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Buck MJ and Lieb JD  (2006) A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet 38(12):1446-51

Abstract: Organisms respond to changes in their environment, and many such responses are initiated at the level of gene transcription. Here, we provide evidence for a previously undiscovered mechanism for directing transcriptional regulators to new binding targets in response to an environmental change. We show that repressor-activator protein 1 (Rap1), a master regulator of yeast metabolism, binds to an expanded target set after glucose depletion despite decreasing protein levels and no evidence of posttranslational modification. Computational analysis predicts that proteins capable of recruiting the chromatin regulator Tup1 act to restrict the binding distribution of Rap1 in the presence of glucose. Deletion of the gene(s) encoding Tup1, recruiters of Tup1 or chromatin regulators recruited by Tup1 cause Rap1 to bind specifically and inappropriately to low-glucose targets. These data, combined with whole-genome measurements of nucleosome occupancy and Tup1 distribution, provide evidence for a mechanism of dynamic target specification that coordinates the genome-wide distribution of intermediate-affinity DNA sequence motifs with chromatin-mediated regulation of accessibility to those sites.

Status: Published Type: Journal Article PubMed ID: 17099712

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
ACA1 ACS1 ADE3 ADH1 AGP1 ANP1 AQY1 ASC1 AST2 ATG19
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AZF1 BDF1 BSC3 BSC5 BUD20 CAB5 CAF40 CAR1 CBP2 CCW12
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Topics Genes linked to topics (#21 - 30 )
CCW14 CDC19 CDC45 CFT1 CIT3 CLN3 CMS1 COG4 COS111 COS5
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Topics Genes linked to topics (#31 - 40 )
CPR4 CSR2 CTS1 CWP2 DBF2 DBF20 DDR2 DIF1 DNM1 DOT6
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Topics Genes linked to topics (#41 - 50 )
DPH5 DTR1 DUR3 DUS3 ECM16 EEB1 EHD3 ENB1 ERG5 EST3
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Topics Genes linked to topics (#51 - 60 )
FAA1 FAS1 FBA1 FRE6 FTR1 FYV1 GAC1 GAT1 GCN4 GCR1
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Topics Genes linked to topics (#61 - 70 )
GEA2 GIS1 GLK1 GLY1 GPD1 GPD2 GPG1 GPM1 GPR1 GTO3
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Topics Genes linked to topics (#71 - 80 )
GUP1 HAP1 HDA1 HIS4 HMLALPHA1 HMS1 HOM6 HSH49 HSP78 HXT6
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Topics Genes linked to topics (#81 - 90 )
ICT1 IGD1 IMT4 IRC15 ISW2 IZH3 JEN1 KTR5 LAA1 LCB2
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Topics Genes linked to topics (#91 - 100 )
LEE1 LEU2 MATALPHA1 MET6 MIG1 MLP1 MLP2 MNN4 MOH1 MON1
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Topics Genes linked to topics (#101 - 110 )
MOT3 MPS2 MRE11 MRM2 MRPL15 MRPL49 MSC6 MSN4 NAT3 NEW1
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Topics Genes linked to topics (#111 - 120 )
NMD5 NOB1 NOT5 NRG1 NUP42 OAF1 ORC2 OYE2 PAU15 PAU16
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Topics Genes linked to topics (#121 - 130 )
PAU4 PAU8 PDC1 PDR11 PEP5 PEX6 PFK27 PGI1 PHO81 PHO84
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Topics Genes linked to topics (#131 - 140 )
PHO88 PHO89 PIM1 PLM2 PMA1 PMP3 PNS1 POC4 POL1 POP6
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Topics Genes linked to topics (#141 - 150 )
PPH22 PPN1 PRE2 PRY1 PRY3 PSA1 PTK2 PUT1 PUT3 PYK2
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Topics Genes linked to topics (#151 - 160 )
