AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
RNA, RibosomalTranscription, GeneticDNA, RibosomalTranscription FactorsBase SequenceRNARNA, BacterialMolecular Sequence DataRNA, Ribosomal, 28SRNA, Ribosomal, 18SRNA, Ribosomal, 5SRNA, Ribosomal, 16SGenes, rRNAGenesNucleic Acid ConformationRNA Polymerase IPhylogenyDNA, Ribosomal SpacerPromoter Regions, GeneticRNA, MessengerNucleic Acid HybridizationRNA, ViralRNA, Small InterferingCell NucleolusRNA, TransferDNA Restriction EnzymesTranscription Factor TFIIIADNA-Directed RNA PolymerasesRNA, Ribosomal, 23SRNA, FungalGene Expression RegulationDNARNA, Ribosomal, 5.8SSequence Analysis, DNAPolymerase Chain ReactionTetrahymenaRNA, ProtozoanRNA SplicingEscherichia coliCloning, MolecularRNA Polymerase IIPlasmidsPol1 Transcription Initiation Complex ProteinsMutationPhysarumSpecies SpecificityRNA, Small NuclearCell NucleusRibosome Subunits, SmallBinding SitesCell LineDNA-Binding ProteinsSequence Homology, Nucleic AcidDNA, BacterialAmino Acid SequenceRNA EditingDNA, FungalSp1 Transcription FactorRibosomesProtein BindingSaccharomyces cerevisiaeHeLa CellsNucleolus Organizer RegionChromatinTrichomonadidaRNA Polymerase IIIDNA, MitochondrialRepetitive Sequences, Nucleic AcidSequence Analysis, RNADNA, RecombinantSingle-Strand Specific DNA and RNA EndonucleasesRestriction MappingGenome, MitochondrialNuclear ProteinsTranscriptional ActivationRNA InterferenceDNA, ProtozoanGenes, BacterialBacteriaRNA Processing, Post-TranscriptionalSequence AlignmentTrans-ActivatorsMetagenomeRNA, UntranslatedProtozoan Infections, AnimalGenes, FungalBradyrhizobiaceaeRNA PrecursorsBase CompositionTranscription Initiation SitePolymorphism, Restriction Fragment LengthModels, GeneticEvolution, MolecularRepressor ProteinsDNA, IntergenicParomomycinTransfectionChromosome MappingXenopusMethylation
PolymeraseSubunitSynthesisProteinsRDNAGenomeNucleolusTypes of RNAMRNAPutativeEukaryoticMoleculesLarge rRNATranscriptionalTranscriptsRibosomesVivoAmino acidsRibonucleicRRNA geneXenopusSingle strandedSpeciesSequenceEncodesMtDNAMammalianGeneticInvolvesPromoterTransfer RNAMessenger RNARegulationChromosomeNucleic acidMethylationPhenotypesChromatin structureTransient expressionInitiationInteractionsSensitivityOligonucleotidePromotersExpressionUpstreamMetabolismMaturationColiCellularNucleotidesTranscriptFunctionalLociRegulatory genesAmplificationGeneticsSequences
Polymerase13
  • c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I. (fhcrc.org)
  • Grandori, Carla and Gomez-Roman, Natividad and Felton-Edkins, Zoe A and Ngouenet, Celine and Galloway, Denise A and Eisenman, Robert N and White, Robert J (2005) c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I. Nature cell biology, 7 (3). (fhcrc.org)
  • c-Myc coordinates cell growth and division through a transcriptional programme that involves both RNA polymerase (Pol) II- and Pol III-transcribed genes. (fhcrc.org)
  • Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. (upenn.edu)
  • The Paralkar Lab has identified that key hematopoietic and leukemic transcription factors bind to rDNA and regulate rRNA transcription, and we are interested in understanding how the binding of cell-type-specific transcription factors regulates the activity of Polymerase I and the transcription of rRNA in normal hematopoiesis, and how this regulation is co-opted in leukemia to drive abundant ribosome biogenesis. (upenn.edu)
  • RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. (nih.gov)
  • Co-transcriptional pre-mRNA processing relies on reversible phosphorylation of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNA polymerase II (RNAP II). (cipsm.de)
  • This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
  • Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I. (wikidata.org)
  • Paradoxically, the rDNA is heavily transcribed by RNA polymerase I (Pol I) to synthesize ribosomal RNA, yet retains several key heterochromatin characteristics such as suppression of recombination and "silencing" of RNA polymerase II (Pol II)-dependent transcription. (hhs.gov)
  • 4. That is, RNA polymerase II reaches forward to find the start point, and RNA polymerase III reaches backward. (printerresource.com)
  • RNA polymerase III promoters differ significantly from RNA polymerase II promoters in that they are located downstream from the transcription start site and within the transcribed segment of the DNA. (printerresource.com)
  • However in contrast to genes transcribed by RNA polymerases II and III, ribosomal gene transcription by RNA polymerase I (Pol I) is species-specific. (prinsesmaximacentrum.nl)
Subunit4
  • The combination of expert knowledge in the fields of transcriptional regulation, chromatin structure and remodeling, ribosomal subunit processing and assembly will allow us to gain further insights in this fascinating topic. (uni-regensburg.de)
