Transcription and gene regulation

ChIP-exo

ChIP-exo, also known as the ChIP-exo assay, is a chromatin immunoprecipitation method introduced in 2011 that digests DNA with lambda exonuclease to map protein-DNA binding sites at near base-pair resolution.

Chromatin accessibility assay

A chromatin accessibility assay measures which genome regions are physically open in a cell population, identifying regulatory elements where transcription factors and other DNA-binding proteins can access DNA.

Chromatin immunoprecipitation

Chromatin immunoprecipitation (ChIP) is an antibody-based method that isolates specific DNA-protein complexes from fragmented chromatin to map where a protein binds, read out by qPCR, microarray, or sequencing.

Oct 20, 2026

Chromatin modifying enzymes

Chromatin modifying enzymes: enzymes that chemically modify DNA or histones (acetylation, methylation, deimination) or remodel nucleosomes to regulate gene accessibility; central to development, imprinting, and cancer, and major drug targets including DNMT, HDAC, and HAT inhibitors.

Chromatin remodeling

Chromatin remodeling is the ATP-dependent alteration of nucleosome position, occupancy, or composition by multi-subunit enzymes, regulating DNA accessibility and falling into four families: SWI/SNF, ISWI, CHD, and INO80.

Chromatin SPT2

SPT2 (SIN1; human SPTY2D1) is a conserved HMG-like chromatin protein and H3/H4 histone chaperone, first found as a suppressor of Ty insertions in yeast, that maintains nucleosomes over transcribed genes and suppresses cryptic transcription.

Chromosome conformation capture

Chromosome conformation capture (3C), developed by Job Dekker in 2002, is a cross-linking, digestion, and ligation method measuring 3D chromatin contacts; derivatives 4C, 5C, Hi-C, and Micro-C map genome architecture from nucleosome to chromosome scale.

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.

Oct 20, 2026

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.

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.

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.

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.

Oct 20, 2026

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.

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.

Demethylation

Demethylation is the removal of methyl groups from compounds, especially DNA demethylation of 5-methylcytosine via passive replication dilution or active TET-mediated oxidation, deamination, and base excision repair pathways.

Di19

Di19 (drought-induced 19) is a family of plant Cys2/His2 zinc-finger transcription factors with two atypical zinc-finger domains, conserved in angiosperms, regulating drought, salt, cold responses, flowering, and development.

DNA methylation

DNA methylation (5-methylcytosine) is an epigenetic mark on cytosine, mostly at CpG sites, written by DNMT1/3 enzymes, erased by TET proteins, silencing promoters, and used in cancer biomarkers and epigenetic aging clocks.

DNA methylation array

A DNA methylation array, or methylation array, is a microarray that measures methylation at hundreds of thousands of CpG sites, used widely in cancer research.

DNA-binding domain

DNA-binding domain (DBD): protein domain recognizing specific DNA sequences, used by transcription factors. Key families: helix-turn-helix/homeodomain, Cys2His2 zinc finger (3% of human genes), winged helix; ~60 amino acids average.

DNase-Seq

DNase-Seq is a sequencing method that maps DNase I hypersensitive sites, the nucleosome-depleted open chromatin regions where regulatory DNA is accessible, across a genome, combining DNase I footprinting with next-generation sequencing.

Downregulation and upregulation

Downregulation and upregulation describe decreased or increased expression of a gene product or receptor. They occur at transcriptional, post-transcriptional, translational, and epigenetic levels, and for GPCRs reflect changes in total receptor number.

E-box

E-box (enhancer box, Ephrussi box): DNA motif 5'-CANNTG-3' bound mainly by bHLH transcription factors as dimers; regulates muscle, neural, circadian, and cancer genes; common variant CACGTG (G-box).

E2F2

E2F2 (E2F transcription factor 2, HGNC:3114) is a human activator E2F transcription factor that binds DP proteins and pRB, controls G1/S cell cycle progression, and acts as tumor suppressor in T cell lymphoma but oncogene in ovarian cancer.

Ecdysteroid receptor

Ecdysteroid receptor (EcR): invertebrate nuclear receptor binding 20-hydroxyecdysone, functioning as an EcR-USP heterodimer, cloned 1991 in Drosophila, target of dibenzoylhydrazine insecticides and gene-switch systems.