• In particular, the NS5B region contained long stem-loop structures of up to 38 internally paired nucleotides which were evolutionarily conserved between human and chimpanzee HGV/GBV-C variants. (ox.ac.uk)
  • Cloning and characterization of two evolutionarily conserved subunits (TFIIIC102 and TFIIIC63) of human TFIIIC and their involvement in functional interactions with TFIIIB and RNA polymerase III. (embl.de)
  • Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ' UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. (nih.gov)
  • Therefore, conserved structures are characteristic evolutionarily signatures of functional RNAs. (biomedcentral.com)
  • It will help you to detect thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. (univie.ac.at)
  • An evolutionarily conserved region of the TDP-43 low-complexity domain (LCD) twenty residues in length can adopt either an α-helical or ß-strand conformation. (bvsalud.org)
  • An evolutionarily conserved region (ECR) of 20 residues within this domain can adopt either of two forms of labile secondary structure. (bvsalud.org)
  • From the viral genome, researchers have deduced the sequences and structures of the viral proteins, hoping to use this information to develop treatments and vaccines for SARS. (sciencedaily.com)
  • It has been proposed that ribosome scanning and start codon selection are regulated by elements in the 5' leader sequence, such as RNA primary sequences (for example, the Kozak sequence context), upstream open reading frames (uORFs), secondary structures, and RNA modifications 4 - 7 . (biorxiv.org)
  • Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
  • However, the accuracy of the native structure derivation of ncRNAs is still not satisfactory, especially on sequences containing pseudoknots. (biomedcentral.com)
  • Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. (biomedcentral.com)
  • Many types of ncRNAs perform their functions through both their sequences and secondary structures, which are defined by the interacting base pairs. (biomedcentral.com)
  • This was not helpful since it included a huge number of sites and sequences that result from spurious (nonfunctional) binding of transcription factors or accidental transcription of random DNA sequences to make junk RNA [see What did the ENCODE Consortium say in 2012? ]. (blogspot.com)
  • 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)
  • They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences. (biomedcentral.com)
  • It models RNA structure in a pair of sequences using a stochastic context free grammar. (biomedcentral.com)
  • While the signal from RNA stability is important when only few sequences are available, more emphasis has to be put on the evolutionary signature in future screens. (biomedcentral.com)
  • The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. (biomedcentral.com)
  • The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data. (biomedcentral.com)
  • Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. (biomedcentral.com)
  • The identification and characterization of macromolecular sequences and their higher-order structures have utilized a very important principle in molecular and evolutionary biology. (biomedcentral.com)
  • Different primary structures (or sequences) can form the same higher-order structure for different RNAs and proteins [ 5 ]. (biomedcentral.com)
  • This comparative method is now widely used in the study for many RNAs, and is the cornerstone for the computational analysis of the deluge of nucleic acid sequences that are determined with next-generation sequencing methodology. (biomedcentral.com)
  • A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. (lookformedical.com)
  • AMINO ACID MOTIFS are often composed of conserved sequences. (lookformedical.com)
  • Transcription regulatory sequences have important role in the pausing of replication/transcription and generation of subgenomic RNAs. (springeropen.com)
  • To validate our hypothesis , we directly compared p68 RNA sequences and the hairpin loop in silico . (lidsen.com)
  • In this study we have carried out a detailed comparison of the structure of the 3′untranslated region (3′UTR) of HGV/GBV-C with that of the upstream NS5B coding sequence. (ox.ac.uk)
  • It has a single-stranded, positive-sense RNA genome of about 9.3 kb and contains a single open reading frame (ORF) encoding two structural (E1 and E2) and five nonstructural (NS2, NS3, NS4, NS5A, and NS5B) proteins. (wikipedia.org)
