Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS |...  Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS |...
Evidence that hfq status influences IS50 transposase expression came from two types of experiments. First, the expression of transposase-lacZ reporter genes in both transcriptional and translational fusion constructs increased significantly under conditions of hfq deficiency. Second, the steady-state level of the native transposase transcript also increased significantly in hfq − . Importantly, the large increase in steady-state transcript level (11-fold) coincided with a less substantial increase in transposase mRNA stability (less than 2-fold increase in half-life). In addition, up-regulation of reporter expression in hfq − for a TLF was almost completely abrogated when the IS50 transposase promoter was replaced by a heterologous promoter. Taken together, these results are consistent with Hfq (or a factor regulated by Hfq) suppressing IS50 transposase expression predominantly at the level of transcription. Notably the suppressive effect of Hfq on IS50 transposase transcription was ...
more infohttps://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-014-0027-z
sRNAMap: Small Noncoding RNA MAP  sRNAMap: Small Noncoding RNA MAP
Small non-coding RNAs (sRNAs) carry out a variety of biological functions and affect protein synthesis and protein activities in prokaryotes. Recently, numerous sRNAs and their targets were identified in Escherichia coli and in other bacteria. It is crucial to have a comprehensive resource concerning the annotation of small non-coding RNAs in microbial genomes. This work presents an integrated database, namely sRNAMap, to collect the sRNA genes, the transcriptional regulators of sRNAs and the sRNA target genes by integrating a variety of biological databases and by surveying literature. In this resource, we collected 397 sRNAs, 62 regulators/sRNAs and 60 sRNAs/targets in seventy microbial genomes. Additionally, more valuable information of the sRNAs, such as the secondary ...
more infohttp://srnamap.mbc.nctu.edu.tw
sRNAPrimerDB -- Official Site  sRNAPrimerDB -- Official Site
The Northern blot method is used to detect specific RNAs that have been separated by size and immobilized onto a membrane (Fig 1). This method can provide specific information regarding the size of a sncRNA and possible precursor structures. Thus, it represents a valuable tool in the discovery and validation of new sncRNAs. In situ hybridization (ISH) is a technology that allows detection of specific nucleic acid sequences in tissue samples at the cellular level (Nielsen, 2012; Urbanek et al., 2015). For detection of individual sncRNA, the ISH technology determines the cellular origin of expression and provides information on expression levels in different tissue compartments and cell populations. This histological expression analysis is of crucial importance for elucidating roles particularly of sncRNAs in molecular and biological processes. ...
more infohttp://123.57.239.141/protocolI
sRNAPrimerDB -- Official Site  sRNAPrimerDB -- Official Site
The Northern blot method is used to detect specific RNAs that have been separated by size and immobilized onto a membrane (Fig 1). This method can provide specific information regarding the size of a sncRNA and possible precursor structures. Thus, it represents a valuable tool in the discovery and validation of new sncRNAs. In situ hybridization (ISH) is a technology that allows detection of specific nucleic acid sequences in tissue samples at the cellular level (Nielsen, 2012; Urbanek et al., 2015). For detection of individual sncRNA, the ISH technology determines the cellular origin of expression and provides information on expression levels in different tissue compartments and cell populations. This histological expression analysis is of crucial importance for elucidating roles particularly of sncRNAs in molecular and biological processes. ...
more infohttp://123.57.239.141:8081/protocolI
Small non-coding RNAs in Streptococci | Frontiers Research Topic  Small non-coding RNAs in Streptococci | Frontiers Research Topic
Gene regulation is a fundamental key for bacteria to responds to environmental changes. In order to adapt to these changes bacteria have evolved and developed different strategies to facilitate tight control of genetic networks in response to diverse extracellular stimuli. The global roles of small noncoding RNAs (sRNAs) started to be interesting in the last years, particularly in regards to bacterial physiology, adaptation and pathogenesis. Beside translational gene regulation (activation or inhibition) through direct interaction with mRNAs, such sRNAs rely on a variety of mechanisms to control their targets, including: (i) sequestering molecules (e.g proteins) or (ii) riboswitches (sensor elements within mRNAs); and (iii) targeting invading cognate DNA, such is the case for CRISPR RNAs (i.e. Clustered Regularly Interspaced Short Palindromic Repeats RNAs). ...