  • Anderson B.J. , Bills M.M. , Egerton J.R. , Mattick J.S. Cloning and expression in E coli of the gene encoding the structural subunit of Bacteroides nodosus fimbriae. (microbiologyresearch.org)
  • A ribosome contains a large and small ribosomal subunit. (dekooktips.com)
  • A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. (colorado.edu)
Synthesis15
  • rRNA synthesis and accumulation occurs rapidly following activation of a conditional MYC-ER allele (coding for a Myc-oestrogen-receptor fusion protein), is resistant to inhibition of Pol II transcription and is markedly reduced by c-MYC RNA interference. (fhcrc.org)
  • Ribosome synthesis involves transcription of ribosomal RNA genes, processing and assembly of ribosomal precursor molecules in the nucleolus and the nucleus, their transport to the cytoplasm and final maturation. (uni-regensburg.de)
  • rRNA transcription rates vary dramatically between different normal cell types in the hematopoietic tree, and leukemic cells have characteristic prominent nucleoli, indicating robust ribosome synthesis. (upenn.edu)
  • Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. (ncsu.edu)
  • The encoded protein is thought to play a role in many cellular processes including response to nucleolar stress, tumor suppression and synthesis of ribosomal DNA. (nih.gov)
  • First, the integration of QIAseq FastSelect in the workflow allows for rapid and efficient removal of ribosomal RNA during the cDNA synthesis reaction. (qiagen.com)
  • A specific nuclear compartment, the nucleolus, and its involvement in ribosomal RNA synthesis, are highlighted. (eur.nl)
  • Three main types of RNA are involved in protein synthesis. (dekooktips.com)
  • What are the three types of RNA and their role in protein synthesis? (dekooktips.com)
  • The three main types of RNA directly involved in protein synthesis are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). (dekooktips.com)
  • The involvement of RNA in such fundamental processes as protein synthesis and RNA processing has led to the idea that ribozymes were more common in early life. (printerresource.com)
  • The most widely understood role of RNA is in protein synthesis, which includes messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA) (see Chapter 2). (printerresource.com)
  • RNA picks up specific amino acids from the cytoplasm of the cell and delivers them to the ribosomes where protein synthesis takes place. (yourgenome.org)
  • Between them, mRNA, rRNA and tRNA are three of the principal players in protein synthesis - the process by which the instructions in your genes are turned into functioning proteins in your cells. (yourgenome.org)
  • In addition, mitochondrial DNA (mtDNA) encodes 2 ribosomal RNA genes and 22 transfer RNA (tRNA) genes necessary for the intramitochondrial synthesis of these 13 polypeptides. (medscape.com)
Proteins22
  • This study aimed to evaluate the expression levels of miR-34a and 11 of its bioinformatically selected target genes and proteins to test their potential dysregulation in RCC. (hindawi.com)
  • Ribosomal proteins (RPs) play important roles in modulating the MDM2-p53 pathway. (elifesciences.org)
  • They seem to think that the gene-centric view requires that everything be attributed to DNA sequences that encode proteins. (blogspot.com)
  • This balance is maintained by the combinatorial activity of transcription factors and chromatin proteins that dictate the transcription of coding gene networks instructing fate choice decisions. (upenn.edu)
  • Nonetheless, MDM2 is in turn regulated by ribosomal proteins (RPs) that binds and suppress the MDM2 E3 ubiquitin ligase activity resulting in the stabilization and activation of p53 [9]. (nanoker-society.org)
  • These ribosomal proteins are found in stoichiometric amounts in the.Approximately 10 L of the extracted DNA was run on 1% gel electrophoresis and visualized under Gel Doc (Bio-rad, Hercules, CA, US). (nanoker-society.org)
  • Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. (ncsu.edu)
  • The achievement, reported in Cell , reveals in unprecedented detail how strands of ribonucleic acid (RNA), cellular molecules that are inherently sticky and prone to misfold, are "chaperoned" by ribosomal proteins into folding properly and forming one of the main components of ribosomes. (scripps.edu)
  • This shows that we now can examine in detail how RNAs fold while they are being synthesized and proteins are assembling on them," says first author Olivier Duss, PhD, a postdoctoral research fellow in the Department of Integrative Structural & Computational Biology at Scripps Research. (scripps.edu)
  • The team used an advanced imaging technology called "zero-mode waveguide single-molecule fluorescence microscopy," which they have adapted in recent years for real-time tracking of RNAs and proteins. (scripps.edu)
