SiRNAsGenomeMiRNAsSingle-strandedGeneEukaryoticDouble-strandedEukaryotesRNAiGenesCleavageBindsAgo2DistinctSmallTranslationComplexSystemsMiRNANcRNAsPost-transcriptionalSiRNANucleic acidsGene expressionMoleculesDsRNARegulatoryRegulationEndogenousInhibitNucleotidesInfectionReplicationProteinRolesTargetExpressionLongSingleReactionGuideEarlyHumanProcess
SiRNAs3
- It is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of approximately 21 to 23 nucleotide siRNAs. (wikipedia.org)
- It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. (biomedcentral.com)
- siRNAs are produced from double-stranded RNAs of viruses and transposable elements, which are processed by the dicer nuclease, one of the essential components of the RNA-Induced Silencing Complexes (RISCs) [ 7 - 9 ]. (biomedcentral.com)
Genome7
- When the dsRNA is exogenous (coming from infection by a virus with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by Dicer. (wikipedia.org)
- The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding genes in the genome. (wikipedia.org)
- These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
- As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). (biomedcentral.com)
- We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. (biomedcentral.com)
- This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. (biomedcentral.com)
- Small RNAs play important roles in many aspects of pre- and post-transcriptional gene regulation, epigenetic modifications, chromosome segregation and genome structure. (biomedcentral.com)
MiRNAs2
- A large number of studies have demonstrated that the synergistic collaboration of a number of microRNAs (miRNAs), their growth factors and their downstream agents is required for the initiation and completion of pathogenesis in the liver. (wjgnet.com)
- The first class of small RNAs identified were the micro RNAs (miRNAs), which are small (~22 nt) non-coding RNAs that regulate gene expression by base pairing to mRNAs where they direct either mRNA cleavage or repress translation [ 8 ]. (biomedcentral.com)
Single-stranded1
- Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger (sense) strand and the guide (antisense) strand. (wikipedia.org)
Gene7
- RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translational or transcriptional repression. (wikipedia.org)
- RNAi is an RNA-dependent gene silencing process that is controlled by RISC and is initiated by short double-stranded RNA molecules in a cell's cytoplasm, where they interact with the catalytic RISC component Argonaute. (wikipedia.org)
- Bioinformatics studies on the genomes of multiple organisms suggest this length maximizes target-gene specificity and minimizes non-specific effects. (wikipedia.org)
- There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)
- The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function. (biomedcentral.com)
- Consequently, the time of day when RNA samples are collected can influence detection of significant changes in gene expression levels. (gene-quantification.de)
- It is also important to consider that quantitation and comparison of gene expression levels across multiple chips requires appropriate normalization. (gene-quantification.de)
Eukaryotic3
- Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
- Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
- Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. (biomedcentral.com)
Double-stranded2
- Exogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer, which binds and cleaves dsRNAs in plants, or short hairpin RNAs (shRNAs) in humans, to produce double-stranded fragments of 20-25 base pairs with a 2-nucleotide overhang at the 3′ end. (wikipedia.org)
- R2D2 carries tandem double-stranded RNA-binding domains to recognize the thermodynamically stable terminus of siRNA duplexes, whereas Dicer-2 the other less stable extremity. (wikipedia.org)
Eukaryotes1
- The discovery of the elaborate and versatile systems of RNA silencing in eukaryotes is one of the pivotal advances in biology of the last decade [ 1 - 6 ]. (biomedcentral.com)
RNAi1
- Two types of small ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. (wikipedia.org)
Genes1
- An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. (biomedcentral.com)
Cleavage1
- Specifically, this is accomplished when the guide strand pairs with a complementary sequence in a mRNA molecule and induces cleavage by Ago2, a catalytic component of the RISC. (wikipedia.org)
Binds2
- The RISC assembly then binds and degrades the target mRNA. (wikipedia.org)
- The RISC-siRNA complex then binds to the target mRNA which is cleaved by the slicer nuclease, another crucial component of RISC, to release the RISC-siRNA which acts as a recyclable catalyst [ 9 , 10 ]. (biomedcentral.com)
Ago21
- The mature miRNA is then loaded onto an Argonaute protein (Ago2 in humans) where it then interacts with and regulates the mRNA target. (biomedcentral.com)
