reprogram somatic cells into induced pluripotent stem cells (Feng et al., 2009). In CD4+ T cells, this analysis revealed a strong association of H3K4me1-marked regions with Ets and Runx motifs, consistent with their known essential roles in T cell development and function (Figure S4C) (Rothenberg and Taghon, 2005). In this cell type, genome-wide data for nucleosome positions, DNase hypersensitivity and mononucleosomal ChIP-Seq for a wide range of histone modifications is available, allowing precise determination of nucleosome positions, chromatin accessibility and histone modifications (Barski et al., 2007; Boyle et al., 2008; Schones et al., 2008). Alignment of H3K4me1 ChIP-Seq, total nucleosome sequence tag positions and DNase I on the Ets motifs enriched in the H3K4me1-marked promoter-distal regions revealed nucleosome phasing around the Ets motif similar to the pattern we observed around PU.1 in PUER cells, which was accompanied by a sharp spike in DNase I hypersensitivity at the Ets site (Figure S4F). This result is in stark contrast to the continuous nucleosome distribution observed when aligning the data on the means of the tag distributions (Figure S4F) and establishes that the central gap in the H3K4me1 pattern over the transcription factor motif is reflective of the absolute nucleosome positions and represents
