RNAsAccumulation of sRNAsMRNAMicroarray analysisBacterialMiRNAExperimentallyMiRNAsBacteriaExtensivelyMycobacteriumRegulatoryPost-transcriptionalEndogenousInduceRNAIIIPathogenicityColiLociProteinRolesGene expression analysisVirulenceSmallAnalysesPatternsMetabolismCaudal fin regenerationEpigeneticRegulation of gene exAbundanceMoleculesAnalysisStrainsAnalyzeChaperoneBehaviorTargetDifferentiallyTestLevelsProcessesResistanceFunctionRoleSpecificTargetsCandidateClinical
RNAs11
- Thus, using publicly available data, I explored the effect of SARS-CoV-2 on the expression of several mitochondrial non-coding RNAs in patients recovering from COVID-19. (frontiersin.org)
- No change in the expression of long non-coding RNAs was detected at any stage of the infection, but up to 43 small mitochondrial RNAs have their expression altered during the recovery from COVID-19. (frontiersin.org)
- Despite these being only preliminary results on a small cohort, the analyses clearly showed that individuals infected by SARS-CoV-2 retain an altered expression of these small RNAs. (frontiersin.org)
- This persistent alteration in the expression of small mitochondrial RNAs might be involved in the long COVID syndrome and further studies are needed to confirm the possibility. (frontiersin.org)
- Small regulatory RNAs (sRNAs) play key roles in modulating gene expression in both prokaryotes and eukaryotes. (biomedcentral.com)
- High-throughput sequencing was used to characterize the expression of small RNAs during zebrafish caudal fin regeneration at zero and four days post amputation using biological triplicate samples. (umaine.edu)
- Micro RNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. (researchsquare.com)
- Several S. aureus small RNAs (sRNAs) regulate virulence. (cdc.gov)
- To coordinate expression of virulence genes during infection, S. aureus uses 2-component systems, transcription factors ( 5 ) and regulatory or small RNAs (sRNAs), which function as positive ( 6 ) or negative ( 7 ) virulence determinants. (cdc.gov)
- The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)
- Our bacterial decoder will also involve the usage of small RNAs, or sRNAs. (igem.org)
Accumulation of sRNAs2
- A limited study had indicated that in Sinorhizobium meliloti the YbeY ortholog regulates the accumulation of sRNAs as well as the target mRNAs, raising the possibility that YbeY may play a previously unrecognized role in bacterial sRNA regulation. (biomedcentral.com)
- Viral titers, disease symptoms and the accumulation of sRNAs (i.e. (biomedcentral.com)
MRNA12
- We have applied a multipronged approach of loss-of-function studies, genome-wide mRNA and sRNA expression profiling, pathway analysis, target prediction, literature mining and network analysis to unravel YbeY-dependent molecular responses of E. coli exposed to hydroxyurea (HU). (biomedcentral.com)
- We successfully identified at least 57 experimentally inferred sRNA-mRNA relationships. (biomedcentral.com)
- Further applying a 'context likelihood of relatedness' algorithm, we reverse engineered the YbeY-dependent Hfq-dependent sRNA-mRNA network as well as YbeY-dependent Hfq-independent sRNA-mRNA network. (biomedcentral.com)
- YbeY extensively modulates Hfq-dependent and independent sRNA-mRNA interactions. (biomedcentral.com)
- In bacteria, numerous sRNAs that range in size from ~50-300 nucleotides in length act on independently transcribed mRNA targets. (biomedcentral.com)
- The most extensively characterized class of bacterial sRNAs are the trans -encoded sRNAs that are encoded distant from the genes for their mRNA targets and that typically have only limited complementarity (10-30 nt) [ 2 ]. (biomedcentral.com)
- Trans- encoded sRNAs form imperfect base-pairing interactions with complementary sequences in their mRNA targets, which are often located at or near ribosome binding sites (RBS), but can also be located upstream of the translation start site as well as deep in the coding regions (CDS) [ 2 ]. (biomedcentral.com)
- Here, we used Translating Ribosome Affinity Purification (TRAP) combined with RNA-seq to allow the characterization of mRNA and sRNA populations associated to polysomes (referred as the translatome). (conicet.gov.ar)
- Biomolecular analyses have revealed that a few SNPs in the promoter sequences and only one SNP in the 5' UTR of mRNA induce the differential expression of , drastically impacting mRNA translation. (cnrs.fr)
- sRNAs can be either cis (A) or trans (B). They can prevent protein synthesis from an mRNA by several methods, including binding to the RBS and preventing ribosome binding or binding to the 5' UTR and recruiting degradative enzymes. (igem.org)
- Some sRNAs positively regulate a gene by binding to a folded mRNA and revealing the RBS. (igem.org)
