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Transcription antitermination protein RfaH
RfaH (sfrB, hlyT) is an E. coli NusG-paralog transcription antiterminator recruited at the ops DNA sequence, suppressing Rho termination on virulence operons, and switching its C-terminal domain from alpha-hairpin to beta-barrel to couple transcription to translation.
Transcription bubble
Transcription bubble: the ~12–14 bp region of unwound single-stranded DNA carried by RNA polymerase during transcription initiation and elongation, formed by σ-factor flip-and-capture in bacteria and TFIIH in eukaryotes.
Transcription elongation factor
Transcription elongation factors are proteins that act on RNA polymerase already transcribing a gene, controlling whether it pauses, resumes, or backtracks; key examples include DSIF, NELF, and P-TEFb.
Transcription elongation factor 1
Transcription elongation factor 1 (Elf1; ELOF1 in humans) is a conserved zinc finger factor of the RNA polymerase II elongation complex, sealing the DNA entry cleft, aiding nucleosome passage, and driving transcription-coupled repair.
Transcription elongation factor GreB
Transcription elongation factor GreB (greB, E. coli, 158 aa) is a bacterial transcript cleavage factor that rescues backtracked RNA polymerase by stimulating endonucleolytic RNA cleavage via its coiled-coil tip residues D41/E44, distinguishing it from GreA by tighter binding and longer cleavage products.
Transcription elongation factor Spt6
Spt6 (Suppressor of Ty 6; SUPT6H in humans) is an essential, conserved histone H3-H4 chaperone and transcription elongation factor that reassembles nucleosomes behind RNA polymerase II, binds Pol II via a tandem SH2 domain, maintains H3K36 methylation, and represses cryptic transcription.
Transcription factor
A transcription factor is a protein that binds specific DNA sequences in enhancer or promoter regions and activates or represses transcription of a particular gene; humans have over 1,500 such genes.
Transcription factor FapR
FapR (fatty acid and phospholipid regulator), bacterial transcriptional repressor of the fap regulon in Gram-positive bacteria such as Bacillus subtilis; malonyl-CoA binding releases it from FapO; hot-dog fold homodimer; used as malonyl-CoA biosensor.
Transcription factor HTH, IscR
IscR (transcription factor HTH, IscR) is an Rrf2-family, helix-turn-helix bacterial transcription factor with a [2Fe-2S] cluster that regulates Fe-S homeostasis, binding type 1 and type 2 DNA motifs via Glu43.
Transcription factor II A
Transcription factor II A (TFIIA) is a eukaryotic general transcription factor of subunits TFIIAα/β and TFIIAγ (53 kDa) that stabilizes TBP/TFIID binding to the TATA box, mediates activator responses, and competes with repressor NC2.
Transcription factor II B
Transcription factor II B (TFIIB) is a eukaryotic general transcription factor that bridges TBP-bound promoters to RNA polymerase II, binds BRE promoter elements, selects transcription start sites, and is conserved in archaea and Pol I/III systems.
Transcription factor II H
Transcription factor II H (TFIIH) is a 10-subunit, ~500 kDa eukaryotic complex with XPB translocase and XPD helicase, essential for RNA polymerase II transcription initiation and nucleotide excision repair; mutations cause xeroderma pigmentosum and trichothiodystrophy.
Transcription factor NusA
NusA (transcription factor NusA) is a conserved bacterial transcription elongation factor, 55 kDa in E. coli, that binds RNA polymerase and modulates pausing, intrinsic termination, and phage lambda N-mediated antitermination.
Transcription factor Opi1/Ccg-8
Opi1 (OPI1/Ccg-8, YHL020C) is the Saccharomyces cerevisiae transcriptional repressor of UAS_INO phospholipid genes; it binds Ino2 in the nucleus, is sequestered at the ER by PA and Scs2, and gives the Opi- inositol-overproducer phenotype when lost.
Transcription initiation factor IIE subunit alpha, N-terminal
TFIIEα N-terminal region: conserved amino-terminal domain of the large TFIIE subunit, carrying an extended winged helix motif (residues 1–115) that binds the Pol II clamp, TFIIEβ, TFIIB, and XPB; archaeal ortholog TFE.
