Glossary
5-azacytidine: A chemical that can effectively remove the methyl groups from nucleic acids. 5-azacytidine is one of many chemical analogs for the nucleoside cytidine. When these analogs are integrated into growing DNA strands, some, including 5-azacytidine, severely inhibit the action of the DNA methyltransferase enzymes that normally methylate DNA.
Acetylation: An enzymatic reaction that results in the addition of an acetyl group to a biochemical.
Activator: Protein in eukaryotic cells that binds to consensus sequences in regulatory promoters or enhancers and affects transcription initiation by stimulating or inhibiting the assembly of the basal transcription apparatus
Cap-trapping: A protocol for capturing full length capped RNAs via chemical biotinylation of the 5' cap and streptavidin capture.
Chromatin: A complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells.
Endonuclease: enzymes that cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain.
Exonucleases: enzymes that cleaves nucleotides one at a time from the end (exo) of a polynucleotide chain.
Epigenetic reprogramming: The process of demethylation, such as in germ cells, when the silencing of imprinted genes is reversed. This process may be mediated by the removal of amino groups by DNA deaminases (removal of an amino group (NH2) from a base).
Epistasis: Type of gene interaction in which a gene at one locus masks or suppresses the effects of a gene at a different locus.
Histones: A family of basic proteins, which associate with DNA in the nucleus and help to condense the DNA into a smaller volume.
Histone code: The combination of all the different modifications that can occur on histones.
Methylation: The addition of a methyl group (-CH3) to a molecule. Methylation of DNA involves cytosine bases of eukaryotic DNA being converted to 5-methylcytosine, resulting in the repression of transcription, particularly in vertebrates and plants. In an interestingly coordinated process, proteins that bind to methylated DNA also form complexes with proteins involved in deacetylation of histones. Therefore, when the DNA is in a methylated state, nearby histones are deacetylated, resulting in compact, semipermanently silent chromatin.
Nucleosome: The basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a histone protein core. This structure is often compared to thread wrapped around a spool.
Occupancy: The spatial-temporal location of a nucleosome on DNA, its "occupancy", is a fundamental mechanism to regulate gene expression.
Phosphorylation: The enzymatic addition of a phosphate group to a protein.
Promoter: DNA sequence to which the transcription apparatus binds so as to initiate transcription; indicates the direction of transcription, which of the two DNA strands is to be read as the template, and the starting point of transcription.
siRNA: Single-stranded RNA molecule (usually from 21 to 25 nucleotides in length) produced by the cleavage and processing of double-stranded RNA; binds to complementary sequences in mRNA and brings about the cleavage and degradation of the mRNA. Some siRNAs bind to complementary sequences in DNA and bring about their methylation.
Tumour suppressor: A gene that normally inhibits cell division. Recessive mutations in such genes often contribute to cancer.