more infohttps://www.frontiersin.org/research-topics/2627/small-non-coding-rnas-in-streptococci
Small RNA library prep with reduced bias and consistent performance  Small RNA library prep with reduced bias and consistent performance
The term "small non-coding RNA" broadly refers to diverse RNA species ~15-150 nucleotides (nt) in size that fulfill biological functions without being translated into proteins. While the involvement of small RNAs in cellular housekeeping processes such as transcript splicing and protein translation has been known since the 1960s, research over the past twenty years has revealed that small RNAs play vital roles in the regulation of gene expression, via both transcriptional and post-transcriptional mechanisms (Choudhuri, 2010). Of the small RNAs involved in gene regulation, the most well-studied are microRNAs (miRNAs; ~22 nt in size), which facilitate post-transcriptional gene silencing by binding specific target mRNAs via base-pair complementarity, and either blocking translation or triggering transcript ...
more infohttp://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/smRNA-seq?sitex=10020:22372:US&PEBCL1=Fz5Y8U2NaGXGUpWn5NcggmS7yd&PEBCL1_pses=ZG5CE26622CC2838A0F248147DA8DAD092E300C9DC517A399E269711F1FDBDCF21545AB7F449C7FBFF5C9A6AD94B72AD568D900F2395399F67
Small RNA library prep with reduced bias and consistent performance  Small RNA library prep with reduced bias and consistent performance
The term "small non-coding RNA" broadly refers to diverse RNA species ~15-150 nucleotides (nt) in size that fulfill biological functions without being translated into proteins. While the involvement of small RNAs in cellular housekeeping processes such as transcript splicing and protein translation has been known since the 1960s, research over the past twenty years has revealed that small RNAs play vital roles in the regulation of gene expression, via both transcriptional and post-transcriptional mechanisms (Choudhuri, 2010). Of the small RNAs involved in gene regulation, the most well-studied are microRNAs (miRNAs; ~22 nt in size), which facilitate post-transcriptional gene silencing by binding specific target mRNAs via base-pair complementarity, and either blocking translation or triggering transcript ...
more infohttp://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/smRNA-seq?sitex=10020:22372:US&PEBCL1=brr6T3ZJr2ZxcK27YO2uTZVB07&PEBCL1_pses=ZG3D11BE890CE399DA771AAB4F7C369DC940A52BE7B2A00156C6DE1E4B7B028095B2E08E9CAE5D0F58FB36DC9D1639C305D7B6251025805666
Small RNA library prep with reduced bias and consistent performance  Small RNA library prep with reduced bias and consistent performance
The term "small non-coding RNA" broadly refers to diverse RNA species ~15-150 nucleotides (nt) in size that fulfill biological functions without being translated into proteins. While the involvement of small RNAs in cellular housekeeping processes such as transcript splicing and protein translation has been known since the 1960s, research over the past twenty years has revealed that small RNAs play vital roles in the regulation of gene expression, via both transcriptional and post-transcriptional mechanisms (Choudhuri, 2010). Of the small RNAs involved in gene regulation, the most well-studied are microRNAs (miRNAs; ~22 nt in size), which facilitate post-transcriptional gene silencing by binding specific target mRNAs via base-pair complementarity, and either blocking translation or triggering transcript ...
