Chromatin organization of transcribed genes in chicken polychromatic erythrocytes.

Transcriptional regulation is impacted by the organization of the genome into chromatin compartments and domains. We previously reported the application of a biochemical fractionation protocol to isolate highly enriched transcribed DNA from chicken polychromatic erythrocytes. In conjunction with next-generation DNA and RNA sequencing as well as chromatin immunoprecipitation-DNA sequencing, we identified all the active chromosomal compartments and determined their structural signatures in relation to expression levels. Highly expressed genes were found in broad dynamically highly acetylated, salt-soluble chromatin compartments, while poorly or moderately expressed genes exhibited a narrow stretch of salt-soluble chromatin limited to their 5' or body region. Here, we present the detailed characteristics, including the location of nucleosome-free regions and CpG islands, of several transcriptionally active chromatin compartments. These chromatin patterns illustrate how the salt solubility profile of a genomic region aids in the annotation of genes expressed in erythroid cells and contributes to the identification of functional features such as regulatory regions.