemical reaction that could be driven by an 'RNA replicase' ribozyme. (elifesciences.org)
- When RNA is copied, one strand acts as a template, and a replicase ribozyme would accurately guide which letters are added to the strand under construction. (elifesciences.org)
- Yet, although ribozymes can be made to copy straight RNA templates this way, folded RNA templates - including the replicase ribozyme itself - impede copying. (elifesciences.org)
- In this apparent paradox, a ribozyme needs to fold to copy RNA, but when folded, is itself copied poorly. (elifesciences.org)
- Biochemical techniques were used to engineer a ribozyme that copies RNA strands by adding letters not one-by-one, but three-by-three. (elifesciences.org)
- Using three-letter 'triplet' building blocks, this new ribozyme can copy various folded RNA strands, including the active part of its own sequence. (elifesciences.org)
Localization1
- TLR7 and TLR8 can recognize both self and viral RNA but seem able to distinguish the presence of viral RNA by detecting their abnormal localization in the endosome rather than a particular RNA motif. (invivogen.com)
Strands3
- Like DNA, strands of RNA contain genetic data. (elifesciences.org)
- RNA strands are made of four different letters attached to each other in a specific order. (elifesciences.org)
- For example, these triplets work together to bind tightly to RNA strands and unravel structures that block RNA copying. (elifesciences.org)
Molecule1
- For early life to be built on RNA, though, this molecule must have had the ability to make copies of itself. (elifesciences.org)
Catalytic2
- RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
- An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. (scienceopen.com)
Maturation1
- Cellular RNAs are regulated at multiple stages, including transcription, RNA maturation and degradation. (nature.com)
Mechanism1
- It proves that the RNA interference mechanism can happen using siRNA in a human. (nanowerk.com)
Transcription1
- Transcription is when RNA is copied from DNA. (wikipedia.org)
Small1
- The functions of small RNAs in fertility, inheritance, and development. (upenn.edu)
Transcriptional2
- We apply EISA to 17 diverse data sets to show that most intronic reads arise from nuclear RNA and changes in intronic read counts accurately predict changes in transcriptional activity. (nature.com)
- Three recent studies based on RNA-seq provided evidence that intronic reads might correlate with transcriptional activity. (nature.com)
Abundance1
- More recently, another group of researchers reported that they had developed a process for optimizing low- abundance RNA, by combining aRNA amplification with template- switching. (genomicglossaries.com)
Synthesis2
- Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease. (nature.com)
- The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. (elifesciences.org)
Mammals1
- Additionally, we show that, in contrast to mammals, modulation of RNA stability does not detectably contribute to dosage compensation of the sex-chromosomes in D. melanogaster. (scilifelab.se)
Biochemical1
- Long non-coding RNAs (lncRNAs) govern fundamental biochemical and cellular processes. (biomedcentral.com)
Exons1
- These are removed in the process of RNA splicing, leaving only exons, regions that will encode the protein. (wikipedia.org)
Populations1
- Researchers at Stanford University used such a method to produce amplified heterogeneous populations of RNA from limited quantities of cDNA. (genomicglossaries.com)
Viral1
- PolyU is a synthetic ssRNA which when complexed to cationic lipids can substitute for viral RNAs in inducing IFN-α production in plasmacytoid dendritic cells (pDC). (invivogen.com)
Researchers1
- In a melanoma cell line that normally lacks miR-211, the researchers introduced miR-211 expression and then used the BRIC-seq method to investigate transcriptome stability dynamics in the presence/absence of miR-211. (news-medical.net)
Transcriptome1
- Due to the development of RNA sequencing technology, the distribution pattern of m6A in the transcriptome has been uncovered. (scienceopen.com)
SiRNA1
- Increased siRNA duplex stability correlates with reduced off-target and elevated on-target effects. (mpg.de)
Stable1
- RNA is inherently less stable than DNA due to its chemical structure. (idtdna.com)
Human1
- Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. (scienceopen.com)
Humans1
- Still, there have been many potential roadblocks to applying RNA interference technology in humans. (nanowerk.com)
Essential2
- Here, we report the effects of variation in the stability of an essential secondary structure element, H1, on intracellular cleavage kinetics. (umassmed.edu)
- Silencing of transposable elements (TEs) is essential for maintaining genome stability. (edu.au)