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Archaeal initiation factors
Archaeal initiation factors are the proteins that assemble a translation-competent ribosome on messenger RNA at the start of protein synthesis in archaea, including aIF1, aIF1A, aIF2, and aIF5B.
Archaeal RNA polymerase
Archaeal RNA polymerase (RNAP) is the single enzyme that transcribes all genes in archaea, with 12 or 13 subunits and a structure closely mirroring eukaryotic RNA polymerase II.
Archaeal transcription
Archaeal transcription: gene expression in Archaea via a single 11–13 subunit RNAP homologous to eukaryotic Pol II, with TBP/TFB/TFE initiation, Spt4/5 and TFS elongation, oligo(dT) intrinsic and FttA/Eta factor-dependent termination.
Archaeal transcription factor B
Archaeal transcription factor B (TFB), homolog of eukaryotic TFIIB and bacterial sigma factors, binds the BRE upstream of the TATA box with TBP and recruits archaeal RNA polymerase; many archaea encode multiple TFB isoforms.
Archaeosine biosynthesis
Archaeosine biosynthesis: archaeal tRNA pathway inserting preQ0 at position 15 via ArcTGT, then converting it to G+ by ArcS/RaSEA (or GAT-QueC, QueF-like in Crenarchaeota), stabilizing the Levitt base pair.
Arginine repressor
Arginine repressor (ArgR, AhrC in Bacillus): hexameric bacterial transcription factor that, with L-arginine as corepressor, binds 18-bp ARG boxes to repress arginine biosynthesis, activate catabolism, and resolve ColE1 plasmid multimers.
Asd RNA motif
Asd (aSD) RNA motif: the anti-Shine-Dalgarno sequence, a conserved CCUCC core at the 3' end of bacterial 16S rRNA that pairs with Shine-Dalgarno mRNA sequences to initiate translation, pauses elongating ribosomes, and varies across species.
Asd-4/GZF3-like, helical region
Asd-4/GZF3-like, helical region (InterPro IPR056998; Pfam PF25026 Asd-4) is a conserved region of fungal GATA transcription factors such as Neurospora ASD4 and yeast Gzf3p, negative regulators of nitrogen catabolic gene expression.
ATAC-seq
ATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) maps genome-wide chromatin accessibility using hyperactive Tn5 transposase to insert adapters into open chromatin; needs 500–50,000 cells, alternative to DNase-seq, FAIRE-seq, MNase-seq.
ATF6
ATF6 (activating transcription factor 6) is an ER membrane sensor of the unfolded protein response; BiP release sends it to the Golgi, where S1P/S2P cleavage yields the bZIP transcription factor ATF6p50 driving chaperone and ERAD genes; loss-of-function variants cause achromatopsia.
ATP-dependent RNA helicase SrmB
SrmB is one of five DEAD-box RNA helicases of Escherichia coli, discovered in 1988 as a suppressor of an L24 ribosomal protein mutation. It aids early 50S ribosomal subunit assembly, tethered via L4/L24 to 23S rRNA, with weak ATPase but strong ATP-independent RNA annealing activity.
AU-rich element
AU-rich element (ARE, adenylate-uridylate-rich element): 50–150 nt AUUUA-rich cis-elements in mRNA 3′UTRs controlling decay, stability, and translation via proteins like TTP and HuR; found in 5–8% of human genes, prominent in cytokine and proto-oncogene transcripts.
AUX/IAA protein
AUX/IAA (auxin/indole-3-acetic acid) proteins are short-lived plant nuclear transcriptional repressors with four conserved domains; auxin-bound TIR1/AFB receptors trigger their ubiquitin-proteasome degradation, freeing ARFs to activate auxin response genes.
Auxin response factor
Auxin response factors (ARFs) are plant-specific B3-family transcription factors, the final effectors of the nuclear auxin pathway, binding AuxREs and regulated by Aux/IAA repressors; classes A, B, C; first cloned 1997.