  • Ribosomes are made of both RNA and proteins, reflecting a molecular partnership that is widely believed to go back nearly to the dawn of life on Earth. (scripps.edu)
  • The findings, according to the researchers, also hint at the existence of unknown RNA assembly factors, most likely proteins, that were not present in their lab-dish-type imaging experiments but are present in cells and boost the efficiency of RNA folding. (scripps.edu)
  • Our study indicates that in ribosomal RNA-folding, and perhaps more generally in RNA-folding in cells, many proteins help fold RNA though weak, transient and semi-specific interactions with it," Duss says. (scripps.edu)
  • The team will now be able to extend this research further to study not only the rest of ribosome assembly, which involves multiple RNA strands and dozens of proteins, but also the many other types of RNA-folding and RNA-protein interaction in cells. (scripps.edu)
  • EVs are small lipid-membrane covered particles and contain RNA, lipids and proteins. (bvsalud.org)
  • DNA methyltransferases are not limited to catalyzing DNA methylation, but also take part in the regulation of gene expression through interactions with other proteins that repress transcription and modify chromatin structure. (caister.com)
  • Specific sets of genes encoding proteins become activated, whereas others are repressed. (eur.nl)
  • RNA is then translated into proteins by structures called ribosomes. (dekooktips.com)
  • Messenger RNA (mRNA) Carries information specifying amino acid sequences of proteins from DNA to ribosomes. (dekooktips.com)
  • Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins. (colorado.edu)
  • rRNA genes contain regions of variable DNA sequence that are unique to the species carrying the … Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. (printerresource.com)
  • Ribonucleic acid, or RNA, plays a key role in turning the instructions held in the DNA of your genome into functional proteins in your cells. (yourgenome.org)
RDNA9
  • Furthermore, by using combined immunofluorescence and rRNA-FISH, we have detected endogenous c-Myc in nucleoli at sites of active ribosomal DNA (rDNA) transcription. (fhcrc.org)
  • Given that rRNA accounts for the bulk of the transcriptional output of the cell, the inability to map datasets to rDNA has historically been a major limitation, and has created a significant knowledge gap in our understanding of the most abundant RNA in the cell. (upenn.edu)
  • The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
  • It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. (ncsu.edu)
  • Such is the case with the rDNA locus, a relatively understudied and unusual form of heterochromatin consisting of tandemly repeated rRNA genes. (hhs.gov)
  • In budding yeast rDNA, transcription of non-coding RNAs from the intergenic spacers must be silenced by the conserved NAD+-dependent histone deacetylase Sir2 to maintain rDNA stability and support replicative lifespan. (hhs.gov)
  • Here we explored the JmjC domain-containing histone demethylase 1B (JHDM1B) function in the epigenetic control of rDNA transcription. (oncotarget.com)
  • In these cellular models, prolonged JHDM1B downregulation triggered a surge of 45S pre-rRNA transcription and processing, associated with a re-modulation of the H3K36me2 levels at rDNA loci and with changes in DNA methylation of specific CpG sites in rDNA genes. (oncotarget.com)
  • Using a human cell line that expresses epitope-tagged yeast TBP, we have isolated a chimeric complex consisting of yeast TBP and human TAFs which faithfully promotes human rDNA transcription in vitro. (prinsesmaximacentrum.nl)
Genome18
  • While loss of wild-type p53 causes fatal damages to the genome, it is not surprising that the TP53 gene is mutated in more than 50% human cancers, and the functions of p53 are often impeded through various mechanisms in the remainder ( Levine and Oren, 2009 ). (elifesciences.org)
  • In addition to genes, there are many other functional parts of the genome. (blogspot.com)
  • Scientists know what they are talking about when they say that the human genome contains about 20,000 protein-coding genes and at least 5,000 genes for non-coding RNAs. (blogspot.com)
  • They are comfortable with the idea that our genome has lots of other functional regions that lie outside of the genes. (blogspot.com)
  • Then they confuse themselves by thinking that knowledgeable experts use the word "gene" as a synonym for all functional sequences in the genome. (blogspot.com)
  • Current bioinformatic pipelines for high-throughput studies like whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like ribosomal DNA. (upenn.edu)
  • A transcription map of the pea chloroplast genome. (ncsu.edu)
  • A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. (ncsu.edu)
  • For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. (ncsu.edu)
