DNA sequence able to be bound by proteins, increasing the likelihood of transcription of a particular gene; cis-acting, located up to 1Mb away from the gene they regulate

method used to analyse protein-DNA interactions, identifying binding sites by combining immunoprecipitation with DNA sequencing

basic proteins acting as spools for DNA to wind around, condensing into nucleosomes allowing the DNA to be tightly packed; prevent tangling or damage to the DNA, and are important in gene regulation and DNA replication

a way of describing the accessibility of DNA by enzymes, between heterochromatin and nucleosome-depleted regions (euchromatin)

a region of DNA with an absence of nucleosomes, typically containing CRMs and actively transcribed genes, and is sensitive to DNases

regions of DNA susceptible to cleavage by DNase; uncondensed DNA, making it accessible to enzymes

method used to assess chromatin accessibility on a genome-wide scale, by probing open chromatin with the hyperactive Tn5 transposase, tagging accessible regions of the genome with sequencing adaptors; more sequence reads indicate greater accessibility of that region

digesting chromosomes with DNase and then sequencing the remaining DNA allows the DNase-sensitive regions to be identified and sequenced separately

process of adding a methyl group; when added to DNA, repressing gene transcription

process of adding acetyl groups to histone proteins, uncondensing the DNA and increasing gene transcription

machine learning technique, inferring a state by the association of that state with another factor that can be observed

field within AI, developing statistical algorithms capable of learning and generalising data, performing tasks without specific instructions

parameter of a hidden Markov model, giving a score for switching between the states and thus controlling the model’s decision to select a given state at any time

a score given in a hidden Markov model giving the likelihood of being in a specific state based on the data

machine learning training technique using unlabelled data

Hidden Markov model used for predicting chromatin states based on histone modification