more infohttp://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/smRNA-seq?sitex=10020:22372:US&PEBCL1=hmHaoM9zOjb2oGBsMNfzrz83I2&PEBCL1_pses=ZG783141B1147214B747726DCDE721F4959B5CA77D8CEBC784467698B274DDCBA296EF296FCFE702ACCCBE23E64C972CC3867D765F583417CD
Paramutation of tobacco transgenes by small RNA-mediated transcriptio…  Paramutation of tobacco transgenes by small RNA-mediated transcriptio…
Detail záznamu - Paramutation of tobacco transgenes by small RNA-mediated transcriptional gene silencing - Detail záznamu - Knihovna Akademie věd České republiky
more infohttps://asep.lib.cas.cz/arl-cav/m-sk/detail-cav_un_epca-0360303-Paramutation-of-tobacco-transgenes-by-small-RNAmediated-transcriptional-gene-silencing/
Systems biology of bacterial small RNAs | Stavans Lab  Systems biology of bacterial small RNAs | Stavans Lab
Small RNAs (sRNAs) are post-transcriptional regulators of gene expression that play fundamental roles in the response of bacterial cells to environmental cues. We study the response of genetic networks and architectural motifs that include sRNAs, as well as the cell-to-cell variability in the expression of genes controlled by sRNAs. To do so, we use fluorescence microscopy and microfluidic techniques that allow us to measure directly the concentrations of fluorescently-tagged target proteins in individual cells as they respond to controlled stimuli, as well as single-molecule fluorescence in-situ hybridization to monitor the response at the target transcript level.. ...
more infohttp://www.weizmann.ac.il/complex/stavans/research-activities/systems-biology-bacterial-small-rnas
sRNAPrimerDB -- Official Site  sRNAPrimerDB -- Official Site
The principle of the one-step real time RT-PCR is illustrated in Fig. 1. The whole detection procedure requires four primers: RP1, RP2, P1 and P2. RP1 contains the P1 and a 11-base sequence that is complimentary to the 3′-end of target sncRNA. RP2 contains P2 and a 11-base sequence that is same with the 5′-end of target sncRNA. The total thermocycling program includes three stages. Stage 1 is the reverse transcription process. In this stage, the RP1 hybridizes with target sncRNA, and then is extended in the presence of Reverse Transcriptase M-MLV (RNase H-) and dNTPs. Since the melting temperature (Tm) of an 11-base sequence is near 37 ℃, this stage is conducted at 37 ℃. In Stage 2, after denaturing at 95 ℃, the RP2 hybridizes with the cDNA of miRNA at 37 ℃, and both sequences are extended in the presence of hot-start Taq polymerase (HS Taq) and dNTPs at 60 ℃. Stage 3 is a conventional PCR process with the primers P1 and P2. ...
more infohttp://123.57.239.141/protocolG
sRNAPrimerDB -- Official Site  sRNAPrimerDB -- Official Site
The principle of the one-step real time RT-PCR is illustrated in Fig. 1. The whole detection procedure requires four primers: RP1, RP2, P1 and P2. RP1 contains the P1 and a 11-base sequence that is complimentary to the 3′-end of target sncRNA. RP2 contains P2 and a 11-base sequence that is same with the 5′-end of target sncRNA. The total thermocycling program includes three stages. Stage 1 is the reverse transcription process. In this stage, the RP1 hybridizes with target sncRNA, and then is extended in the presence of Reverse Transcriptase M-MLV (RNase H-) and dNTPs. Since the melting temperature (Tm) of an 11-base sequence is near 37 ℃, this stage is conducted at 37 ℃. In Stage 2, after denaturing at 95 ℃, the RP2 hybridizes with the cDNA of miRNA at 37 ℃, and both sequences are extended in the presence of hot-start Taq polymerase (HS Taq) and dNTPs at 60 ℃. Stage 3 is a conventional PCR process with the primers P1 and P2. ...
more infohttp://123.57.239.141:8081/protocolG
Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA | The EMBO Journal  Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA | The EMBO Journal
Research into post‐transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ‐dependent sRNAs are largely unknown. Here, we report in Salmonella Typhimurium the mode‐of‐action of RaiZ, a ProQ‐dependent sRNA that is made from the 3′ end of the mRNA encoding ribosome‐inactivating protein RaiA. We show that RaiZ is a base‐pairing sRNA that represses in trans the mRNA of histone‐like protein ...
