DNA is organized in the cell nucleus by way of a chromatin structure, which is shaped and maintained by many chromatin marks, such as histone tail modifications (e.g., H3K4me1), transcription factors (e.g., GATA1) and chromatin modifiers (e.g., EZH2).
The genome-wide occurrence of such chromatin marks can be captured using assays such as Chromatin Immunoprecipitation Sequencing (ChIP-Seq).
Chromatin states describe the combinatorial occurrence of multiple chromatin marks, using software such as
ChromHMM and
Segway, etc).