  • The DENV genome is a single-stranded positive-sense RNA of ≈11,000 nucleotides (nt) that encodes 3 structural proteins (capsid, membrane, and envelope) and 7 nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) ( 3 ). (cdc.gov)
  • The genome of the SARS virus is a single strand of RNA that folds into regular repeating patterns to form secondary structures such as helices. (sciencedaily.com)
  • But could the structure of the RNA genome itself also be a target for antiviral drugs? (sciencedaily.com)
  • This element sits at one end of the viral genome, and, as the researchers show, its sequence is highly conserved in related coronaviruses. (sciencedaily.com)
  • Furthermore, unlike the rest of the SARS genome, which changes rapidly, the s2m element is absolutely conserved in SARS variants obtained from patients during the SARS epidemic. (sciencedaily.com)
  • Pospiviroidae's type species, potato spindle tuber viroid (PSTVd), has a rod-like secondary structure ∼360-nt-long genome that can be functionally and structurally divided into five domains: (i) terminal left, (ii) pathogenicity (P), (iii) central (C) containing the conserved central region, (iv) variable (v) and (5) terminal right (TR) (5). (degruyter.com)
  • Shortening of the 5'-terminus of the daughter strand, caused by the removal of the terminal RNA-primer and the subsequent incomplete replication of linear DNA molecules, is observed during the genome replication occurring upon cell fission. (actanaturae.ru)
  • 2021. Exploring the druggability of conserved RNA regulatory elements in the SARS-CoV-2 genome . (uni-frankfurt.de)
  • In participating UK research institutions, investigators can publish open access in Genome Research, Genes & Development, RNA, and Learning & Memory without article publication charges and all staff can read the entire renowned Cold Spring Harbor journal collection. (cshlpress.com)
  • SARS-CoV-2 bears positive sense RNA genome that has organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. (springeropen.com)
  • The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) that causes the global pandemic illness COVID-19 has a 29.9 kb positive sense single strand RNA genome (Kim et al. (springeropen.com)
  • Inside the host environment, the RNA genome goes through a complicated replication/transcription process. (springeropen.com)
  • In order to translate the viral proteins and package the RNA genome into virion particles, the SARS-CoV-2 enters the host cell and undergoes replication of the positive sense RNA genome. (springeropen.com)
  • In the process, the negative sense RNA genome is created. (springeropen.com)
  • Therefore, in this study investigation of conserved secondary structure pattern was performed nearby the initiation codon/TRS that might be important in pausing of transcription during negative sense RNA synthesis of the SARS-CoV-2 genome. (springeropen.com)
  • The negative sense RNA is firstly generated through the replication/transcription of positive sense RNA genome. (springeropen.com)
  • The negative sense RNA will serve as template for positive sense RNA genome and subgenomic messenger RNAs (or subgenomic RNAs) (Sawicki et al. (springeropen.com)
  • The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
  • Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
  • More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
  • Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
  • DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp, are putative RNA helicases. (thermofisher.com)
  • DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular procsses involving RNA binding and alteration of RNA secondary structure. (nih.gov)
  • Using the yeast structure as a template, we have modeled the homologous domains from elongin A and CRSP70 and identified a conserved positively charged patch on the surface of all three proteins, which may be involved in conserved functional interactions with the transcriptional machinery. (embl.de)
  • His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
  • Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
  • The first three RNAs identified - messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA) were associated with the translation of RNA to proteins - protein synthesis. (biomedcentral.com)
  • While DNA is known to carry genetic information from one generation to the next, and proteins are capable of forming three-dimensional structures that catalyze chemical reactions, the function of RNA was perceived as the carrier of the information to code for amino acids in a protein, serve as a scaffold for proteins in the ribosome, and attach amino acids to the growing protein chain during protein synthesis. (biomedcentral.com)
