The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as histones.
[9] The current understanding and interpretation of histones comes from two large scale projects: ENCODE and the Epigenomic roadmap.
This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome.
[12] A look in to the data obtained led to the definition of chromatin states based on histone modifications.
[15] H3K4me allows binding of MDB and increased activity of DNMT1 which could give rise to CpG island methylator phenotype (CIMP).
CIMP is a type of colorectal cancers caused by the inactivation of many tumor suppressor genes from epigenetic effects.
It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells.
ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region.
Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes.