RNA and gene regulation

Bru-seq

Bru-seq is a metabolic-labeling sequencing method, introduced in 2013, that captures newly transcribed RNA by pulse-labeling living cells with bromouridine, measuring active transcription and mapping it across the genome.

C-terminal binding protein

C-terminal binding protein (CtBP; CTBP1/CTBP2) is an NAD(H)-binding animal transcriptional corepressor descended from dehydrogenases, recruited via PXDLS motifs to repress development, EMT, and cancer genes.

C19MC miRNA cluster

C19MC (chromosome 19 miRNA cluster) is a primate-specific, paternally imprinted cluster of 46 miRNA genes at 19q13.41, expressed almost exclusively in the placenta and undifferentiated stem cells, regulating trophoblast innate immunity and serving as a biomarker of pregnancy complications.

Cajal body

The Cajal body, also called a coiled body, is a small, membraneless compartment in the cell nucleus that concentrates the machinery for assembling and recycling spliceosomal snRNPs.

Cancer-associated long non-coding RNAs

Cancer-associated long non-coding RNAs (lncRNAs) are non-protein-coding transcripts linked to cancer initiation, progression, drug response, or patient outcome; thousands of associations are reported, but only one FDA-approved diagnostic exists.

Cap analysis of gene expression

Cap analysis of gene expression (CAGE) is a transcriptomics method, reported in 2003, that sequences the capped 5' ends of RNAs to map transcription start sites and quantify promoter activity.

Capping enzyme

Capping enzyme (RNGTT), the eukaryotic RNA guanylyltransferase that adds the 5′ GMP cap to mRNA via a lysyl-GMP intermediate, recruited by Ser5-phosphorylated Pol II CTD; distinct viral capping enzymes are antiviral targets.

Carboxy-terminal domain of RNA polymerase II

The carboxy-terminal domain (CTD) of RNA polymerase II is the intrinsically disordered YSPTSPS-repeat tail of the Rpb1 subunit, phosphorylated as polymerase moves through genes to recruit capping, splicing, and processing enzymes.

CarD, C-terminal domain

The CarD C-terminal domain (CarD-CTD), also called the DNA-binding domain, is the all-alpha-helical domain at residues 67–162 of mycobacterial CarD, which wedges tryptophan W85 into promoter DNA to stabilize the transcription bubble.

CAT tailing

CAT tailing is a laboratory method for measuring poly(A) tail length on RNA, combining RNA circularization with tailing plus template switching to create a sequenceable tail.

Catabolite control protein A

Catabolite control protein A (CcpA), LacI/GalR-family transcription regulator of Gram-positive bacteria; with corepressor HPr-Ser46-P binds cre operators, mediating carbon catabolite repression, virulence, and antibiotic resistance links.

CCA-adding enzyme

CCA-adding enzyme (ATP(CTP):tRNA nucleotidyltransferase) is a template-independent RNA polymerase adding the CCA end to tRNA. Two unrelated classes, archaeal class I and bacterial/eukaryotic class II, share a catalytic core but differ in nucleotide-selection mechanism.

CDKN2B-AS1

CDKN2B-AS1 (ANRIL) is a human long non-coding RNA gene at 9p21.3, antisense to CDKN2B, that silences CDKN2A/B via PRC1/PRC2 and is the strongest genetic susceptibility locus for cardiovascular disease, also linked to diabetes, cancers, and glaucoma.

CDR1 antisense RNA

CDR1 antisense RNA, also known as CDR1as, is a circular RNA from the X chromosome, highly enriched in brain tissue and carrying more than 70 binding sites for miR-7.

CEL-seq

CEL-seq is a single-cell RNA sequencing method, introduced in 2012, that barcodes each cell's RNA during reverse transcription and amplifies transcripts linearly by in vitro transcription.

CELF family

The CELF family (CUG-BP and Elav-like family), also called BRUNOL, is a group of six RNA-binding proteins, CELF1 through CELF6, that regulate alternative splicing, mRNA stability, and translation.

CELF1-mediated mRNA decay

CELF1-mediated mRNA decay is a regulative mRNA decay pathway in which CELF1 (CUGBP1) binds GU-rich elements in 3′UTRs and recruits the PARN deadenylase to shorten target mRNA half-lives.

Cemdisiran

Cemdisiran (ALN-CC5, ALN-62643) is an investigational GalNAc-conjugated siRNA from Alnylam/Regeneron that silences liver C5 mRNA; subcutaneous, long-acting, in Phase 3 for PNH, myasthenia gravis, and geographic atrophy.

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.

Chloroplastic group IIB intron splicing facilitator CRS2-like

Chloroplastic group IIB intron splicing facilitator CRS2-like (IPR048076): plant protein family homologous to maize CRS2, a peptidyl-tRNA hydrolase-derived, 23 kDa chloroplast stroma protein that splices nine subgroup IIB introns with CAF1 or CAF2.

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.

Chromatin isolation by RNA purification sequencing

Chromatin isolation by RNA purification sequencing (ChIRP-seq) is a hybridization-capture method, reported in 2011, that maps the genomic binding sites of one chosen RNA by 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.