Epigenetics glossary

Discover our epigenetics glossary with definitions covering the need-to-know terms in epigenetics.

Key termDefinition
3C (Chromosome Conformation Capture)A technique used to quantify specific chromatin interactions of interest in vivo. Cross-linked restriction digested chromatin fragments are circularized to detect interacting DNA regions by PCR.
4C (Circular Chromosome Conformation Capture)A 3C derivative technique used to detect unknown DNA regions that interact with a region of interest. Unknown DNA interacters are amplified by primers binding in the known region which are then detected by microarray.
5C (Chromosome Conformation Capture Carbon Copy)A 3C derivative technique used for in depth detection of DNA interacters with a DNA region of interest. 5C primers anneal across ligation junctions to amply the unknown interacting DNA library which is then characterized with microarray or next-generation sequencing.
5-Carboxylcytosine (5-caC)The final oxidised derivative of 5-methylcytosine during its active demethylation by the TET enzymes.  It may serve yet unknown biological functions as its own epigenetic mark.
5-Formylcytosine (5-fc)the penultimate oxidised derivative of 5-methylcytosine during its active demethylation by the TET enzymes. It is enriched at poised enhancers and other regulatory regions.
5-hydroxymethylcytosine (5hmC)The first oxidized derivative of 5-methylcytosine during its active demethylation by the TET enzymes. It is enriched in the mammalian brain and germ cells and may act as its own epigenetic mark.
AcetylationThe covalent addition of an acetyl group to a macromolecule, most commonly protein lysine and arginine residues. When present on histones it neutralizes their positive charge allowing nucleosome decompation and enhanced gene expression.
BiotinylationThe covalent linkage of a biotin molecule to a macromolecule such as DNA or protein to serve as a tag. Biotin is bound rapidly and strongly by avidin and streptavidin proteins creating conjugates coupled to fluorophores to detect the tagged macromolecule target.   
Bisulfite conversionTreatment of DNA with sodium bisulfite converting unmethylated cytosine to uracil while leaving 5-methylcytosine (and 5-hydroxymethylcytosine) intact.
Bisulfite sequencingAmplification of bisulfite converted DNA with PCR followed by DNA sequencing to differentiate unmodified cytosine from 5-methylcytosine. It can be applied to specific regions or the entire genome.
BiTS-4C seq (Batch isolate Tissue Specific 4C-seq)A method to detect chromatin interactions at a locus of interest in a specific cell type, often in a multicellular embryo. After crosslinking nuclei are sorted using flow cytometry then subjected to the remainder of the 4C protocol in parallel to the whole embryo for comparison.
Capture CA high throughput, high resolution 3C technique in which oligonucleotide capture technology (OCT) is used after standard 3C to examine interactions occurring at hundreds of regions of interest simultaneously.
CentromereA specific DNA region where each pair of sister chromatids are connected during mitosis.
Chromatin in situ proximity (ChrISP)A technique for single-cell analysis of proximities between two chromatin fibers in 3-D at high resolution. It is similar to in situ proximity ligation assay (ISPLA) except proximities are visualized by a fluorescent connector oligonucleotide forming a circular DNA.
ChIP on ChIPChromatin immunoprecipitation (ChIP) using an antibody against a protein or histone modification of interest coupled to microarray to detect enriched DNA regions.
CitrullinationAlso known as deamination, is the post-translational modification of the amino acid arginine to citrulline in a protein, reducing its positive charge.
Combined Bisulfite Restriction Analysis (COBRA)A technique to quantify DNA methylation at a specific locus from a very small amount of DNA by bisulfite PCR followed by restriction digestion at converted sites.
Constitutive heterochromatinRegions of DNA—particularly telomeres, centromeres, and other repetitive sequences—that are characterized by highly compacted transcriptionally inactive chromatin that generally cannot become active.
CRISPRA genome editing system utilizing the CRISPR/Cas9 endonuclease which is targeted to a DNA region of interest by a specific guide RNA to induce DNA double strand breaks.
Cross-linking ligation and sequencing of hybrids (CLASH)A UV cross-linking, ligation, and sequencing-based technique for the analysis of RNA-RNA interactions occurring in the proximity of an RNA binding protein of interest.
De novo methylationThe methylation of cytosines in CpG sites that are unmethylated on both DNA strands by de novo DNMTs.
DeamidationThe removal of an amide group from a protein, particularly converting asparagine residues to a mixture of isoaspartate and aspartate. It is involved in targeting proteins for degradation.
DeiminationAlso known as citrullination, is the post-translational modification of the amino acid arginine to citrulline in a protein, reducing its positive charge.
e4C (enhanced 4C)Technique for the detection of more weakly associated, distal DNA interactions than conventional 4C by the addition of a ChIP step to the 4C protocol.
Facultative heterochromatinTightly compacted heterochromatin which forms in a region of DNA that can also from transcriptionally active euchromatin depending on the context, for example X-inactivation.
FISH (fluorescence in situ hybridization)A microscopy technique used to localized a specific DNA sequence on chromosomes using a fluorescently labeled probe.
FormylationThe addition of a formyl group. In epigenetics, formylation of histone lysine residues enhances DNA binding and blocks methylation and acetylation.
