Nucleosome Retention in Human Sperm Figure 3. GC-content predicts variation in nucleosome retention among gene classes and at distal regulatory regions. GC-content signatures around the start sites of (A) housekeeping genes (black), (B) tissue-specific genes (genes expressed in a single tissue, blue) and (C) developmental regulators (red). Average nucleosome retention in sperm (E–G), average nucleosome occupancy in T-cells (I–K), and average nucleosome affinity around the start sites (M–O) of the same three classes of genes. Nucleosome retention in sperm, but not occupancy in T-cells, mirrors the GC-content and the intrinsic nucleosome affinity. The three gene classes contain 7,308 housekeeping genes, 1,686 tissue-specific genes and 538 transcription factors that regulate development. GC-content (D), nucleosome retention in sperm (H), nucleosome occupancy in T-cells (L), and nucleosome affinity (P) are also enriched at DNase I hypersensitive sites (HS) identified in embryonic stem (ES) cells. The average scores were calculated from 64,217 DNase I HS sites from ES cells located at least 1 kb away from any gene. doi:10.1371/journal.pgen.1002036.g003 Nucleosome retention at distal regulatory regions In addition to gene start sites, many regulatory regions in the human genome are also GC-rich with high predicted intrinsic nucleosome affinity [34,54]. Using DNase I hypersensitive sites in ES cells to identify putative distal regulatory regions that function in the early embryo, we find that they are also associated with nucleosome retention in sperm (Figure 3H). Thus, in addition to the promoters of developmental regulators and housekeeping genes, nucleosomes are also retained in mature sperm at distal regulatory regions that are active in the early embryo. In all cases, PLoS Genetics | www.plosgenetics.org 5 April 2011 | Volume 7 | Issue 4 | e1002036