- sRNAs are very short transcripts of RNA (usually ~100 base pairs in E. coli ) that are used in bacteria to positively or negatively regulate genes at the translational level by binding to the mRNA of the gene and either occluding the ribosomal binding site (RBS) and preventing ribosome binding or recruiting nucleases to degrade the mRNA. (igem.org)
Microarray analysis2
- From this set of candidate genes, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS (Sigma 38). (wikipedia.org)
- Of 54 detectable E. coli sRNAs in our microarray analysis, 30 sRNAs showed a differential expression upon HU stress, of which 28 sRNAs displayed a YbeY-dependent change in expression. (biomedcentral.com)
Bacterial5
- Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth. (wikipedia.org)
- Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. (biomedcentral.com)
- Other bacterial sRNAs, referred to as cis -encoded sRNAs, are present in close proximity to their targets, such as upstream, opposite of the 5′ UTR of the target, or between two genes in an operon [ 2 ]. (biomedcentral.com)
- Like microRNAs (miRNAs) in eukaryotes, trans -acting bacterial sRNAs appear to recognize their targets by a seed-pairing mechanism using seeds as small as 6-7 nucleotides. (biomedcentral.com)
- Using sRNAs in our bacterial decoder will help us achieve on/off behavior rather than intermediate levels of outputs, since sRNAs do little at low concentrations but demonstrate strong regulation at high concentrations. (igem.org)
MiRNA2
- Developmental changes in barley microRNA expression profiles coupled with miRNA targets analysis. (edu.pl)
- Id of miRNA differential appearance We initial normalized miRNA-sequence data from 18 libraries as transcripts per million (TPM). (clinical-research-informatics.com)
Experimentally2
- A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. (wikipedia.org)
- The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. (wikipedia.org)
MiRNAs4
- In our study, we identified miRNAs in hops and their expression patterns in the roots of susceptible and resistant hop cultivars in the early stages of infection with the fungus V. nonalfalfae . (researchsquare.com)
- MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. (peerj.com)
- Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus . (peerj.com)
- In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research. (peerj.com)
Bacteria5
- 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)
- The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. (frontiersin.org)
- Gaining a deeper insight into how sRNAs recognize and interact with their targets is crucial to understanding the mechanism of sRNA action and function in bacteria at a molecular level. (biomedcentral.com)
- Recently, synthetic biologists have been focusing on creating logic gates in bacteria by controlling gene expression at various levels: transcription, translation, and post-translational processes. (igem.org)
- The roles and mechanisms of sRNAs in bacteria currently comprise a very prominent topic in the field of biology, and many sRNAs have been extensively studied and characterized. (igem.org)
Extensively1
Mycobacterium1
- Mycobacterium tuberculosis sRNA Pseudomonas sRNA Bacillus subtilis BSR sRNAs Caenorhabditis elegans sRNA Bacteroides thetaiotaomicron sRNA List of RNA structure prediction software Hershberg R, Altuvia S, Margalit H (April 2003). (wikipedia.org)
Regulatory2
- The differential expression of these tRNA derived fragments and previous research into gene silencing by sRNA suggest that these other sRNA have the potential to play a regulatory role in zebrafish caudal fin regeneration. (umaine.edu)
- There are ≈160 sRNAs in the Staphylococcal Regulatory RNA database ( 8 ). (cdc.gov)
Post-transcriptional1
- Regulation of gene expression occurs at multiple levels within eukaryotic cells, including chromatin-based, transcriptional and post-transcriptional events. (conicet.gov.ar)
Endogenous1
- Worthy of note, in yeast cells expressing DCL4, 21- and 22-nt sRNAs are associated with endogenous loci. (biomedcentral.com)
Induce1
- Esr41 sequence is not present in nonpathogenic E. coli K12, but the sRNA can induce cell motility in K12 as well, suggesting that target genes controlled by Esr41 are present in both E.coli. (wikipedia.org)
RNAIII4
- RNAIII, RsaE, and SprD in Staphylococcus aureus as well as CyaR sRNAs), target recognition is structure-driven using C-rich stretches that are located within accessible loop regions [ 3 ]. (biomedcentral.com)
- Expression of RNAIII was lower in strains from septic shock patients than in strains from colonized patients. (cdc.gov)
