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English: Graphic representation of eukaryotic transcriptional machinery. (A) Basal eukaryotic transcriptional machinery; members of the transcription factor II (TFII) family of proteins associate with RNA polymerase II (RNApolII) in an ordered manner to form the pre-initiation complex. The core promoter region, containing transcription factor binding sites (TFBS) and the transcriptional start site, is bound by the pre-initiation complex and RNApolII is directed to begin transcription of target genes. (B) cis-regulatory DNA sequences modulating eukaryotic transcription. Distant cis-regulatory sequences (CRSs), such as enhancers and silencers (located up to 1Mbp from the target promoter), associate with additional TFs (Xn) and form indirect interactions with the target promoter. Subsequently, transcriptional outputs are modified depending on the nature of the associated CRS; increases in transcript quantity (enhancer function—green arrows) or reduction/abolition of transcription (silencer function—red T-bars). In order for enhancer/silencer sequences to interact with target promoters DNA must be modified to “loop out” the interspaced DNA. Other recognised classes of regulatory sequences include insulators: Barrier-form insulators prevent chromatin condensation from repressing active regulatory regions setting up regulatory boundaries; Enhancer-blocking (EB) insulators maintain the specificity of CRS interactions by blocking regulatory sequences from impinging on neighbouring genes. Finally, locus control regions are described as regions containing multiple CRSs, they function in concert to confer correct temporal and/or spatial specificity of the target gene.