  • In the vast majority of eukaryotes, OXPHOS is operated by genes encoded by two genomes - most in the nuclear genome (nDNA) and 37 in the short circular mitochondrial genome (mtDNA). (biorxiv.org)
  • Whereas most regions of the genome are constantly methylated these elements are mainly kept free of methylation thereby facilitating the establishment of an open chromatin structure and of initiation of transcription. (caister.com)
  • Besides its role in the regulation of genes, DNA methylation silences repetitive elements and appears to be important for the stability of the mammalian genome. (caister.com)
  • CTCF is a protein that mediates distinct processes of gene regulation, including transcription and the structural organization of the genome. (eur.nl)
  • Heterochromatin is generally repressive to transcription and plays important roles in maintaining genome stability, whether it is through facilitating centromere function, telomere protection, or suppressing recombination between the underlying DNA repeats to help maintain genomic integrity. (hhs.gov)
  • Two other major roles for noncoding RNA are in genome defense and in genetic regulation. (printerresource.com)
  • Using an RNA genome, many viruses are known to encode their genetic information. (printerresource.com)
  • A. Ribosomal RNA analysis StructRNAfinder - predicts and annotates RNA families in transcript or genome sequences. (printerresource.com)
  • A deletion anywhere in the mitochondrial genome may affect transcription or translation of genes that were not affected by the deletion. (medscape.com)
Nucleolus1
Types of RNA11
MRNA15
  • Nuclear and cytoplasmic mRNAs for several phytochrome-regulated genes were examined in Pisum seedlings in order to investigate possible light effects on mRNA partitioning between the nucleus and cytoplasm. (ncsu.edu)
  • mRNA steady state levels of the chlorophyll a/b-binding protein of photosystem II, ferredoxin I, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 and pEA207, two other light-responsive genes, were determined during chlorophyll photooxidation. (ncsu.edu)
  • Quantitative-real time-reverse transcription PCR (Q-RT-PCR) is widely used and is a sensitive and robust technique for the detection and quantification of often rare mRNA targets [ 3 ]. (biomedcentral.com)
  • RNA sequencing of microRNAs (miRNAs) derived from EVs (EV-miRNAs) and mRNA transcripts from blood cells was used for the construction of signaling networks reflecting endocannabinoid and miRNA communication by EVs to target immune cells. (bvsalud.org)
  • Researchers can also utilize mRNA enrichment kits (sold separately) and focus RNA-seq library construction on protein coding mRNAs. (qiagen.com)
  • RNA-seq libraries have been successfully constructed from high-quality total RNA, fragmented FFPE RNA and enriched mRNA. (qiagen.com)
  • RNA processing in chloroplasts includes mRNA 5′- and 3′-end processing, intron splicing, and intercistronic cleavages of polycistronic messages, as well as typical tRNA and rRNA processing. (dekooktips.com)
  • They are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). (dekooktips.com)
  • Additional RNAs are involved in gene regulation and mRNA degradation. (dekooktips.com)
  • Messenger RNA (mRNA) carries the instructions from the nucleus to the cytoplasm. (dekooktips.com)
  • mRNA is produced in the nucleus, as are all RNAs. (dekooktips.com)
  • In this video, we will learn how to describe the components that make up RNA molecules and differentiate between tRNA, mRNA, and rRNA. (nagwa.com)
  • Targeted disruption of the gene encoding D4Rs reduces the amplitude of the contrast sensitivity rhythm by reducing daytime sensitivity and abolishes the rhythmic expression of Npas2 and Adcy1 mRNA in the ganglion cell layer (GCL) of the retina. (jneurosci.org)
  • Messenger RNA (mRNA) is formed in the nucleus on the 3' coding (antisense) strand of the DNA in the process of transcription . (yourgenome.org)
  • mRNA molecules move to the surface of the ribosomes, carrying instructions from the genes in the nucleus about the protein which needs to be synthesised. (yourgenome.org)
Putative4
  • These findings indicate miR-34a along with its putative target genes could play a role in RCC tumorigenesis and progression. (hindawi.com)
  • The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. (yeastgenome.org)
  • Sequence and primer extension analysis revealed the presence of putative genes encoding tRNA lle and tRNA Ala within the 16S-23S spacer region, as well as a number of potential regulatory features. (microbiologyresearch.org)
  • These elements included a single promoter, which was mapped upstream of the 16S rRNA gene and which was similar to Escherichia coli consensus promoter sequences, an AT-rich upstream region, a GC-rich motif that may be involved in stringent control, leader and spacer antitermination sequences, sites for ribonuclease processing, and a putative factor-independent terminator sequence. (microbiologyresearch.org)