Distinct1
- Each class of small RNAs is synthesized by a distinct mechanism and each has discrete biological functions. (biomedcentral.com)
Small3
- Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. (biomedcentral.com)
- A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. (biomedcentral.com)
- Another class of important small RNAs is the piRNAs. (biomedcentral.com)
Translation1
- Once mRNA is degraded, post-transcriptional silencing occurs as protein translation is prevented. (wikipedia.org)
Complex1
- The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC). (wikipedia.org)
Systems1
- Annotation of the rhesus GeneChip is under continuous revision with large percentages of probesets under multiple annotation systems having undergone multiple reassignments between March 2007 and November 2008. (gene-quantification.de)
MiRNA7
- Two types of small ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. (wikipedia.org)
- For example, the non-coding RNA can be small nucleolar RNA (snoRNA), microRNA (miRNA), small interfering RNA (siRNA), and/or Piwi-interacting RNAs (piRNA). (justia.com)
- Ten of them identified an over- or downregulated gene signature, 5 found microRNA (miRNA) signature. (hindawi.com)
- Overrepresented groups of targets include mRNAs coding for transcription factors, components of the miRNA machinery, and other proteins involved in translational regulation, as well as components of the ubiquitin machinery, representing novel feedback loops in gene regulation. (gene-quantification.org)
- Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at http://www.microrna.org Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes. (gene-quantification.org)
- The first cancer-targeted microRNA (miRNA) drug - MRX34, a liposome-based miR-34 mimic - entered Phase I clinical trials in patients with advanced hepatocellular carcinoma in April 2013, and miRNA therapeutics are attracting special attention from both academia and biotechnology companies. (gene-quantification.eu)
- Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. (gene-quantification.eu)
NcRNAs3
- ncRNAs are encoded within the genomes of both eukaryotic and prokaryotic organisms and represent a novel layer of cell regulation and function that rivals the diversity and function of protein-coding mRNAs (for review, see Mattick 2007). (nih.gov)
- Genome-wide sequencing approaches have lead to the discovery of non-coding RNAs (ncRNAs), which account for approximately 98% of the entire genome output, compared to the remaining 2% corresponding to protein-coding transcripts ( 14 ). (frontiersin.org)
- Evolutionary studies have demonstrated that the increase in organisms complexity corresponds to a decrease in the abundance of protein-coding genes and a concomitant rise in the number of ncRNAs, indicating that regulatory RNA diversification has been critical to increase vertebrate complexity ( 15 , 16 ). (frontiersin.org)
Post-transcriptional3
- Once mRNA is degraded, post-transcriptional silencing occurs as protein translation is prevented. (wikipedia.org)
- The efficacy of macrophage- mediated inflammatory response relies on the coordinated expression of key factors, which expression is finely regulated at both transcriptional and post-transcriptional level. (frontiersin.org)
- The efficacy of macrophage-mediated inflammatory responses relies on the coordinated expression of key proteins involved in macrophage activation and polarization processes, whose expression is finely regulated at both transcriptional and post-transcriptional levels ( 4 - 9 ). (frontiersin.org)
SiRNA4
- Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger (sense) strand and the guide (antisense) strand. (wikipedia.org)
- R2D2 carries tandem double-stranded RNA-binding domains to recognize the thermodynamically stable terminus of siRNA duplexes, whereas Dicer-2 the other less stable extremity. (wikipedia.org)
- RNAi screens are primarily conducted using synthetic small interfering RNA (siRNA) or plasmid-encoded short hairpin RNA (shRNA). (nih.gov)
- Cleavage is mediated by a single strand of the siRNA duplex termed the guide strand, after loading into the RNA-induced silencing complex (RISC). (nih.gov)
Nucleic acids5
- Methods for analyzing RNA can entail reverse transcription of the desired RNA, followed by preamplification and amplification of selected target nucleic acids. (justia.com)
- The invention relates to methods useful for analyzing the nucleic acids, e.g., genomic DNA or RNA (e.g., non-coding RNA or mRNA), of small populations of cells or single cells. (justia.com)
- An obstacle to the rapid and reliable analysis of genomic DNA or RNA (e.g., non-coding RNA or mRNA) from small samples or single cells has been that the reproducibility of conventional polymerase chain reaction (PCR) has been inadequate to ensure that all target nucleic acids of interest are amplified sufficiently to be detected. (justia.com)