more infohttp://emboj.embopress.org/content/early/2017/03/23/embj.201696127
Genes  | Free Full-Text | Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms | HTML  Genes | Free Full-Text | Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms | HTML
With the advent of new and improved high-throughput sequencing technologies in the last few years, a growing number of novel classes of small RNA, other than miRNAs or siRNA, has emerged, which appear as new actors in gene expression regulation. tRNA-derived small RNAs represent one of these novel members that are, surprisingly, among the most conserved class of small RNAs throughout evolution. They could represent the most primitive small RNA pathways from which the well-known canonical RNA silencing pathways reported in higher eukaryotes evolved. This review aims to make a compilation of the most relevant research literature in this field with the purpose of shedding light on the relation of these primitive tRNA-derived molecules with the gene silencing machinery.
more infohttp://www.mdpi.com/2073-4425/3/4/603/htm
miRNA Entry for MI0000270  miRNA Entry for MI0000270
In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. MicroRNAs (miRNAs) are transcribed as ~70 nucleotide precursors and subsequently processed by the RNase-III type enzyme Dicer to give a ~22 nucleotide mature product. In this case the mature sequence comes from the 5' arm of the precursor. They target and modulate protein expression by inhibiting translation and / or inducing degradation of target messenger RNAs. This new class of genes has recently been shown to play a central role in malignant transformation. miRNA are downregulated in many tumors and thus appear to function as tumor suppressor genes. The mature products miR-181a, miR-181b, miR-181c or miR-181d are thought to have regulatory roles at posttranscriptional level, through complementarity to target mRNAs. miR-181 which has been predicted or experimentally ...
more infohttp://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000270
Aptamer and Sequencing Core - John Rossi  Aptamer and Sequencing Core - John Rossi
The goal of this program is to develop cell targeted approaches to delivering small non-coding RNA directed transcriptional gene silencing and RNA directed Pddl...
more infohttp://grantome.com/grant/NIH/P01-AI099783-01-7517
Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA | The EMBO Journal  Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA | The EMBO Journal
The vast majority of currently known ProQ‐binding sRNAs are of unknown function (Smirnov et al, 2016). We have previously observed that asRNAs are enriched in the ProQ interactome, suggesting that this protein may be involved in gene expression regulation via perfect base pairing with cis‐encoded mRNA targets. Some of these asRNAs and their regulatory mechanisms have been characterized, including members of the Sib, Rdl, and IstR families of type I antitoxins, the transposon‐associated art200 and the intergenic cis‐acting SraG sRNAs (Darfeuille et al, 2007; Ellis et al, 2015; Fontaine et al, 2016; Han et al, 2010; Kawano, 2012; Mok et al, 2010). Some other ProQ‐associated sRNAs are derived from transcriptional attenuators (SraF, rimP leader) or have been proposed to function as trans‐encoded base‐pairing sRNAs (SraL) (Argaman et al, 2001; Naville & Gautheret, 2010; Nechooshtan et al, 2009; ...
more infohttp://d2ni3bh4dzb2ig.cloudfront.net/content/36/8/1029
Difference between revisions of Gama:Projects - OpenWetWare  Difference between revisions of "Gama:Projects" - OpenWetWare
HIV infection occurs following a series of virus-host interactions that culminate in the integration of viral DNA into the host cell genome. This process results in the generation of a pool of latently infected CD4 T cells, resistant to therapies that target replicating viruses, and constitutes a major viral reservoir. It is hoped that drugs that prevent the establishment of this pool, such as Raltegravir, may help to address this problem. Regulatory small non-coding RNAs are likely to impact on the molecular processes of the HIV life-cycle particularly through the regulation of the cellular pathways of T cell activation. With this reasoning we have performed a deep-sequencing analysis of the profile of small RNA expression in primary human naïve CD4 T cells, and upon T cell activation and HIV infection. Our preliminary data showed a differential expression of miRNAs upon cell activation, and/or HIV infection, which is ...