Transcription Initiation Site
Transcription initiation site (transcription start site, TSS), the +1 nucleotide where RNA polymerase begins synthesizing RNA; clustered in transcription start regions, shaped by core promoter elements (TATA, INR, BRE, DPE), and mapped genome-wide by CAGE and RAMPAGE.
Transcription regulator HTH, GntR
GntR (PF00392, HTH_GntR) is a large bacterial transcription factor family named after the Bacillus subtilis gluconate operon repressor, with a winged helix-turn-helix DNA-binding domain, metabolite-sensing C-terminal domain, and FadR, HutC, MocR, YtrA, AraR, PlmA subfamilies.
Transcription regulator Rrf2
Rrf2 transcription regulator family: widespread bacterial dimeric winged-HTH repressors (IscR, NsrR, RirA, CymR, RsrR) that sense NO, iron, redox, and cysteine, often via iron-sulfur cluster cofactors.
Transcription regulator, HycA
HycA (formate hydrogenlyase regulatory protein), also HYCA_ECOLI, is a bacterial antiactivator encoded by the promoter-proximal hycA gene of the hyc operon; it represses FHL by counteracting FhlA, and its deletion boosts hydrogen production.
Transcription termination factor Rho
Rho (ρ-factor), bacterial transcription termination factor discovered by Jeff Roberts in E. coli in 1969; a ring-shaped hexameric ATP-dependent RNA helicase that binds C-rich rut sites and dissociates RNA polymerase.
Transcriptional Activation
Transcriptional activation is the increase in a gene's transcription rate, occurring when DNA-bound activator proteins recruit or stimulate RNA polymerase assembly at the gene's promoter.
Transcriptional antitermination N peptide
Transcriptional antitermination N peptide: the arginine-rich motif of bacteriophage lambda N protein that binds the boxB RNA hairpin, recruits Nus factors, and converts RNA polymerase into a termination-resistant, processive form.
Transcriptional coactivator
Transcriptional coactivators are non-DNA-binding proteins recruited by transcription factors to boost gene expression, including Mediator, CBP/p300, and the SRC family; they integrate signaling, drive disease, and are drug targets via SMIs, PROTACs, and molecular glues.
Transcriptional regulator SgrR
SgrR (formerly yabN) is an E. coli winged-helix transcription factor, 551 aa, that senses glucose-phosphate stress and activates sgrS transcription; divergently transcribed from sgrS, with homologs mainly in Enterobacteriaceae.
Transcriptional regulator SirC
SirC (HilC, SprA; UniProt P0CL09) is a 295-amino-acid AraC-family transcription factor encoded in Salmonella typhimurium SPI1 that positively regulates the invasion type III secretion system through a HilA-independent pathway.
Transcriptional regulator UL34
Transcriptional regulator UL34 (pUL34), HCMV gene UL34 product, is a nuclear sequence-specific DNA-binding repressor of the US3 and US9 immune evasion genes, essential for HCMV replication; distinct from HSV UL34 membrane protein.
Transcriptional Regulatory Elements
Transcriptional regulatory elements: DNA sequences (promoters, enhancers, silencers, insulators, locus control regions) that control gene transcription via transcription factors, coactivators, and chromatin mechanisms.
Transcriptional regulatory protein RcsA
RcsA is an unstable LuxR-family auxiliary transcriptional regulator in E. coli and other enteric bacteria; with RcsB it activates colanic acid capsule (cps) genes, is degraded by Lon protease (5-min half-life), and is regulated by H-NS and DsrA.
Transcriptional regulatory protein RcsB
RcsB is a transcriptional regulatory protein serving as the response regulator of the Rcs phosphorelay in Enterobacteriaceae, controlling more than 5% of genes, including those for capsules, biofilms, and virulence.
Transcriptome
Transcriptome: the complete set of RNA transcripts in a cell or tissue, also called gene readouts. Measured by RNA-seq, microarrays, single-cell, spatial, and long-read methods; differs between cells despite identical genomes.