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RNA polymerase II holoenzyme
RNA polymerase II holoenzyme: a preformed eukaryotic transcription complex of Pol II with general transcription factors TFIIB, TFIIE, TFIIF, TFIIH, and Mediator/SRB proteins, discovered in yeast and mammalian cells for promoter recognition and regulated initiation.
RNA polymerase III
RNA polymerase III, or Pol III, is one of the three major eukaryotic nuclear RNA polymerases, making about 15% of cellular RNA in growing cells, including tRNA and 5S rRNA.
RNA polymerase inhibitor
An RNA polymerase inhibitor is a molecule that blocks transcription by binding RNA polymerase; rifamycins and fidaxomicin treat bacterial infections, while alpha-amanitin poisons human cells.
RNA polymerase sigma factor 54
RNA polymerase sigma factor 54 (σ54, σN, RpoN) is a 54 kDa bacterial sigma factor recognizing −24/−12 promoters; unlike σ70 it needs AAA+ enhancer-binding protein ATPases to open DNA.
RNA polymerase-binding transcription factor DksA
DksA (DnaK suppressor protein, dksA) is a 151-amino-acid E. coli transcription factor that binds RNA polymerase's secondary channel, not DNA, and with ppGpp represses rRNA promoters up to 20-fold while activating amino acid biosynthesis promoters during the stringent response.
RNA splicing
RNA splicing removes introns from pre-mRNA and joins exons to make mature mRNA, mainly via the spliceosome (U1-U6 snRNAs plus >50 proteins). Discovered as split genes by Sharp and Roberts in 1977; over 95% of human multi-exon genes are alternatively spliced.
RNA Stability
RNA stability: how long mRNA resists degradation, in cells (bacterial half-lives of minutes, eukaryotic hours, ARE-mediated decay) and as medicines (frozen mRNA-LNP vaccines, cold-chain limits, stabilization strategies).
RNA structure prediction
RNA structure prediction is the computational task of inferring an RNA molecule's folded structure from its sequence, usually as base-pair secondary structure and increasingly as full-atom 3D models.
RNA-binding protein
RNA-binding proteins (RBPs) are proteins that bind RNA to regulate splicing, stability, localization, and translation; about 1,600 human RBPs (roughly 7.5% of protein-coding genes) carry domains such as RRM and KH, and are mapped by CLIP-seq and computational prediction.
RNA-binding protein FUS
FUS (fused in sarcoma), historically TLS, is an RNA-binding protein regulating transcription, RNA processing, and DNA repair; gene fusions drive liposarcoma, and mutations cause familial ALS.
RNA-directed DNA methylation
RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic pathway in which small interfering RNAs guide repressive DNA methylation, silencing transposons and repeats; it was discovered in viroid-infected tobacco.
RNA-induced silencing complex
RNA-induced silencing complex (RISC): ribonucleoprotein effector of RNA interference, minimally one Argonaute protein plus a 20-30 nt guide RNA (siRNA, miRNA, or piRNA); human AGO2 is the only slicer, and GW182 mediates slicer-independent silencing.
RNA-Seq
RNA-seq (RNA sequencing) is a transcriptome-wide method that converts isolated RNA into cDNA and sequences it to measure gene expression; variants include scRNA-seq, long-read RNA-seq, and clinical applications.
RNAi as antiviral immunity
RNAi as antiviral immunity describes how RNA interference acts as a sequence-specific antiviral immune system in fungi, plants, and invertebrates, where viral RNA is cut into siRNAs that guide its destruction.
RNAi Therapeutics
RNAi therapeutics are siRNA drugs that silence disease genes via the RISC/Argonaute pathway; first FDA approval was patisiran (2018), with seven approved siRNAs delivered by lipid nanoparticles or GalNAc conjugates.
RNAIII
RNAIII is the 514-nucleotide dual-function regulatory RNA of the Staphylococcus aureus agr quorum-sensing system; it encodes delta-hemolysin and represses surface-protein mRNAs while activating toxin genes, driving the switch from colonization to toxin production.
Robert W. Malone
Robert W. Malone, American physician and biotechnologist; Salk Institute graduate student behind 1989 PNAS and 1990 Science mRNA-delivery papers; later a prominent COVID-19 vaccine critic whose inventor claims fact-checkers and peers reject.
Roquin
Roquin (Roquin-1/RC3H1 and Roquin-2/RC3H2) are RNA-binding E3-ligase-domain proteins that repress immune mRNAs such as ICOS by binding CDE/ADE stem-loops via the ROQ domain; the sanroque M199R mutation causes lupus-like autoimmunity in mice.
RpoB
RpoB (rpoB) is the bacterial gene encoding the beta subunit of DNA-dependent RNA polymerase; its 81-bp RRDR mutations cause rifampicin resistance and underpin TB molecular diagnostics like Xpert, with I491F as a diagnostic-escape mutation.
RpoS (σ38)
RpoS (σS, σ38, KatF) is the alternative sigma factor of E. coli RNA polymerase and master regulator of the general stress response, induced in stationary phase and starvation, controlling over 500 stress-survival genes.
rRNA Genes
rRNA genes (rDNA) are the genes transcribed to produce the RNA components of ribosomes, occurring across prokaryotes, archaea, and eukaryotes. In eukaryotes they form tandem repeats.
rRNA phylogenetics
rRNA phylogenetics infers evolutionary relationships from ribosomal RNA sequences, chiefly bacterial and archaeal 16S and eukaryotic 18S rRNA, and is the most widely used approach for reconstructing microbial phylogeny.
rRNA processing and modification
rRNA processing and modification are the cleavage and site-specific chemical changes that convert a 47S precursor transcript into the mature 18S, 5.8S, and 28S ribosomal RNAs, guided by snoRNPs.
rRNA-processing protein Efg1
rRNA-processing protein Efg1 (Exit from G1 protein 1, YGR272C) is a 233-aa nucleolar assembly factor of yeast 90S pre-ribosomes, required for 18S rRNA processing at A1/A2 sites; distinct from Candida Efg1 and mitochondrial EFG1.
RSD-2, N-terminal
RSD-2, N-terminal: the N-terminal region of RSD-2, a motif-less Caenorhabditis elegans protein required for systemic RNAi that interacts with Tudor-domain protein RSD-6 and lacks close homologs outside nematodes.
RT-qPCR analysis
RT-qPCR analysis is a bench biology method that measures the abundance of a chosen RNA by copying it into complementary DNA and quantifying that cDNA with real-time quantitative PCR.
Runt domain
Runt domain: the conserved 128-amino-acid DNA-binding and CBFβ-heterodimerization domain of Runx transcription factors (RUNX1/2/3), named after Drosophila runt, central to hematopoiesis, osteogenesis, and core-binding-factor leukemias.
RyhB
RyhB is an E. coli small regulatory RNA discovered in 2002 by Massé and Gottesman. Fur-repressed under iron repletion, it mediates the iron-sparing response, repressing iron-using enzymes (sdhCDAB, sodB) and promoting siderophore synthesis.
SBDS
SBDS, the Shwachman-Bodian-Diamond syndrome gene on chromosome 7, encodes a 250-amino-acid ribosome maturation factor that with EFL1 releases eIF6 from 60S pre-ribosomes; biallelic mutations cause Shwachman-Diamond syndrome.
Sds3-like
Sds3-like (SDS3/SUDS3) proteins are conserved corepressor subunits of SIN3 histone deacetylase complexes, stabilizing the 1-2 MDa Sin3L/Rpd3L assembly via coiled-coil dimerization and Sin3A HID binding; loss causes aneuploid cell lethality.