Eukaryotic1
Molecules3
  • The imaging feat clarifies how RNA molecules fold-and might one day translate into better medicines for a host of diseases. (scripps.edu)
  • More generally, the research offers biologists a powerful new approach to the study of RNA molecules, hundreds of thousands of which are active at any given time in a typical cell. (scripps.edu)
  • RNA is closely related to DNA, but it contains a different sugar - ribose - and the base uracil (U) replaces thymine (T). The other bases, adenine (A), cytosine (C) and guanine (G), are common in both molecules. (yourgenome.org)
Large rRNA1
  • Remarkably, silencing of these non-coding RNAs by Sir2 actually requires Pol I-dependent transcription of the large rRNA coding genes. (hhs.gov)
Transcriptional7
  • This study indicates that chloroplast genes are often grouped into multigene transcriptional units which can be cotranscribed, and that light-stimulated plastid development involves changes in the relative abundance of the overlapping RNAs of different length that result from transcription of these genes or gene clusters. (ncsu.edu)
  • Emphasis is given to the diversity of different responses observed with different genes and evidence for light effects at both transcriptional and post‐transcriptional levels. (ncsu.edu)
  • This gene encodes a nucleolar transcriptional regulator that was first identified by its ability to bind specifically to the Myb proto-oncogene protein. (nih.gov)
  • Expression of the reporter construct is also affected by proximity to highly expressed ribosomal RNA operons depending on the relative orientation of transcription despite being insulated by strong transcriptional terminators, in a manner consistent with supercoiling competition. (biorxiv.org)
  • Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. (biorxiv.org)
  • Baylis H.A. , Bibb M.J. Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomjces A3(2). (microbiologyresearch.org)
  • Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. (bvsalud.org)
Transcripts7
  • All transcripts detected were more abundant (as a fraction of total cellular RNA) in light grown plants than in plants entirely in the dark. (ncsu.edu)
  • Transcripts from each of five light-regulated genes exhibited different responses to a variety of light treatments, but for each transcript we observed a characteristic linear relationship between nuclear and cytoplasmic levels over a wide range of total transcript abundance. (ncsu.edu)
  • Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
  • To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. (biorxiv.org)
  • These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
  • The final RNA-seq libraries created using the QIAseq FastSelect RNA Library Kits retain strand and directionality of the original transcript, increasing the accuracy of the final mapped transcripts and quantification. (qiagen.com)
  • To such effect, I want to perform an RNA-Seq experiment in order to analyze potential rRNA transcripts isoforms and processing sites. (printerresource.com)
Ribosomes1
Vivo3
  • Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
  • However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
  • Finally, mtDNA transcription termination sites have been either mapped in-vitro, or were associated with MTERF binding sites ( Christianson and Clayton 1986 ), thus, again, limiting the capability to in-vivo map transcription terminations sites in diverse organisms. (biorxiv.org)
Amino acids1
Ribonucleic1
  • and assignment of the genera Cardiobacterium, Dichelobacter, and Suttonella to Cardio-bacteriaceae fam nov in the gamma division of Proteobacteria based on 16S ribosomal ribonucleic acid sequence comparisons. (microbiologyresearch.org)
RRNA gene2
  • The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. (uni-wuerzburg.de)
  • Distel, D. L., DeLong, E. F., and Waterbury, J. Epub … Bacterial Identification by 16S rRNA Gene Sequence Analysis Background All bacteria contain 16S ribosomal RNA (rRNA) genes of approximately 1500 base pairs (bp) in length. (printerresource.com)
Xenopus1
Single stranded4
  • This class of noncoding RNAs is small, single stranded, and 19-25 nucleotide long that act as negative regulators involved in posttranscriptional silencing of the gene expression [ 5 ]. (hindawi.com)
  • RNA is a single-stranded nucleic acid that is composed of three main elements: a nitrogenous base, a five-carbon sugar and a phosphate group. (dekooktips.com)
  • RNA is normally single-stranded, while DNA is double-stranded. (nagwa.com)
  • Notice that RNA has one sugar phosphate backbone because it's single-stranded, while DNA has two because it's double-stranded. (nagwa.com)
