Mainly sourced from Wikipedia but arranged as per my train of thought.
Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation. Histone H3 is one of the core histone proteins (the others are H2A, H2B and H4) involved in the structure of chromatin in eukaryotic cells. H3 is involved with the structure of the nucleosomes of the 'beads on a string' structure and H3 is the most extensively modified of the five histones.
Nucleosomes are 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.
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication.
The common nomenclature of histone modifications is:
The name of the histone (e.g. H3)
The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein
The type of modification (Me: methyl, P: phosphate, Ac: acetyl, Ub: ubiquitin)
So H3K27Ac denotes the acetylation of the 27th residue (a lysine) from the start (i.e. the N-terminal) of the H3 protein.
Histone acetyltransferases (HAT) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA. In general, histone acetylation is linked to transcriptional activation and associated with euchromatin. Histone modification levels and gene expression are well correlated; the levels of a single modification (H3K27ac) can be used to faithfully model gene expression (Karlic et al., 2010 PNAS).
Chemical modifications (e.g. methylation and acylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K27Ac histone mark across the genome as determined by a ChIP-seq assay. The H3K27Ac histone mark is the acetylation of lysine 27 of the H3 histone protein, and it is thought to enhance transcription possibly by blocking the spread of the repressive histone mark H3K27Me3 (from the ENCODE track on the UCSC Genome Browser).
ChIP-sequencing, also known as ChIP-seq, is used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to precisely map global binding sites for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations.
The ChIP process enriches specific crosslinked DNA-protein complexes using an antibody against a protein of interest. It can be used to precisely map global binding sites for any protein of interest.
ChIP-seq: welcome to the new frontier