- When RNAIII was associated with expression of sprD, colonizing strains could be discriminated from strains in patients with bloodstream infections, including patients with sepsis and septic shock. (cdc.gov)
- Monitoring expression of RNAIII and sprD could help determine severity of bloodstream infections. (cdc.gov)
Pathogenicity1
- Small pathogenicity island sRNAs sprB and sprC were clade specific. (cdc.gov)
Coli3
- These loci will include false positives, so the number of sRNA genes in E. coli is likely to be less than 275. (wikipedia.org)
- Cell motility enhancing sRNA named Esr41, was discovered in intergenic region of pathogenic enterohemorrhagic E.coli (EHEC) O157:H7 Sakai. (wikipedia.org)
- Esre sRNA, for "essential small RNA in E. coli", is located in 3′ moiety of yigP gene (also known as ubiJ), which is involved in coenzyme Q8 biosynthesis in Escherichia coli and Salmonella enterica serovar Typhimurium. (wikipedia.org)
Loci1
- 275 potential sRNA-encoding loci were identified computationally using the QRNA program. (wikipedia.org)
Protein6
- UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein. (wikipedia.org)
- The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. (uni-stuttgart.de)
- In this study, Gia1, a non-pheromone GPCR (G protein-coupled receptor) with sexual-specific expression in Fusarium graminearum, is found to be essential for ascosporogenesis. (bvsalud.org)
- To decipher the molecular basis for the variation in expression and protein production among strains, different regulation levels were analyzed in representative clinical isolates and reference strains. (cnrs.fr)
- Thirty five protein had been indicated for its expression in any five regenerating time items from the manage trials. (kinasepathway.com)
- Because quantitation to Western blotting of immunoprecipitates is inherently sensitive, a contradistinction in protein expression of Ly108-1 and Ly108-2 could not be excluded. (upb.ro)
Roles2
- Several of the sRNAs exhibited specific expression patterns during high cell density fermentation and are differentially expressed in the presence of multiple chemicals, suggesting they may play roles during stress conditions. (wikipedia.org)
- YbeY-dependent sRNAs have central roles in modulating cellular response to HU stress. (biomedcentral.com)
Gene expression analysis2
- This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. (frontiersin.org)
- The second thing you want to do is Quantification of target RNA molecules - crucial for the differential gene expression analysis, where you aim to determine which genes are upregulated/downregulated across your samples. (novogene.com)
Virulence1
Small2
- For the most part these other small RNA (sRNA), such as transfer RNA (tRNA) derived fragments, ribosomal RNA (rRNA) derived fragments, and small nucleolar RNA, are disregarded. (umaine.edu)
- Tags were annotated to various sRNA classes through sequence alignment to small RNA and genome databases in a hierarchical fashion. (umaine.edu)
Analyses2
- This analyses showed that microRNA and tRNA derived fragments were the most abundant sRNA types. (umaine.edu)
- TEtranscripts is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments. (cshl.edu)
Patterns2
- Other research groups might be more interested in analyzing a shift in cellular transcriptomic footprints across time to determine the time-scale gene expression patterns. (novogene.com)
- For an organism that lacks a high-quality reference genome, the de novo assembly of its transcriptome is a useful method for researchers to find the transcripts or genes responsive to various treatments and to better understand the expression patterns of the candidate genes. (biomedcentral.com)
Metabolism2
- Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. (uni-stuttgart.de)
- Transcriptome analysis revealed that NO mediated LPS-induced HA production via upregulating the expressions of critical genes associated with central carbon metabolism and downstream HA biosynthesis genes. (bvsalud.org)
Caudal fin regeneration1
- We've got examined the biomechanism of zebrafish caudal fin regeneration in various moment items according to differential proteomics strategies. (kinasepathway.com)
Epigenetic1
- Epigenetic regulation is necessary for the production of differentiated cells throughout plant development, as well as maintaining the stability and integrity of the gene expression profiles. (ac.ir)
Regulation of gene ex2
- The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae . (biomedcentral.com)
- The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. (ac.ir)
Abundance2
- The observed abundance and the differential expression of the various types of sRNA were analyzed. (umaine.edu)
