RNA and gene regulation

Cis-encoded antisense RNA

A cis-encoded antisense RNA is a small regulatory RNA transcribed from the same genetic locus as its target, on the opposite DNA strand, making it fully complementary to one target.

Cis-natural antisense transcript

Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the opposite DNA strand of the same locus as a sense gene, overlapping it with perfect complementarity; widespread in eukaryotes, they regulate expression via siRNAs, chromatin remodeling, splicing, and translation control.

Cis-regulatory element

Cis-regulatory element (CRE): non-coding DNA regulating transcription of nearby genes; classes include promoters, enhancers, silencers, and insulators; mapped genome-wide by ENCODE and engineered synthetically for cell-type-specific gene expression.

Class I aminoacyl-tRNA synthetases

Class I aminoacyl-tRNA synthetases are enzymes that charge transfer RNAs with amino acids, defined by a Rossmann fold carrying the HIGH and KMSKS motifs; they attach 11 of the 22 coded amino acids.

Class II aminoacyl-tRNA synthetases

Class II aminoacyl-tRNA synthetases are the ten-member family of tRNA-charging enzymes with an antiparallel beta-sheet catalytic fold, recognized in 1990, that charge 11 of the 22 coded amino acids.

CLIP-Seq

CLIP-Seq, cross-linking immunoprecipitation followed by sequencing, maps the RNA transcripts a specific RNA-binding protein contacts inside cells, down to exact nucleotides in modern variants like iCLIP and eCLIP.

Coilin

Coilin, also called p80-coilin and encoded by the gene COIL, is an 80-kilodalton protein whose depletion eliminates Cajal bodies, where snRNPs mature about 10 times faster.

Combined oxidative phosphorylation defect type 11

Combined oxidative phosphorylation defect type 11 (COXPD11, RMND1 disease) is a rare autosomal recessive mitochondrial translation disorder causing neonatal hypotonia, lactic acidosis, deafness, developmental delay, and frequent kidney disease, OMIM 614922.

Combined oxidative phosphorylation defect type 23

COXPD23, also called combined oxidative phosphorylation deficiency 23, is an ultrarare autosomal recessive mitochondrial disease caused by biallelic GTPBP3 variants, presenting with lactic acidosis, hypertrophic cardiomyopathy, and encephalopathy in infancy or childhood.

Competence pheromone ComX, Bacillus-type

ComX, Bacillus-type: isoprenylated peptide quorum-sensing pheromone of Bacillus subtilis; 55-residue precursor cleaved by ComQ to a modified decapeptide that activates the ComP-ComA two-component system, with strain-specific pherotypes under diversifying selection.

Competence protein ComK

Competence protein ComK is the master regulator of natural competence in Bacillus subtilis, activating DNA uptake genes through an all-or-nothing switch active in only 5 to 10% of cells.

Competing endogenous RNA

Competing endogenous RNAs (ceRNAs): transcripts such as lncRNAs, circRNAs, pseudogenes, and mRNAs sharing microRNA response elements that compete for shared miRNAs, forming ceRNET regulatory networks; hypothesis proposed in 2011, with quantitative controversy over physiological scale.

Conjugal transfer repressor TrbA

TrbA is the 13.5 kDa global repressor of IncP-1 plasmid RK2/RP4, encoded at the trb operon start, that represses conjugative transfer promoters and cooperates with KorB as a clamp-locking co-repressor.

Consensus Sequence

Consensus sequence: a representative DNA, RNA, or protein sequence taking the most frequent residue at each aligned position; used for motifs, CODEHOP primers, and protein design, but weak for motif search.

Conserved non-coding sequence

Conserved non-coding sequences (CNEs, conserved non-coding elements) are non-protein-coding DNA stretches maintained by purifying selection across species. About 3.5% of the human genome is CNEs; they act mostly as developmental enhancers in genomic regulatory blocks.

Corepressor (genetics)

Corepressor (genetics): proteins or metabolites that help repressors shut off transcription. Eukaryotic examples NCoR/SMRT (1995) recruit HDAC complexes; bacterial corepressors like tryptophan activate repressors.

CPEB

CPEB (cytoplasmic polyadenylation element binding protein) family: CPEB1–4 in vertebrates, Orb/Orb2 in Drosophila; sequence-specific mRNA binding proteins controlling poly(A) tail length, translation, oocyte maturation, senescence, cancer, and memory.

CpG Islands

CpG islands are CpG-rich, typically unmethylated DNA stretches, several hundred to a few thousand base pairs long, found mostly at gene promoters; promoter hypermethylation silences tumor suppressor genes in cancer.

CpG site

CpG site: a cytosine-guanine dinucleotide in DNA, the main target of vertebrate DNA methylation. Also called CpG dinucleotide. Established by DNMT3A/B, maintained by DNMT1 with UHRF1; CpG islands stay unmethylated; methylated CpGs are mutation hotspots.

CREB phosphorylation

CREB phosphorylation: phosphorylation of the CREB transcription factor, chiefly at Ser133 in its kinase-inducible domain, by PKA, CaMKs, RSK, MSK1/2, and MAPKAPK2, enabling CBP/p300 recruitment and cAMP-, calcium-, and stress-responsive gene transcription.

CREB-binding protein

CREB-binding protein (CBP, KAT3A, CREBBP) is a ~265 kDa transcriptional coactivator and lysine acetyltransferase recruited by phosphorylated CREB; loss causes Rubinstein–Taybi syndrome and frequent B-cell lymphoma inactivation.

CRISPR activation

CRISPR activation (CRISPRa) is a gene regulation method that increases expression of endogenous genes without cutting DNA, using dCas9 fused to activator domains; it was first demonstrated in 2013.

CRISPR interference

CRISPR interference (CRISPRi) is a gene repression technique in which a dead Cas9 protein blocks transcription without cutting DNA, introduced by Lei Qi and colleagues in 2013.

CRISPR RNA

CRISPR RNA (crRNA) is the target-complementary guide RNA of CRISPR-Cas systems, processed from pre-crRNA with tracrRNA and RNase III in type II systems, fused into sgRNA for Cas9, and used standalone in Cas12a and Cas13 editing and diagnostics.

Oct 22, 2026

CRISPR-responsive hydrogel

A CRISPR-responsive hydrogel is a polymer or DNA network that changes when CRISPR enzymes such as Cas12a recognize a target sequence, releasing cargo or producing a diagnostic signal.

Cross-domain homology of translation factors

Cross-domain homology of translation factors traces which translation GTPases across bacteria, archaea, and eukaryotes descend from a common ancestor and which arose convergently, including release and recycling factors.

Cross-linking and immunoprecipitation

Cross-linking and immunoprecipitation (CLIP) is a method for identifying the RNA targets of RNA-binding proteins in living cells, combining UV cross-linking with immunoprecipitation and sequencing.

CUT&Tag

CUT&Tag (Cleavage Under Targets and Tagmentation) is an antibody-based sequencing method mapping histone modifications and chromatin proteins, working from as few as 100 cells in one day.

Cyclin-dependent kinase 7

Cyclin-dependent kinase 7 (CDK7), with cyclin H and MAT1, forms CAK activating CDKs 1/2/4/6 and is a TFIIH kinase phosphorylating Pol II CTD Ser5/Ser7; targeted by covalent inhibitors THZ1 and YKL-5-124 and clinical candidates ICEC0942, SY-1365, SY-5609, LY3405105.