THI7 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
TEL2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
UTP20 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
FAS2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HIS3 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
INO2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MHR1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
LEU2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YGL039W DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
CIS3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
LEU1 DOWN in 'Abf1 mutant' vs 'Abf1 wild type control'
CHL1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ARO8 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
(Sample) organism/Saccharomyces cerevisiae
ICS2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
MRPL27 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
BUD4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MSA2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPS25B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
(Factor value) GENOTYPE/Abf1 wild type control
YDR089W DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YNL146C-A UP in 'Rap1 mutant' vs 'Rap1 wild type control'
URA3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
IRC18 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
MRPL24 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
SNF3 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
PUB1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HHO1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
IDP2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPS22B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ABF1 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
YJL218W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
YDR034W-B UP in 'Abf1 mutant' vs 'Abf1 wild type control'
MET17 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YIR043C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ENV9 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
COS10 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
GSC2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YJR008W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
NPL3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YER137C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
(Sample) genotype/Rap1 wild type control
ARG3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
VAC17 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
IMD1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ERC1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YDR461C-A UP in 'Rap1 mutant' vs 'Rap1 wild type control'
YBR197C DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ISC1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YGR093W DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
COS6 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PUT1 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
PGA1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
Analysis of 'Abf1 mutant' vs 'Abf1 wild type control'
YPL113C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
TIP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RPL7A DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
LEU4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HXT2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MMR1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YGR021W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
NDL1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
TOS1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
GUP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ZRT1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YHP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ALD3 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
RPL13A DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
snR70 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
DIA4 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
NIT3 DOWN in 'Abf1 mutant' vs 'Abf1 wild type control'
RPR1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPL7B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SPA2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
NUP49 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
GLY1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RPS7B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
BTN2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
YOR203W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
HIS4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
FAS1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SCW10 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ARG5,6 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PCA1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
TEC1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
(Sample) genotype/Abf1 wild type control
OPI10 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
CYC7 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
CPR4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MET6 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
TNA1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RPL18B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ATG8 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
CAN1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YRA1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ECM33 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YGL188C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
MET14 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
GIC1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
OPI3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
KSH1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YBL059W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ACT1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MET5 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PAB1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
AVT4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YPK9 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RNR4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PGI1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RTS3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SIM1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SFG1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HXK2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RPS1A DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
CDC26 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ERG25 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
OM45 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
TOS6 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MOG1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
OST3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HOM2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
BTN2 UP in 'Abf1 mutant' vs 'Abf1 wild type control'
TTI1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PSY1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPL14B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SRL1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SCP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RCK2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
AIM33 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
LCL2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PHO4 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PMI40 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YLR040C UP in 'Abf1 mutant' vs 'Abf1 wild type control'
ORC6 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
GAS3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
DBP2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
DNF2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HUG1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MET28 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
FMC1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ARO9 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
QDR2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
PIC2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
YAR029W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
TAF2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ALG3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ARE1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
KAP120 DOWN in 'Abf1 mutant' vs 'Abf1 wild type control'
Analysis of 'Rap1 mutant' vs 'Rap1 wild type control'
CLB1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MLP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SAM3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ALD3 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
ARO10 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
YKL177W UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RAD28 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPS0B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YOR192C-C DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SRS2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
IMG2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RPA190 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
RPL17B DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
HTB2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MUP1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YOL019W DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YEL023C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
KRE6 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YKR012C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
(Factor value) GENOTYPE/Rap1 wild type control
Abf1 and Rap1 are General Regulatory Factors that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing, and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. We have used microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37 C. We combined this data with published ChIP-chip studies and motif analysis to identify probable direct targets for Abf1 and Rap1. We also identified a substantial number of genes likely to bind Rap1 or Abf1, but not affected by loss of GRF binding. Interestingly, the results strongly suggest that Rap1 can contribute to gene activation from farther upstream than can Abf1. Also, consistent with previous work, more genes that bind Abf1 are unaffected by loss of binding than those that bind Rap1. Finally, we showed for several such genes that the Abf1 C-terminal region, which contains the putative activation domain, is not needed to confer this peculiar \"memory effect\" that allows continued transcription after loss of Abf1 binding. Experiment Overall Design: Three replicates each of rap1 ts and abf1 ts yeast were grown at 25 C and shifted to 37 C, along with matched wild type controls, prior to RNA isolation. The ts mutants lose DNA binding at 37 C.
YOR292C UP in 'Rap1 mutant' vs 'Rap1 wild type control'
GCD11 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
FMP43 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
RAX1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
FKS1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YMR027W DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
SVS1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ADE2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
ASC1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
YDR476C DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
POP8 DOWN in 'Abf1 mutant' vs 'Abf1 wild type control'
ARG1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
TUB2 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
JNM1 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
KES1 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'
MDL2 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
PET191 UP in 'Rap1 mutant' vs 'Rap1 wild type control'
STR3 DOWN in 'Rap1 mutant' vs 'Rap1 wild type control'