more infohttps://openwetware.org/wiki/?title=Gama:Projects&diff=504459&oldid=501467
Newsletter63 | Arraystar  Newsletter63 | Arraystar
tRFs & tiRNAs: small RNAs with distinct and varied functions tRNA is known to be an adaptor molecule to decode and translate mRNA into protein. However, recent studies have discovered tRNAs to be a major source of small non-coding RNAs, with their abundance levels often higher than microRNAs. tRNA derived fragments (tRF) and tRNA halves (tiRNA) are generated from tRNAs by precise biogenesis processes (Fig. 1), having distinct and varied functions to [1-3]:. ...
more infohttps://www.arraystar.com/resources/newsletter63/
Unravelling the function of small RNAs  Unravelling the function of small RNAs
Small non-coding RNAs (ncRNAs) play a hitherto unrecognised role in regulation of gene expression. To broaden knowledge on the function and evolution of these molecules, a EU project investigated various classes of regulatory ...
more infohttps://phys.org/news/2012-08-unravelling-function-small-rnas.html
Browsing  by Subject Microbiology  Browsing by Subject "Microbiology"
Micro RNAs (miRNAs) are a class of highly conserved small non-coding RNAs that play an important part in the post-transcriptional regulation of gene expression. A substantial number of miRNAs have been proposed as biomarkers ...
more infohttps://aran.library.nuigalway.ie/xmlui/browse?value=Microbiology&type=subject
MicroRNAs as novel endogenous targets for regulation and therapeutic treatments - MedChemComm (RSC Publishing)  MicroRNAs as novel endogenous targets for regulation and therapeutic treatments - MedChemComm (RSC Publishing)
MicroRNAs (miRNAs) are small non-coding RNAs that have been identified as key endogenous biomolecules that are able to regulate gene expression at the post-transcriptional level. The abnormal expression or function of miRNAs has been demonstrated to be closely related to the occurrence or development of various hum
more infohttp://pubs.rsc.org/en/content/articlelanding/2018/md/c7md00285h
Difference between revisions of Gama - OpenWetWare  Difference between revisions of "Gama" - OpenWetWare
Our research focuses on the characterization and modeling of post-transcriptional regulatory networks involved in the coordination of gene expression programs in vertebrates, using a combination of cell and molecular biology studies with genomics and bioinformatics approaches. We are particularly interested in regulatory events determined by small non-coding RNAs and the interaction of RNA binding proteins with mRNA untranslated sequence elements (UTRs)and how they can be targeted to influence on gene expression outputs for therapeutic applications. ...
more infohttps://openwetware.org/wiki/?title=Gama&diff=576660&oldid=504472
KRIBB: Search Results  KRIBB: Search Results
Integrated genomic analysis of recurrence-associated small non-coding RNAs in oesophageal cancer / H J Jang; H S Lee; B M Burt; G K Lee; K A Yoon; Y Y Park; B H Sohn; S B Kim; M S Kim; J M Lee; J Joo; S C Kim; J S Yun; K J Na; Y L Choi; Jong Lyul Park; Seon-Young Kim; Y S Lee; L Han; H Liang; D Mak; J K Burks; J I Zo; D S Sugarbaker; Y M Shim; J S Lee , 2017 ...
more infohttps://repository.kribb.re.kr/simple-search?query=%28%28author%3A%22B+Kim%22%29%29&order=title-asc&start=120
In Vivo Regulated Release and Function of Extracellular Small RNAs | Global Research Projects  In Vivo Regulated Release and Function of Extracellular Small RNAs | Global Research Projects
There is a desperate need for new means to diagnose and treat most human diseases. Extracellular small RNAs provide great promise. In particular, recent findings provide strong evidence for their utility as biomarkers. Furthermore, very recent work shows functional roles for at least a subset of the extracellular small RNAs, which provides an opportunity for their manipulation in the treatment of disease. However, as the field is so recent with only anecdotal evidence in limited systems, there remains a fundamental gap in our knowledge of how wide spread the phenomenon of functional extracellular small RNAs really is and how can its potential be fully realized. This U19 Center's long-term goal is to uncover paradigms of extracellular small RNA function in health and disease and apply those paradigms to clinically relevant settings including biomarker discovery and ...
more infohttp://globalprojects.ucsf.edu/project/vivo-regulated-release-and-function-extracellular-small-rnas