FRET (Förster resonance energy transfer)An extremely sensitive technique to measure distances between molecules using light sensitive chromophores.
GlycosylationThe chemical linkage of a carbohydrate to another molecule such as a lipid or protein. It serves many functions including protein folding, cell adhesion, and protein-ligand binding.
HemimethylatedDNA that is methylated at a cytosine of a CpG site of one strand, but not the same CpG of the other strand. These sites occur after cell division, and are recognized and methylated by the maintenance DNA methyltransferase DNMT1.
HistonePositively charged proteins that stabilize and compact DNA. Post-translational modifications to histones serve as important regulators of gene expression and other chromatin processes.
Histone CodeThe hypothesis that different histone modifications code for specific chromatin states. Further, these modifications form a combinatorial code to heritably control gene expression. 
Histone MethyltransferaseEnzymes which serve to methylate histone lysine or arginine residues. Individual histone methyltransferases typically act on very specific histone residues.
Histone VariantAlternate histone proteins that differ slightly in amino acid sequence from the canonical histone. They have unique functional properties and chromosomal distributions.
HydroxylatedRefers to the addition of a hydroxyl group (OH-) to a molecule. Hydroxylation of DNA and histone methylation serves as the first step in their active demethylation.
HypermethylationAn increase in methylation of a particular region, usually referring to a gain of DNA cytosine methylation.
HypomethylationA decrease in methylation of a particular region, usually referring to a loss DNA cytosine methylation.
ImprintingThe expression of alleles of a gene in a parent-of-origin specific manner accomplished by DNA cytosine methylation. A paternally imprinted gene shows maternal expression and paternal methylation, while a maternally imprinted gene shows the reverse.
ISH: in situ hybridizationA technique for localization of a specific DNA or RNA within a tissue section using a labelled nucleic acid probe. Fluorescence (FISH) and chromogenic (CISH) detection are the two main methods of probe visualization.
Long non-coding RNANon-protein coding RNAs that are 200 base pairs or longer that are highly regulated, but many of their functions remain elusive.
Loss of imprinting (LOI)Alteration of imprinted gene expression caused by aberrant DNA methylation or deletion of regulatory DNA sequences.
MalonylationThe addition of a malonyl group to a histone lysine residue which serves a yet-to-be-determined function.
Methylated DNA Immunoprecipitation (Methyl-DIP or MeDIP)The detection of methylated DNA by chromatin immunoprecipitation using an antibody against 5-methylcytosine.
MethylationThe addition of a methyl (CH¬3) group to a molecule. It can occur at DNA cytosine nucleotides and represses gene expression or at histone lysine or arginine residues which are repressive or activating depending on the residue.  
microRNA (miRNA)Single-stranded, non-protein coding RNAs about 21-24 nucleotides in length expressed in plants and animals. They bind to their target gene’s 3’ untranslated region and block transcription or promote degradation. 
NeddylationThe conjugation of the ubiquitin-like protein NEDD8 to a lysine residue of a protein target. NEDD8 modification can alter target protein conformation and binding to partners and has a role in cell growth and survival.
O-GlcNAcylationThe addition of the β-D-N-acetylglucosamine monosaccharide to target protein serine or threonine residues. It competes with phosphorylation for these residues and as such is believed to have a reciprocal role in regulating protein function.
PhosphorylationThe addition of a phosphate (PO4-3) group to target protein serine or threonine residues. It alters many protein conformations and functions, acting as an on/off switch.
Piwi-interacting RNA (piRNA)Are single-stranded, non-protein coding RNAs about 26-31 nucleotides in length expressed in animals. They are more abundant and less conserved than microRNAs and function to silence gene expression by forming repressive piwi protein-piRNA complexes.
Polycomb-group (PcG)Family of proteins that regulate developmental gene expression during development, usually by methylating histone H3 lysine 27 at target promoters.
Small activating RNA (saRNA)A special subtype of double-stranded RNA (dsRNA) that promote target gene expression through dsRNA-induced transcriptional activation (RNAa).
Small interfering RNAs (siRNA)Non-protein-coding, double stranded RNA molecules 20-25 nucleotides in length with 2 nucleotide 3’ overhangs. They promote target mRNA degradation through the RNA interference (RNAi) pathway.
SuccinylationThe addition of a succinyl group to a protein lysine residue. It alters the lysine charge from +1 to -1 but its exact role remains unknown. 
SUMOylationThe addition of a Small Ubiquitin-like Modifier (SUMO) protein to a target protein. This modification is involved in trafficking proteins to the nucleus among many other processes.
TelomereA repetitive DNA sequence at the end of a chromosome that protects from DNA replication-induced shortening or other damage. Telomerase reverse transcriptase lengthens the telomere after it is shortened during DNA replication.
Trithorax-group (trxG) proteinsA diverse group of proteins that maintain gene expression—particularly during development—by acting in large complexes that depositing histone H3 lysine 4 trimethylation.
UbiquitinationThe addition of one or a chain of ubiquitin proteins to a protein target. It often targets the protein for degradation but can also alter its localization, conformation, or binding.
X-inactivationThe condensation of chromatin and silencing of gene expression on one X-chromosome to compensate for the additional dosage of genes in female mammalian cells compared to male.
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