Box. Functional definition of some terms utilized for the description of molecular mechanisms involved in the control of gene expression.

Transcription factors are proteins that control the activity of genes. These proteins recognize specific DNA sequences located within promoter sequences (= regulatory sequences located immediately in front of the gene) and/or enhancer sequences (= regulatory sequences that can be located upstream, within, or downstream of the gene). Activators are transcription factors that increase transcriptions when bound to promoter or enhancer sequences, while repressors are transcription factors that decrease transcription when occupying such sequences. Frequently, transcription factors bind to specific DNA elements as pairs. When such pairs are composed of two identical proteins, they are called homodimers, when they consist of two different proteins, they are called heterodiiners. For example, the two activators CLOCK and BMALI bind as heterodirners to socalled E-Box motifs (with the sequence CACGTG), located within promoter and enhancer sequences of the genes mPerl and mPerJ (murine Period gene 1 and murine Period gene 2).

The repression of gene transcription is also called “silencing Epigenetic silencing” is a stable form of silencing that involves covalent modifications of chromatin constituents, either as methyl groups on cytosine bases of the DNA or as various posttranslational modifications on certain amino acids within histories- Histories are proteins that package DNA into protein-DNA complexes called chromatin within cell nuclei.

Orthologs are genes that show a high DNA sequence similarity between different organisms - say humans, mice, and flies - and that perform equivalent function in these organisms.