  • RNA is capable of forming complex three-dimensional structure like proteins. (biomedcentral.com)
  • And like proteins these higher-order structures catalyze reactions. (biomedcentral.com)
  • Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. (lookformedical.com)
  • This is referred to as the primary structure of proteins. (lookformedical.com)
  • Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure. (lookformedical.com)
  • Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. (upf.edu)
  • Myelinating Schwann cells form a myelin sheath around a single axon and express high levels of myelin-related proteins and messenger RNA (mRNA). (medscape.com)
  • 2020. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy . (uni-frankfurt.de)
  • Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. (biomedcentral.com)
  • Human transcription factor IIIC (hTFIIIC) is a multisubunit complex that mediates transcription of class III genes through direct recognition of promoters (for tRNA and virus-associated RNA genes) or promoter-TFIIIA complexes (for the 5S RNA gene) and subsequent recruitment of TFIIIB and RNA polymerase III. (embl.de)
  • 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)
  • Here we found a highly conserved RNA secondarystructure, the regulatory B12 element, which is widely distributed in theupstream regions of cobalamin biosynthetic/transport genes in eubacteria.In addition, the binding signal (CBL-box) for a hypothetical B12 regulatorwas identified in some archaea. (embl-heidelberg.de)
  • Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. (biomedcentral.com)
  • Microbial structured RNAs are involved in biological processes ranging from cis -antisense regulation to targeted regulation of diverse sets of genes [ 1 ]. (biomedcentral.com)
  • A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. (lookformedical.com)
  • The surface view of the crystal structure of RBMS1 protein is shown bound with the bases of nucleotides of c-myc promoter. (neelsb.com)
  • We determined the 2.57 Å crystal structure of RBMS1 in its promoter DNA bound state that provided atomic-resolution insight into specific binding of individual nucleotides of DNA with the protein. (neelsb.com)
  • We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. (biomedcentral.com)
  • Viral RNA was extracted by using a High Pure RNA extraction kit (Roche Diagnostics, Mannheim, Germany) according to the manufacturer's instructions, transcribed to cDNA, and amplified by polymerase chain reaction, as described previously ( 8 ). (cdc.gov)
  • We have previously solved the structures of domains II and III, which stimulate arrested polymerase II elongation complexes in order to resume transcription. (embl.de)
  • Domain I also interacts with the transcriptionally active RNA polymerase II holoenzyme and therefore, may have a function unrelated to the previously described transcription elongation activity of TFIIS. (embl.de)
  • Yeast RNA polymerase II subunit RPB9. (embl.de)
  • The RPB9 subunit of RNA polymerase II regulates transcription elongation activity and is required for the action of the transcription elongation factor, TFIIS. (embl.de)
  • A conserved charged stretch in the linker region (residues 89-95, DPTLPR) mediated the interaction with RNA polymerase II. (embl.de)
  • For example, transcript elongation factor TFIIS is highly conserved among eukaryotes, and yet the TFIIS protein from Saccharomyces cerevisiae cannot function with mammalian RNA polymerase II and vice versa. (embl.de)
  • Yeast domain II alone is able to bind yeast RNA polymerase II with the same affinity as the full-length TFIIS protein, and this domain was expected to confer the species selectivity. (embl.de)
  • These 30 amino acids may physically orient domains II and III to support functional interactions between TFIIS and RNA polymerase II. (embl.de)
  • In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. (pasteur.fr)
  • 2020 ). RNA-dependent RNA polymerase (RdRp) is the nsp-12 that has the important property to backtracking that causes long pausing at specific site (Dulin et al. (springeropen.com)
  • These canonical subgenomic RNAs are thought to be generated through the complex mechanism that involves pausing of negative sense RNA synthesis by RNA-dependent RNA polymerase (RdRp) (Alexandersen et al. (springeropen.com)
  • Finding a similar 90° kink in a region of ribosomal RNA that binds factors necessary for the initiation of protein synthesis, the researchers speculate that the SARS virus may use the s2m element to hijack its host cell's protein synthesis machinery. (sciencedaily.com)
  • Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. (mdpi.com)
  • Background: Metazoans transcribe many long non-coding RNAs (lncRNAs) that are poorly conserved and whose function remains unknown. (upf.edu)
  • They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. (thermofisher.com)
  • Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. (biomedcentral.com)
  • Using in planta nucleotide-resolution mRNA structurome probing, we discovered that this stress-induced switch in translation is mediated by highly structured regions detected downstream of uAUGs in TE-up transcripts. (biorxiv.org)
  • Conservation of the RNA helicases suggests that mRNA structurome remodelling is a general mechanism for stress-induced translation across kingdoms. (biorxiv.org)
  • Unlike miRNAs whose central function is to restrain mRNA translation by inducing degradation, lncRNAs can act as numerous roles to exert their functions by directly or indirectly interacting with DNA, RNA or protein, even can encode some short peptides (Fig. 3 a-d) [ 6 ]. (biomedcentral.com)
  • Here, we highlight that an important RNA sequence region, encompassing an exon-intron hairpin loop (also called IDX-rasISS1), of the H-Ras pre-mRNA may encode an ncRNA that regulates p68 RNA helicase. (lidsen.com)
  • Loss of function mutations in TERT , the telomerase reverse transcriptase gene, and TR (also known as TERC ), the telomerase RNA, underlie up to 20% and 3% of familial and sporadic pulmonary fibrosis cases, respectively [ 8 ], [ 9 ]. (ersjournals.com)
  • Telomerase is an enzyme that maintains telomeres, the protective structures at the ends of chromosomes. (escholarship.org)
  • Telomerase has two essential components, the protein component telomerase reverse transcriptase (TERT) and the telomerase RNA (TER). (escholarship.org)
  • TER also has several conserved secondary and tertiary structures known to be important for telomerase function. (escholarship.org)
  • It consists of two major components: telomerase RNA (TER) and reverse transcriptase (TERT). (actanaturae.ru)
  • The present review summarizes data on the structure, biogenesis, and functions of telomerase. (actanaturae.ru)
  • Telomerase consists of two major components: reverse transcriptase (TERT) and telomerase RNA (TER), which contains the template domain for the telomere repeat synthesis [ 9 ]. (actanaturae.ru)
  • Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
  • Early studies showed that FinO specifically binds the 3' transcriptional terminator structure of FinP in a manner that critically relies on both the GC-rich hairpin and 3' polypyrimidine tail that define the terminator 16 , and further work showed that the base of the hairpin and 3' tail are both strongly protected from ribonuclease degradation by FinO 17 . (nature.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)
  • 2020 ). According to previous research model, it was suggested that strand exchange or 5′ leader (5′ UTR) sequence to body (RNA) fusion occurs at TRS during negative sense RNA synthesis (Kim et al. (springeropen.com)
  • Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. (biomedcentral.com)
  • In this work, we use SVM-based feature selection to derive the consensus abstract shape of homologous ncRNAs and apply the predicted shape to structure prediction including pseudoknots. (biomedcentral.com)
  • Of the characterized secondary structures of ncRNAs, Watson-Crick (C-G and A-U) and wobble base p airs (G-U) are most commonly seen. (biomedcentral.com)
  • As knowing the secondary structure provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs, deriving the secondary structures of ncRNAs remains an important research topic in RNA informatics. (biomedcentral.com)
  • Pseudoknot is an important structural motif in secondary structures of many types of ncRNAs. (biomedcentral.com)
  • Many computational methods have been used to determine the native structure of ncRNAs. (biomedcentral.com)
  • Non-coding RNAs (ncRNAs) have emerged as one of the most abundant regulatory molecules. (lidsen.com)
  • Long noncoding RNAs (lncRNAs) are a class of endogenous, non-protein coding RNAs that are highly linked to various cellular functions and pathological process. (biomedcentral.com)
  • Complete nucleotide sequencing of RNA of NIID04-27, -31, and -47 and partial sequencing of NIID04-41 were performed. (cdc.gov)
  • The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. (nature.com)