Species4
  • Of these, 3,114 were single genes confined to a single species. (blogspot.com)
  • Because of small differences in the 16S ribosomal gene, the primers are specific to organisms only of the M. tuberculosis complex ( M. tuberculosis, M. bovis, M. africanum, M. microti ) and only these species are detected. (vin.com)
  • The simple workflow utilizes the FastSelect RNA removal reagents to suppress ribosomal RNA and other unwanted RNAs to enable gene expression and transcript identification from a variety of model systems including human, mouse, rat and related species, plants, yeast, zebrafish, flies, worms and bacteria. (qiagen.com)
  • The complete solution includes online access to the RNA-seq analysis portal (for supported species), which allows researchers to start with FASTQ files and perform read alignment, differential gene expression and pathway analysis. (qiagen.com)
Sequence8
  • A gene is a DNA sequence that is transcribed to produce a functional product. (blogspot.com)
  • Finally, they misunderstand the term "gene-centric" where the word "gene" is used metaphorically to refer to any DNA sequence that functions in population genetics and evolution. (blogspot.com)
  • A small target sequence within this gene is amplified (billions of copies are made) using PCR. (vin.com)
  • This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. (biorxiv.org)
  • Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)
  • Microarrays, by making use of the sequence resources created in genomic projects, are a powerful technology capable of measuring the expression levels of thousands of genes simultaneously and have dramatically expedited comprehensive understanding of gene expression profiles for disease development. (biomedcentral.com)
  • Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing. (wikidata.org)
  • In mammals, cytosine methylation at CpG positions of the DNA sequence is one of the hallmarks of epigenetic gene silencing. (caister.com)
Encodes2
  • Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide. (ncsu.edu)
  • The AR1 gene, which encodes the TGMV coat protein, was transcribed transiently in leaf discs after agroinoculation of TGMV A DNA. (ncsu.edu)
MtDNA3
  • Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. (biorxiv.org)
  • Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged. (biorxiv.org)
  • The proposed mechanism is based on the knowledge that transcription of mtDNA is polycistronic, which means that all genes encoded on the heavy and light strands are transcribed as 2 large precursor RNA strands. (medscape.com)
Mammalian2
  • The question is, how many of these gene families show gain or loss of numbers during mammalian evolution? (blogspot.com)
  • DNA methylation patterns change dynamically during mammalian development and lineage specification, yet scarce information is available about how DNA methylation affects gene expression profiles upon differentiation. (cipsm.de)
Genetic5
  • With the recognition that DNA was the genetic material, the word "gene" took on an additional meaning as a physical unit of function. (blogspot.com)
  • Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. (yeastgenome.org)
  • This is why DNA is preferred by organisms as a support for genetic information, and short-lived RNA is preferred for transient messages in the cell. (nagwa.com)
  • Before we get into this, let's first review how RNA can transmit genetic information contained in DNA to the rest of the cell. (nagwa.com)
  • It is RNA which makes it possible for DNA to act as the genetic material, in spite of being trapped in the nucleus of the cell. (yourgenome.org)
Involves1
  • Our study demonstrates a circadian rhythm of contrast sensitivity that peaks during the daytime, and that its regulation involves interactions of D4Rs, the clock gene Npas2 , and the clock-controlled gene adenylyl cyclase 1 ( Adcy1 ) in a subset of retinal ganglion cells (RGCs). (jneurosci.org)
Promoter2
  • The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. (ncsu.edu)
  • During evolution, CpG rich regions, so-called CpG islands, have been established as prominent features of promoter regions of genes. (caister.com)
Transfer RNA2
  • Transfer RNA (tRNA) is found in the cytoplasm and has a complex shape. (yourgenome.org)
  • These subsequently cleave into separate RNA strands, including transfer RNA strands. (medscape.com)
Messenger RNA1
  • In 1961, French scientists François Jacob and Jacques Monod hypothesized the existence of an intermediary between DNA and its protein products, which they called messenger RNA. (dekooktips.com)
Regulation6
  • As a graduate student he worked on fundamental aspects of regulation of expression of genes. (wikipedia.org)
  • He interrupted his postdoctoral studies at MIT briefly the summer of 1973 to serve as a visiting professor at the University of Copenhagen Faculty of Health and Medical Sciences, where he continued his work on the regulation of gene expression in bacteria. (wikipedia.org)