BACE1-AS
BACE1-AS (BACE1AS, BACE1-AS1, NCRNA00177) is a human long non-coding antisense RNA at 11q23.3 that stabilizes BACE1 mRNA, elevating beta-secretase and amyloid-beta in Alzheimer's disease via a feed-forward loop.
Bacterial initiation factor
Bacterial initiation factors IF1, IF2, IF3 (infA, infB, infC) are the three proteins bacteria use to start translation, versus 12+ in eukaryotes; IF2 is a GTPase recruiting fMet-tRNA, IF3 the fidelity factor.
Bacterial RNA polymerase
Bacterial RNA polymerase (RNAP, DNA-directed RNA polymerase, EC 2.7.7.6): the α2ββ′ω core enzyme plus sigma factors that transcribes all bacterial RNA; rifamycin antibiotic target with rpoB-mediated resistance.
Bacterial small RNA
Bacterial small RNA (sRNA), 50–350 nt regulatory RNAs that base-pair with mRNAs or bind proteins, often aided by the Hfq chaperone, controlling stress, metabolism, virulence, and antibiotic resistance; includes cis/trans-encoded and dual-function peptide-coding sRNAs.
Bacterial sRNA discovery methods
Bacterial sRNA discovery methods combine genome-wide transcriptomics such as dRNA-seq and RNA-seq, computational gene prediction, and experimental validation to identify small regulatory RNAs in bacteria.
Bacterial transcription
Bacterial transcription is the copying of bacterial DNA into messenger RNA by RNA polymerase, whose sigma factors recognize promoters; the enzyme is also a proven target for antibiotics.
Bacterial translation
Bacterial translation: protein synthesis on 70S ribosomes via initiation, elongation, termination, recycling. Uses three factors IF1, IF2, IF3, fMet-tRNA, and Shine-Dalgarno/16S rRNA pairing for start codon selection.
Barbara J. Graves
Barbara J. Graves is an American biochemist and Professor Emerita of Oncological Sciences at the University of Utah, known for mechanistic studies of ETS transcription factors.
Basic helix-loop-helix transcription factors
Basic helix-loop-helix (bHLH) transcription factors are dimeric eukaryotic regulators with a ~60-amino-acid basic helix-loop-helix domain that binds E-box CANNTG motifs; over 100 human members regulate neurogenesis, myogenesis, hematopoiesis, and cancer-related programs.
BC200 lncRNA
BC200 (BCYRN1) is a 200-nucleotide primate brain cytoplasmic lncRNA on chromosome 2, transcribed by Pol III from an Alu element, that represses dendritic translation via eIF4A/eIF4B/PABP and is elevated in several cancers, notably breast cancer, as a blood biomarker.
BET protein
A BET protein, short for bromodomain and extra-terminal domain, is one of four chromatin readers (BRD2, BRD3, BRD4, BRDT) that bind acetylated histones and control gene transcription.
BHRF1 microRNA cluster (Epstein–Barr virus)
The BHRF1 microRNA cluster is a set of three microRNA precursors encoded by Epstein–Barr virus at the BHRF1 gene locus, expressed at high levels in latency III.
Biofilm regulator BssR
BssR (formerly YliH, gene bssR) is a 127-amino-acid regulatory protein of Escherichia coli K-12 that represses biofilm formation in glucose-containing media by modulating indole and AI-2 quorum-sensing signals.
Biogenesis of circular RNA by back-splicing
Biogenesis of circular RNA by back-splicing is the non-canonical splicing that joins a downstream 5′ donor to an upstream 3′ acceptor, closing RNA into a covalent circle.
BioNTech
BioNTech SE (BNTX), German biotech in Mainz founded 2008 by Sahin, Türeci, Huber; co-developed Comirnaty, the first approved mRNA COVID-19 vaccine, with Pfizer; now building an oncology pipeline toward a multi-product company by 2030.
Bisulfite sequencing
Bisulfite sequencing (BS-Seq, WGBS, RRBS) measures DNA methylation at single-base resolution: sodium bisulfite converts unmethylated cytosine to uracil while 5mC resists, so C/(C+T) read counts reveal methylation, developed by Frommer et al. 1992.