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.

Cell Lines

Cells that have been continually passaged over a long period of time and have acquired homogenous genotypic and phenotypic characteristics. Cell lines can be finite or continuous. An immortalised or continuous cell line has acquired the ability to proliferate indefinitely, either through genetic mutations or artificial modifications. A finite cell line has been sub-cultured for 20-80 passages after which they senesce. Cell lines are preferably used for convenience as they are easy to handle and widely published. However, they are less preferred as a biologically relevant option, since they have lost the true characteristics of the original tissue from which they were isolated.

Chromatin

A complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells.

Cis-acting elements

Elements that affect the expression of the gene next to them

Cryptic genetic variation

means that a genome can contain mutations whose phenotypic effects are invisible because they are suppressed or buffered, but under rare conditions they become visible and subject to selection pressure.

Dominant negative

If a mutation has a dominant negative effect, the presence of the mutated version interferes with the function of the healthy allele, an effect known as haplo-insufficiency, where there is simply not enough expression of the functional copy of the gene to produce the expected phenotype

Endonuclease

enzymes that cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain.

Exonuclease

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.

Forward genetics

Forward genetics (or a forward genetic screen) is an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism; forward genetics starts with a phenotype and moves towards identifying the gene(s) responsible

Genetic screen

A genetic screen or mutagenesis screen is an experimental technique used to identify and select for individuals who possess a phenotype of interest in a mutagenized population.

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.

Negative selection

In natural selection, negative selection or purifying selection is the selective removal of alleles that are deleterious. If DNA sequence has not changed at the rate expected of neutral changes fixed by random genetic drift then it is under negative selection.

Nucleoside

The combination of a base (A,C, G, or T) connected to the number one carbon of the sugar (deoxyribose).

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.

Nucleotide

A nucleoside with a phosphate group attached to the 5' OH group of the sugar (deoxyribose). A linear sequence of nucleotides is created by connecting a nucleotide's 5' phosphate to the 3' OH group of the upstream nucleotide.

Occupancy

The spatial-temporal location of a nucleosome on DNA, its "occupancy", is a fundamental mechanism to regulate gene expression.

Penetrance

The proportion of individuals carrying an allele (or a genotype) that also express the trait (phenotype) associated with it.

Phosphorylation

The enzymatic addition of a phosphate group to a protein.

Positive selection

Positive natural selection is the force that drives the increase in prevalence of advantageous traits

Primary cell

Cells isolated directly from human or animal tissue using enzymatic or mechanical methods. Once isolated, they are placed in an artificial environment in plastic or glass containers supported with specialised medium containing essential nutrients and growth factors to support proliferation. Primary cells could be of two types – adherent or suspension. Adherent cells require attachment for growth and are said to be anchorage-dependent cells. The adherent cells are usually derived from tissues of organs. Suspension cells do not require attachment for growth and are said to be anchorage-independent cells. All suspension cells are isolated from blood system. Although primary cells usually have a limited lifespan, they offer a huge number of advantages compared to cell lines.

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.

Reverse genetics

Reverse genetics (or a reverse genetic screen) analyses the phenotype of an organism following the disruption of a known gene; reverse genetics starts with a known gene and assays the effect of its disruption by analysing the resultant phenotypes

Senescence

The gradual deterioration of function characteristic of most complex lifeforms, arguably found in all biological kingdoms, that on the level of the organism increases mortality after maturation.

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.

Trans-acting transcription factors

DNA-binding proteins encoded by genes in other parts of the genome

Tumour suppressor

A gene that normally inhibits cell division. Recessive mutations in such genes often contribute to cancer.