- Some genes only show a high expression abundance under specific conditions or treatments, which means that multiple organs or time-series sampling need to be performed to obtain more transcripts. (biomedcentral.com)
Molecules1
- DCL4 was shown to be functional in processing dsRNA-like molecules in vitro and in vivo into 21- and 22-nt sRNAs. (biomedcentral.com)
Analysis7
- In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. (uni-stuttgart.de)
- Currently, most expression analysis software packates are not optimized for handling the complexities involved in quantifying highly repetitive regions of the genome, especially transposable elements (TE), from short sequencing reads. (cshl.edu)
- In addition, TEtranscripts combines multiple libraries and perform differential analysis using DESeq2. (cshl.edu)
- TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. (cshl.edu)
- In our article „ mdRNAseq analysis of marine microbial communities from the northern Red Sea ", which was published in Scientific Reports, we have employed Differential RNA-Seq to analyze the primary transcriptomes of a complex marine microbiome sample. (cyanolab.de)
- This technique, not previously used for metatranscriptomics, is powerful for the simultaneous identification of transcriptional start sites (i.e., the suite of active promoters) and the analysis of gene expression at community-wide scale. (cyanolab.de)
- Comparison of RNA isolation methods on RNA-SEQ: Implications for differential expression and meta-analysis. (labtecsp.com)
Strains2
- We investigated presence and expression of 8 sRNAs in 83 S. aureus strains from 42 patients with sepsis or septic shock and 41 asymptomatic colonized carriers. (cdc.gov)
- We investigated differences in sRNA gene content and expression levels in S. aureus strains isolated from patients with bloodstream infections and from asymptomatic carriers. (cdc.gov)
Analyze1
- To analyze RNA-Seq expression data for genomes included in the platform, a pipeline is integrated in MicroScope. (cns.fr)
Chaperone1
- The Hfq chaperone binds to A/U rich regions of sRNAs that are often located near the stem-loop structures as well as to the poly (U) regions at the 3′ end of the sRNAs [ 7 ]. (biomedcentral.com)
Behavior1
- Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. (peerj.com)
Target1
- Isolates associated with colonization might have sRNAs with target expression different from those of disease isolates. (cdc.gov)
Differentially1
- Three months meats were recognized as differentially governed regarding renewal depending on differential in-gel electrophoresis evaluation relating to the manage as well as rejuvenating flesh. (kinasepathway.com)
Test2
- 4) test of differential expression between samples of distinct experimental conditions. (cns.fr)
- A pivotal prospective, cross-sectional clinical trial comprising 8920 eligible participants was used to evaluate the sensitivity and specificity of the mt-sRNA test compared with a colonoscopy. (cdc.gov)
Levels1
- Compared to microarray-based transcriptomics, RNA-Seq provides direct access to the structure of transcripts, is not limited to a list of predefined transcripts, and covers a larger dynamic range of expression levels. (cns.fr)
Processes1
- They can modulate various biochemical and physiological processes, including plant response and resistance to fungal pathogens, by regulating the expression of numerous genes. (researchsquare.com)
Resistance1
- Loss of ybeY function, which results in a marked resistance to HU, had global affects on sRNA-mediated gene expression. (biomedcentral.com)
Function1
- Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. (uni-stuttgart.de)
Role1
- Their consultants in population of a advanced Role acquired Some Moreover Additionally implemented, only least by the 24th Opposites, so there were a balance in use for companies of 2013Proceedings %, and they used put mutatis mutandis to stylistic dequeues and sRNAs. (bcvsolutions.com)
Specific1
- To do that, you need to consider your research objectives: for instance, some projects are interested 'only' in comparing transcriptomic profiles across samples in different experimental conditions (e.g Treatment vs. Control), or between different tissue types, to identify tissue-specific gene expression. (novogene.com)
Targets1
- Fusion studies have revealed that seed regions of RybB or MicC sRNAs are sufficient to guide the recognition of targets [ 3 ]. (biomedcentral.com)
Candidate2
- A screen for sRNA genes based on homology to Salmonella and Klebsiella identified 59 candidate sRNA genes. (wikipedia.org)
- Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. (frontiersin.org)
Clinical1
- Six sRNAs had variable expression not correlated with clinical status. (cdc.gov)