Global nucleosome occupancy in yeast

Table 1 Transcription factors that tend to associate with nucleosome-depleted promoters

Transcription factor	Pathway	Number of targets	Nucleosome-depleted
Rap1	Biosynthesis	291	35%
Fhl1	Biosynthesis	137	48%
Swi4	Cell cycle	165	36%
Hsf1	Environmental response	114	35%
Gat3	Metabolism	119	31%
Cin5	Environmental response	200	23%
Phd1	Metabolism	138	25%
Dal81	Metabolism	70	34%
Ndd1	Cell cycle	122	26%
Yap6	Environmental response	123	26%
Fkh2	Cell cycle	145	24%
Pdr1	Environmental response	103	27%
Ino4	Metabolism	118	25%
Smp1	Environmental response	99	27%
Yap5	Environmental response	113	26%
Ash1	Development	41	41%

Transcription factors are ranked according to the significance of their association with nucleosome-depleted promoters, as determined by a hypergeometric model. Shown are the 16 top-ranked factors along with relevant physiologic pathway, number of promoters bound [1], and percent of target promoters that are nucleosome-depleted. Factors found previously to be functionally cooperative are indicated [22].

ISSN: 1474-760X