  • this covariation suggests that when one nucleotide of a predicted structured motif undergoes mutation, a compensatory mutation of the complementary base-pairing nucleotide is also observed, preserving the overall structure [ 3 , 4 ]. (biomedcentral.com)
  • It is recently shown that using the abstract shapes, which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions, can improve the performance of structure prediction. (biomedcentral.com)
  • Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. (nih.gov)
  • The latter, dubbed structure conservation index (SCI), is thus a measure for structural conservation only. (biomedcentral.com)
  • In this paper, we revisit the problem and propose a series of other possible strategies to measure structural conservation and compare their performance on a large data set of structural RNA families. (biomedcentral.com)
  • This indicates that an inhibitory feedback mechanism acting on the p68 RNA helicase is mediated by higher structural levels of the hairpin-loop. (lidsen.com)
  • The idea of abstract shapes has long been used to characterize different types of structures. (biomedcentral.com)
  • While the size of the folding space of an RNA sequence increases exponentially with the sequence length [ 10 ], many possible folding only differ in the details of the loop and helix regions and hence have the same abstract shape. (biomedcentral.com)
  • In response to immune induction, uORF-inhibition is alleviated by three Ded1p/DDX3X-homologous RNA helicases which unwind the RNA structures, allowing ribosomes to bypass the inhibitory uORFs and upregulate defence protein production. (biorxiv.org)
  • p65 functions in Tetrahymena by binding TER and reorganizing important RNA motifs, placing them in the correct orientation to facilitate TERT binding. (escholarship.org)
  • The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. (lookformedical.com)
  • Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations. (biomedcentral.com)
  • We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. (biomedcentral.com)
  • They mediate RNA-protein/RNA-RNA interactions in many different biological pathways and some even show enzymatic activity themselves. (biomedcentral.com)
  • We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. (biomedcentral.com)
  • At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
  • Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. (degruyter.com)
  • Upon inoculation, mature Pospiviroidae RNA molecules enter the plant cell nucleus. (degruyter.com)
  • These then fold and bend in three dimensions to form complex tertiary structures. (sciencedaily.com)
  • This strong sequence conservation indicates that the tertiary structure of s2m could be important for viral function, and when the researchers solved the three-dimensional crystal structure of the element, they found that it had a unique tertiary structure. (sciencedaily.com)
  • Jan. 11, 2022 Tertiary lymphoid structures are formations that occur outside of the lymphatic system. (sciencedaily.com)
  • A native structure is a structure that forms conformationally folding in native state before forming the tertiary structure. (biomedcentral.com)
  • Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. (lookformedical.com)
  • We describe the cognate cDNA cloning and characterization of two subunits (hTFIIIC63 and hTFIIIC102) that are present within a DNA-binding subcomplex (TFIIIC2) of TFIIIC and are related in structure and function to two yeast TFIIIC subunits (yTFIIIC95 and yTFIIIC131) previously shown to interact, respectively, with the promoter (A box) and with a subunit of yeast TFIIIB. (embl.de)
  • We then further characterized this domain, demonstrating that it binds a conserved region of the RNA and affects basepairing interactions in an important stem-loop region of the RNA. (escholarship.org)
  • Hepatitis G virus and GB virus C (GBV-C) are RNA viruses that were independently identified in 1995, and were subsequently found to be two isolates of the same virus. (wikipedia.org)
  • Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. (pasteur.fr)
  • Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp. (biomedcentral.com)
  • It therefore represents an attractive model to study the diversity of RNA viruses. (biomedcentral.com)
  • KCBP is a microtubule (MT) minus-end-directed kinesin widely conserved in plants. (go.jp)
  • sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
  • Moreover, recent global ribosome-sequencing (Ribo-seq, sequencing of ribosome-protected RNA fragments) studies have shown that uORFs are a prevalent feature in eukaryotic mRNAs, not limited to these few well-studied examples 19 - 21 . (biorxiv.org)