QCR6 QDR2 RAD2 RAP1 RAS1 RCF2 RDN25-1 RGI2 RHO3 RIA1
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Cellular Location blue ball
Function/Process blue ball
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Topics Genes linked to topics (#161 - 170 )
RIB3 RNR2 RNR4 RPA190 RPA34 RPC31 RPH1 RPL11B RPL12A RPL12B
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Topics Genes linked to topics (#171 - 180 )
RPL13A RPL14B RPL15A RPL16A RPL16B RPL17A RPL17B RPL19A RPL1A RPL20A
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Topics Genes linked to topics (#181 - 190 )
RPL20B RPL21A RPL21B RPL22A RPL23A RPL23B RPL25 RPL26A RPL27A RPL28
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Topics Genes linked to topics (#191 - 200 )
RPL2A RPL2B RPL31B RPL32 RPL34A RPL34B RPL35A RPL35B RPL36A RPL37A
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Topics Genes linked to topics (#201 - 210 )
RPL38 RPL41A RPL43A RPL5 RPL6A RPL7B RPL8A RPL8B RPL9A RPP0
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Topics Genes linked to topics (#211 - 220 )
RPP1B RPS0B RPS10A RPS10B RPS11B RPS12 RPS13 RPS14A RPS14B RPS15
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Topics Genes linked to topics (#221 - 230 )
RPS16A RPS18A RPS19A RPS19B RPS1A RPS1B RPS21A RPS21B RPS22A RPS23A
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Topics Genes linked to topics (#231 - 240 )
RPS24A RPS24B RPS25A RPS25B RPS27A RPS27B RPS29A RPS29B RPS3 RPS30A
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#241 - 250 )
RPS30B RPS4A RPS4B RPS5 RPS6A RPS6B RPS7B RPS8A RPS9A RPS9B
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#251 - 260 )
RTC4 RVS167 RXT3 SEC59 SEC8 SED1 SFT1 SGA1 SGV1 SHE9
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Topics Genes linked to topics (#261 - 270 )
SIP4 SIZ1 SKO1 SKP2 SKS1 SKT5 SNF4 SNR17A SPG4 SPO20
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Mutants/Phenotypes blue ball
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Topics Genes linked to topics (#271 - 280 )
SRO9 SRP40 SSB1 SSF2 SSN8 SST2 SUF2 SUR1 SUT1 SUT2
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Topics Genes linked to topics (#281 - 290 )
SYC1 TAX4 TDH2 TEF1 THI4 TIM21 TMA10 TOS8 TPI1 TRX2
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Topics Genes linked to topics (#291 - 300 )
TUP1 TVP15 TYE7 UBI4 UBP2 UFO1 UGO1 UGX2 URA3 USV1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball
Function/Process blue ball
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Topics Genes linked to topics (#301 - 310 )
UTP15 UTP4 VEL1 VHS1 VMA6 VPS8 VTS1 WHI2 YAP6 YAR075W
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Topics Genes linked to topics (#311 - 320 )
YAT1 YBL028C YBL029W YBR090C YCF1 YCK2 YCL076W YCR006C YCR025C YDR042C
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Topics Genes linked to topics (#321 - 330 )
YDR186C YDR541C YDR543C YEL057C YEL075C YER034W YER130C YER158C YFL034W YFL064C
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Topics Genes linked to topics (#331 - 340 )
YFT2 YGL260W YGR050C YGR283C YHR033W YIL055C YIL175W YIL177C YIR016W YJL225C
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Topics Genes linked to topics (#341 - 350 )
YKL031W YLL065W YLL067C YLR413W YML133C YML6 YMR082C YMR086C-A YMR144W YMR265C
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Topics Genes linked to topics (#351 - 360 )
YMR295C YNL010W YNL144C YNL190W YOR268C YOR302W YOR338W YOR342C YOR365C YOR387C
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Topics Genes linked to topics (#361 - 366 )
YPL162C YPR202W YPT31 YRF1-3 ZEO1 ZRT3
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