Figure 1

Microstates and graphs. A fragment of a graph is shown (below), with three vertices, i, j and k, and several labelled, directed edges. Vertex i is expanded into a microstate, or snapshot of a DNA state (above), showing some of the features that can be represented (not to scale). Here, a hypothetical promoter region of a gene is shown. Features include sequence-specific transcription factors bound to DNA (grey shapes), additional recruited components, such as transcriptional co-regulators (orange shapes), general-purpose transcriptional machinery, such as Mediator (yellow), general transcription factors (GTFs, blue-green) and RNA Pol II (magenta), along with chromatin remodellers and enzymatic factors that modify the histone tails of nucleosomes (blue shapes). Potential post-translational modifications of transcription factors, co-regulators and histone tails are shown by the corresponding symbols, along with DNA methylation. Distal enhancers may participate through 3D chromatin conformation, such as DNA looping. CTD is the carboxy terminal domain of RNA Pol II. 3D, three dimensional; CTD, carboxy terminal domain; GTF, general transcription factor; Pol, polymerase; Ac, acetylation; Me, methylation; P, phosphorylation; Ub, ubiquitination.