  • Finally, alternative splicing microarrays containing apoptosis targets were incubated to verify whether pre-mRNAs other than H-Ras could also present a similar hairpin loop structure regulated by p68 RNA helicase. (lidsen.com)
  • This gene encodes a DEXD/H box RNA helicase that functions as an antiviral factor and promotes RIG-I-like receptor-mediated signaling. (nih.gov)
  • Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection. (pasteur.fr)
  • Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. (pasteur.fr)
  • Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)
  • Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the LCD. (bvsalud.org)
  • Under normal conditions wherein methionine residues are reduced, the ECR forms a labile cross-ß structure that enables RNA granule condensation. (bvsalud.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)
  • In this thesis research, I describe our attempts to better understand how conserved elements of TERT and TER assemble to form a functional enzyme. (escholarship.org)
  • Scott and colleagues used this approach to hypothesize that the function of the s2m element involves interaction with a conserved host factor during the SARS life cycle. (sciencedaily.com)
  • In this work we used a biochemical technique known as site-directed hydroxyl radical probing to identify sites of interaction between protein and RNA within the enzyme. (escholarship.org)
  • Our work uncovered a specific interaction between a conserved RNA element known as the template boundary element (TBE) and a conserved protein element known as the CP2 motif. (escholarship.org)
  • Presumably, this process involves the interaction between the host's bromodomain-containing viroid RNA-binding protein 1 (VIRP1) and the viroid's TR domain (6). (degruyter.com)
  • Small RNAs (sRNAs) control a variety of physiological responses across bacterial species 1 . (nature.com)
  • Domain I is conserved in evolution from yeast to human species and is homologous to the transcription factors elongin A and CRSP70. (embl.de)
  • However, the results presented here indicate that domain II is insufficient to confer species selectivity, and a primary determinant lies in a 30-amino acid highly conserved linker region connecting domain II with domain III. (embl.de)
  • This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. (biomedcentral.com)
  • Programmable antivirals to target conserved essential shapes in pandemic viral genomes. (cdc.gov)
  • Though computationally expensive, mining intergenic regions of large metagenomic datasets is necessary for us to find structured RNAs in these largely unexplored regions of microbial genomes. (biomedcentral.com)
  • Since then, he has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and his main field of interest is RNA-interference (RNAi) and RNA-directed DNA methylation (RdDM) in plants. (degruyter.com)
  • The prediction of similar structures in the same region of hepatitis C virus may allow the functions of these structures to be determined with a more tractable experimental model. (ox.ac.uk)
  • Using predicted shapes in structure prediction allows us to achieve approximate 29% higher sensitivity and 10% higher positive predictive value than other pseudoknot prediction tools. (biomedcentral.com)
  • The combination of mass data analysis and SVM-based feature selection makes our approach a promising method for shape and structure prediction. (biomedcentral.com)
  • With advances in sequencing technologies and structure prediction, more pseudoknot structures are expected to be disclosed. (biomedcentral.com)
  • The predicted shape will then be used to guide structure prediction. (biomedcentral.com)
  • As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. (biomedcentral.com)
  • We report the genetic characterization of RNA from DENV-1 isolates from these patients. (cdc.gov)
  • RPB9 comprises two zinc ribbon domains joined by a conserved linker region. (embl.de)
  • Since then, she has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and her main field of interest is RNA-interference (RNAi) and viroid biology in plants. (degruyter.com)
  • Furthermore, RNAi assays containing the hairpin loop as an miRNA precursor were conducted, using the pTer vector, to explore the effects on 68 RNA helicase expression levels. (lidsen.com)
  • These RNAi analyses were quantified by Western blots (using anti-p68 RNA helicase and anti-EIF 2 α ) and Fluc/Rluc 3'UTRs/CDS assays. (lidsen.com)