- The nucleic acids generated, e.g., from a single cell's genomic DNA or RNA, can be subjected to preamplification. (justia.com)
- The secreted cell-free nucleic acids, small microRNAs, circulating tumor cells and proteins act as early diagnostic biomarkers of breast tumor. (biomedcentral.com)
Gene expression2
- This means that in contrast to RNA molecules generated during gene expression (i.e., messenger RNA [mRNA] molecules), they are not used as templates for the synthesis of proteins. (nih.gov)
- Fifteen years after the discovery of RNA silencing, we are only just beginning to understand the depth and complexity of how these RNAs regulate gene expression and to consider their role in shaping the evolutionary history of higher eukaryotes. (gene-quantification.eu)
Molecules1
- It is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of approximately 21 to 23 nucleotide siRNAs. (wikipedia.org)
DsRNA1
- When the dsRNA is exogenous (coming from infection by a virus with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by Dicer. (wikipedia.org)
Regulatory1
- 2009. MicroRNAs: target recognition and regulatory functions. (virosin.org)
Regulation3
- The widespread regulation of microRNA biogenesis, function and decay. (gene-quantification.eu)
- Regulation of mRNA translation and stability by microRNAs. (virosin.org)
- We further review the impact of microRNA-dependent regulation of tumor-associated macrophages and the relative implication for tumor biology. (frontiersin.org)
Endogenous2
- 2014. Replication of many human viruses is refractory to inhibition by endogenous cellular microRNAs. (virosin.org)
- 2013. How do viruses avoid inhibition by endogenous cellular microRNAs? (virosin.org)
Inhibit1
- In this review, we highlight the essential molecular mechanisms underlying the different phases of inflammation that are targeted by microRNAs to inhibit or accelerate restoration to tissue integrity and homeostasis. (frontiersin.org)
Nucleotides1
- Small RNA guides-microRNAs, small interfering RNAs, and repeat-associated small interfering RNAs, 21 to 30 nucleotides in length-shape diverse cellular pathways, from chromosome architecture to stem cell maintenance. (gene-quantification.eu)
Infection1
- We have conducted crosslinking, immunoprecipitation, and sequencing (CLIP-seq) to characterize N interactions with host and viral RNAs during infection. (mdpi.com)
Replication2
- RVFV's nucleocapsid protein (N) is an RNA-binding protein that is necessary for viral transcription, replication, and the production of nascent viral particles. (mdpi.com)
- In the present study, we investigated the role of miR-135a in regulating HCV life cycle and showed that it preferentially enhances viral genome replication. (virosin.org)
Protein1
- Experimental support for the validity of the method comes from known targets and from strong enrichment of predicted targets in mRNAs associated with the fragile X mental retardation protein in mammals. (gene-quantification.org)
Roles1
- Several studies have provided compelling evidence that microRNAs play pivotal roles in modulating macrophage activation, polarization, tissue infiltration, and resolution of inflammation. (frontiersin.org)
Target1
- Bioinformatics studies on the genomes of multiple organisms suggest this length maximizes target-gene specificity and minimizes non-specific effects. (wikipedia.org)
Expression2
- 220-plex microRNA expression profile of a single cell. (gene-quantification.org)
- Facile means for quantifying microRNA expression by real-time PCR. (gene-quantification.org)
Long2
- Only one screened long noncoding RNA (lncRNA) was associated with radiosensitivity but was made in colorectal cancer cell lines and was written in Chinese and therefore was excluded. (hindawi.com)
- Prion diseases typically have long pre-clinical incubation periods during which time the infectious prion particle and infectivity steadily propagate in the brain. (prolekarniky.cz)
Single1
- MicroRNA quantitation from a single cell by PCR using SYBR Green detection and LNA-based primers. (gene-quantification.org)
Reaction1
- When DNA is produced from RNA, e.g., by reverse transcription, preamplification can then be carried out in the same reaction mixture. (justia.com)
Guide1
- The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC). (wikipedia.org)
Early1
- CTCs, CTC-specific microRNAs and circulatory miRs are collectively predictive of an early metastatic spread with prospective implications as therapeutic tools for targeting metastatic cells. (biomedcentral.com)
Human1
- Human microRNA targets. (gene-quantification.org)
Process1
- In this process, the involvement of multiple immune cells is critical. (frontiersin.org)