Skip to main content
. Author manuscript; available in PMC: 2009 Oct 1.
Published in final edited form as: Nat Methods. 2009 Mar 22;6(4):283–289. doi: 10.1038/nmeth.1313

Fig. 5. Higher-order patterns of DNA accessibility.

Fig. 5

(a) Mapped DNase I cleavages relative to 5,006 TSSs29. Four major clusters are exposed by k-means analysis (red, blue, green and purple bars, respectively). In the red cluster, maximal DNase I cleavage occurs in a stereotypic ∼50 bp band ∼100 bp upstream of the TSS (grey arrowhead, top). In the blue, green and purple clusters, the extent and intensity of DNase I cleavage upstream of the TSS widens to the -1, -2, and -3 nucleosomes (respectively). (b) Spatial restriction of footprints near TSSs. Distribution of footprints matching Reb1, Abf1, Rap1, Mcm1, Pdr3, Cbf1 and Hsf1 relative to the TSSs (dashed black lines) and start codons of 1,260 genes sorted by the length of the 5′UTR. Enrichment within a ∼50 bp region centered ∼100 bp upstream of the TSS (dashed red lines). (c) DNase I cleavage profiles aligned relative to Reb1, Abf1, Rap1 and Mcm1 footprints. (d) mRNA abundance for genes found in each of the four clusters correlates with the accessibility of the promoters of those genes (colors as in a; median expression denoted by a black bar).