  • See the article ' Lone pair pi contacts and structure signatures of r(UNCG) tetraloops, Z-turns, and Z-steps: A WebFR3D Survey ' by Zirbel and Auffinger (2022) for information about oxygen stacking interactions and for examples of WebFR3D searches and how to construct them. (bgsu.edu)
  • With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. (biomedcentral.com)
  • In the present bioinformatics analysis, a consensus secondary structure was identified among negative sense subgenomic RNAs of SARS-CoV-2. (springeropen.com)
  • In the current study, the bioinformatics analysis of negative sense subgenomic RNAs was performed that revealed a consensus hairpin loop secondary structure. (springeropen.com)
  • However, the time interval between GBV-C infection and clearance of viraemia (detection of GBV-C RNA in plasma) is not known. (wikipedia.org)
  • Of these 5 patients, 4 had a primary DENV infection and 1 had a primary dengue infection and a secondary flavivirus infection. (cdc.gov)
  • This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. (frontiersin.org)
  • Structure of a conserved domain common to the transcription factors TFIIS, elongin A, and CRSP70. (embl.de)
  • To elucidate the relationship between the structure and transcription elongation function of RPB9, we initiated a mutagenesis study on the Saccharomyces cerevisiae homologue. (embl.de)
  • This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production. (springeropen.com)
  • Although the conserved role of TRS has been identified/proposed in the pausing of transcription, the role of RNA secondary structure has not been identified in this perspective. (springeropen.com)
  • Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. (biomedcentral.com)
  • Functional constraints lead to evolutionary conservation of the RNA structure that in many cases can exceed the level of sequence conservation. (biomedcentral.com)
  • The ssRNA(+), likely transferred into the nucleolus, is finally processed by a type III RNase and a DNA LIGASE into unit-length circular RNAs (8) ( Figure 1 ). (degruyter.com)
  • Using a combination of covariance scanning and analysis of variability at synonymous sites, we previously demonstrated that the coding regions of HGV/GBV-C may contain extensive secondary structure of undefined function (Simmonds & Smith, Journal of Virology 73, 5787-5794, 1999). (ox.ac.uk)
  • By investigation of free energies on folding, secondary structure predictive algorithms and analysis of covariance between HGV/GBV-C genotypes 1-4 and the more distantly related HGV/GBV-C chimpanzee variant, we obtained evidence for extensive RNA secondary structure formation in both regions. (ox.ac.uk)
  • Surrounding the open reading frame (ORF) are 5´ and 3´ noncoding regions (NCRs) that form RNA secondary structures ( 4 ). (cdc.gov)
  • Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. (degruyter.com)
  • Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. (biomedcentral.com)
  • We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2-12 double-stranded RNA fragments. (biomedcentral.com)
  • The function of histone modifying epigenetic regulators and noncoding RNA as central mediators of epithelial stem cell renewal and differentiation represent major emerging areas of study in the lab. (stanford.edu)
  • Initially, two observations prompted the present study: i) previous results revealed down-regulation of p68 RNA helicase resulting from overexpression of the IDX hairpin loop in HeLa cells, and ii) the secondary structure of the IDX hairpin loop resembles pri-miRNAs, implying that an miRNA could be processed from the hairpin loop-containing pri-miRNA and regulate 68 RNA helicase. (lidsen.com)
  • Moreover, a similar effect on p68 RNA helicase-mediated interference is observed during the upregulation of the hairpin loop. (lidsen.com)
  • Finally, we also identified a similar hairpin loop-like structure in an alternative splicing region of MAPK12/ERK6. (lidsen.com)
  • Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. (nih.gov)
  • And RNA is being associated with many previously known functions in the cell, and equally if not more significant, RNA is being associated with many newly identified functions. (biomedcentral.com)
  • We have solved the structure of domain I of yeast TFIIS using NMR spectroscopy. (embl.de)
  • A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. (biomedcentral.com)
  • Because vitamin B-12 is highly conserved through the enterohepatic circulation, cobalamin deficiency from malabsorption develops after 2-5 years and deficiency from dietary inadequacy in vegetarians develops after 10-20 years. (medscape.com)