TABLE 3.

Genes on chromosome III with cryptic transcripts^a

Gene	Nucleosome level in spt6-1004	Spt6 level	RNAP II level
LDB16	−0.24	0.46	1.49
BUD3	−0.02	−0.22	−1.11
DCC1	−0.14	−0.34	−0.33
AGP1	−0.48	0.27	0.43
ATG22	0.09	−0.13	−0.16
YCL042W	−0.71	0.69	1.92
MRC1	−0.01	−0.21	−1.0
POL4	0.02	−0.05	0.23
YCR016W	0.01	−0.02	−0.38
CWH43	−0.08	−0.10	−0.07
MAK32	−0.05	−0.17	−0.68
SYP1	−0.20	0.01	0.01
RBK1	−0.29	0.24	0.67
RRT12	−0.29	0.30	0.09
RAD18	0.23	−0.09	−0.93
SSK22	0.03	−0.27	−0.53
SRB8	0.11	−0.36	−1.0
FIG2	−0.06	−0.16	−0.63
CDC39	0.00	0.32	−0.37
RDS1	0.14	−0.42	−1.4
AAD3	0.11	−0.54	−0.83

^aThe RNAP II occupancy (log₂ IP/no Ab) and Spt6 occupancy (log₂ HA/no tag) determined by our ChIP-chip assay are compared to the nucleosome occupancy signals (log₂ spt6-1004/wild type) across coding regions for genes on chromosome III known to have short transcripts in the spt6-1004 mutant.