  • Little is known however about how rRNA transcription is regulated and fine-tuned across normal and malignant tissues, and whether this regulation can be targeted for leukemia treatment. (upenn.edu)
  • These findings provide insight into the regulation of naturally occurring genes and specific rules for optimizing control of synthetic biology constructs. (biorxiv.org)
  • It gives an introduction to gene regulation and how this process is influenced by chromatin modifications, nuclear organization and compartmentation. (eur.nl)
  • The accessibility and transcription of ribosomal genes is controlled at several levels, with their epigenetic regulation being one of the most important. (oncotarget.com)
Chromosome4
  • MicroRNA-34a gene (MIR-34A) that is located on chromosome 1p36 belongs to one of evolutionary-conserved miRNA families (MIR-34 family) that consists of three members: MIR-34A, MIR-34B, and MIR-34C [ 10 ]. (hindawi.com)
  • Even in wild-type “Chinese Spring”, the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. (ncsu.edu)
  • Human chromosome 15q11-q13 is a critical region for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and most of the genes are under the condition of imprinting mechanism. (researchgate.net)
  • The epigenetic modification of DNA with 5-methylcytosine is an important regulatory event involved in chromatin structure, genomic imprinting, inactivation of the X chromosome, transcription, and retrotransposon silencing. (caister.com)
Nucleic acid1
  • RNA is a nucleic acid similar to DNA, but with only a single, helical strand of bases. (yourgenome.org)
Methylation1
  • Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. (ncsu.edu)
Phenotypes3
  • Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (yeastgenome.org)
  • Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes. (yeastgenome.org)
  • A knowledge graph of biological entities such as genes, gene functions, diseases, phenotypes and chemicals. (edu.sa)
Chromatin structure1
Transient expression2
  • Transient expression of heterologous RNAs using tomato golden mosaic virus. (ncsu.edu)
  • The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
Initiation3
  • Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. (nih.gov)
  • Transcription takes place in three steps: initiation, elongation, and termination. (dekooktips.com)
  • Basic mechanisms of transcription initiation are conserved from yeast to man. (prinsesmaximacentrum.nl)
Interactions2
  • This involved the transcription, or copying out from its corresponding gene, of a ribosomal RNA, and initial interactions of this RNA strand with a ribosomal protein. (scripps.edu)
  • A key finding was that the ribosomal protein partners guide the folding of the RNA strand through multiple temporary interactions with the strand, well before they nestle into their final places in the folded RNA-protein molecule. (scripps.edu)
Sensitivity2
  • DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat. (ncsu.edu)
  • Characterization of the impact of the MYBBP1A gene and rs3809849 on asparaginase sensitivity and cellular functions. (nih.gov)
Oligonucleotide2
  • The short-oligonucleotide-based Affymetrix GeneChip ® arrays utilize multiple probes for each gene with an automated control for the experimental process from hybridization to quantification and thus provide reliable and comparable data [ 2 ]. (biomedcentral.com)
  • A., 1992, The use of 16S ribosomal RNA targeted oligonucleotide probes to study competition between ruminai fibrolytic bacteria. (printerresource.com)
Promoters2
  • Transcription is controlled by regulatory sequences such as promoters, operators, and enhancers but these are not part of the gene. (blogspot.com)
  • Boros I. , Csordés-Tôth E. , Kiss A. , Tôrôk I. , Udvardy K. , Venetianer P. Identification of two new promoters probably involved in the transcription of a ribosomal RNA gene of Escherichia coli. (microbiologyresearch.org)
Expression12
  • An aberrant miRNA expression could contribute to cancer development and progression [ 6 , 7 ] and could affect their target genes that are involved in many biological processes, such as cell differentiation, proliferation, apoptosis, metabolism, and development [ 8 ]. (hindawi.com)
  • In addition, downregulation in expression of 18S ribosomal RNA was also observed in all treated HT-29 cells. (nanoker-society.org)
  • This was confirmed by fluorescence imaging to measure the level of expression of 18S ribosomal RNA in live cell images. (nanoker-society.org)
  • Patterns of phytochrome-induced gene expression in etiolated pea buds. (ncsu.edu)
  • Photobleaching was found to affect the expression of the various genes in different ways. (ncsu.edu)
  • Sixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. (biomedcentral.com)
  • For example, microarray technology has been used to compare gene expression profiles between normal and diseased cells and this has led to dramatic advances in the understanding of cellular processes at the molecular level [ 1 ]. (biomedcentral.com)
  • An appropriate internal control for Q-RT-PCR should be expressed stably across all data samples and if this is true, measurement of genes relative to the internal control will reflect the real gene expression. (biomedcentral.com)
  • The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. (biomedcentral.com)
  • This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. (biomedcentral.com)
  • Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. (biomedcentral.com)
  • 6. I want to study ribosomal RNA expression and potential processing sites in bacteria. (printerresource.com)
Upstream1
  • One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. (ncsu.edu)
Metabolism1
  • The problem with this part of the book (the part about the molecular gene) is that the authors seem to be confused about the difference between a molecular gene and the view that "genes" are the only thing that count in genetics, evolution, metabolism etc. (blogspot.com)
Maturation1
  • Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. (nih.gov)
Coli2
Cellular1
  • GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies ( Molecular Function , Biological Process , and Cellular Component ), a reference, and an evidence code. (yeastgenome.org)
Nucleotides2
  • and modifying RNA nucleotides either at the ends of an RNA or within the body of the RNA. (dekooktips.com)
  • RNA and DNA are both considered nucleic acids which are made up of repeating subunits called nucleotides. (nagwa.com)
Transcript2
  • The presence of CTCs in 43 blood samples from patients with metastatic melanoma was evaluated using a combination of immunocytochemistry and transcript analyses of five genes by RT-PCR and 19 genes by droplet digital PCR (ddPCR), whereby a CTC score was calculated. (nature.com)
  • Second, during reverse transcription, each transcript incorporates a unique sample ID. (qiagen.com)
Functional3
  • There are two types of genes: protein-coding genes and those that specify a functional noncoding RNA (i.e ribosomal RNA, lincRNA). (blogspot.com)
  • Thus, when they recognize that important functional elements exist outside of genes, they conclude that the gene-centric view is fatally flawed. (blogspot.com)
  • However, in many cases, the RNA needs further processing before it is functional. (printerresource.com)
Loci4
  • Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. (ncsu.edu)
  • Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. (ncsu.edu)
  • Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. (ncsu.edu)
  • These loci (rrnA, rrnB and rrnC) were isolated on recombinant lambda clones, and comprised 16S, 23S and 5S rRNA genes closely linked in that order. (microbiologyresearch.org)
Regulatory genes1
  • They talk about "structural genes" and imply that the discovery of "regulatory genes" altered our concept of the gene but these terms were never used by experts in the way that the authors imagine (p. 66). (blogspot.com)
Amplification3
  • Recent technological advances have seen the introduction of methods that detect mycobacteria by amplification of mycobacterial nucleic acids (DNA or RNA) followed by detection of the amplification product. (vin.com)
  • At present, two amplification methods have been FDA approved for detection of M. tuberculosis from sputum in humans: the Amplicor system (Roche Molecular Systems, Branchburg, NJ) and the AMTD system (Gen-Probe Inc., San Diego, CA). The Amplicor system has as its target the mycobacterial 16S ribosomal RNA gene. (vin.com)
  • The AMTD system amplifies the ribosomal RNA through a method termed Transcription Mediated Amplification (TMA). (vin.com)
Genetics2
  • Because of my interest in this topic, I was intrigued by the title of a new book, The Gene: from Genetics to Postgenomics . (blogspot.com)
  • This leads us to their second goal where they try to convince us that the definition of "gene" is fatally flawed because genes aren't the only things that play an important role in genetics. (blogspot.com)
Sequences3
  • Non-experts may not be familiar with the topic and they may have many misconceptions about genes and DNA sequences but we don't base our science on the views of non-experts. (blogspot.com)
  • I suspect they are thinking of a gene as coding sequences but you have to struggle to interpret their view of the molecular definition. (blogspot.com)
  • Berg K.L. , Squires C. , Squires C.L. Ribosomal RNA operon anti-termination Function of leader and spacer region box B-box A sequences and their conservation in diverse microorganisms. (microbiologyresearch.org)