FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter

Abstract

Transcriptional activators and coactivators overcome repression by chromatin, but regulation of chromatin disassembly and coactivator binding to promoters is poorly understood. Activation of the yeast HO gene follows the sequential binding of both sequence-specific DNA-binding proteins and coactivators during the cell cycle. Here, we show that the nucleosome disassembly occurs in waves both along the length of the promoter and during the cell cycle. Different chromatin modifiers are required for chromatin disassembly at different regions of the promoter, with Swi/Snf, the FACT chromatin reorganizer, and the Asf1 histone chaperone each required for nucleosome eviction at distinct promoter regions. FACT and Asf1 both bind to upstream elements of the HO promoter well before the gene is transcribed. The Swi/Snf, SAGA, and Mediator coactivators bind first to the far upstream promoter region and subsequently to a promoter proximal region, and FACT and Asf1 are both required for this coactivator re-recruitment.

Fig 1. Nucleosome eviction occurs in waves along the HO Promoter

A. DY6669 cells (GALp::CDC20) with a GALp::CDC20 allele were synchronized in mitosis by removing galactose, followed by release by addition of galactose (t = 0). The CDC20 arrest is at the G2/M transition, and HO expression at 40 min following release corresponds to late G1 phase. Nucleosome occupancy was measured by H3 ChIP using samples taken at various times after the release. This data along with additional time points are shown in Suppl Fig S1. The DNA in the experiment was sheared to an average of 350 bp, as opposed to approximately 550 bp in the other ChIP experiments. URS1, URS2, the Swi5 and SBF binding sites are shown for the HO promoter, where the ATG represents +1 and the transcription start site is at −20. Error bars in ChIP assays reflect the standard deviation of three replicate PCRs. B. The data from panel A, along with additional time points, is plotted as a function of time for PCR intervals centered at −1528, −729, −349, and −55.

Fig 2. Histone acetylation, Swi5, and pol II ChIPs at the HO promoter

DY6669 cells (GALp::CDC20) were used for ChIPs for H3(K14)-Ac (A), H4-Ac (B), histone H3 (C), and RNA pol II (F). The H3(K14)-Ac and H4-Ac ChIPs are normalized to the ChIP of total H3. D. HO mRNA measured by RT-qPCR from synchronized DY8602 (GALp::CDC20 SWI2-Myc). E. Swi5-Myc ChIP with synchronized DY6542 (GALp::CDC20 SWI5-Myc). Error bars in ChIP or RT-qPCR assays reflect the standard deviation of three replicate PCRs.

Fig 3. Coactivators bind first to URS1 and then to URS2 at the HO promoter

Binding of Swi/Snf, SAGA, and Mediator to HO URS1 and URS2 were analyzed by ChIP in synchronized cells. The following cells were used: A. DY8602 (GALp::CDC20 SWI2-Myc), B. DY12752 (GALp::CDC20 GCN5-Myc), C. DY8460 (GALp::CDC20 GAL11-Myc), D. DY10790 (GALp::CDC20 SWI2-Myc pob3), E. DY12750 (GALp::CDC20 GCN5-Myc pob3), F. DY12748 (GALp::CDC20 GAL11-Myc pob3), G. DY12964 (GALp::CDC20 SWI2-Myc asf1), H. DY12927 (GALp::CDC20 GCN5-Myc asf1), I. DY13137 (GALp::CDC20 GAL11-Myc asf1). Error bars in ChIP assays reflect the standard deviation of three replicate PCRs.

Fig 4. FACT mutants are sensitive to Asf1 levels

A. HO expression is reduced in pob3 and asf1 mutants. RNA was isolated from log phase wild type (DY150), pob3 (DY7379), and asf1 (DY12869) strains, and HO, PIR1, and CLN2 expression measured by RT-qPCR. Error bars in RT-qPCR assays reflect the standard deviation of three replicate PCRs. B. Double mutants affecting FACT and Asf1 are additive. Serial ten fold dilutions of strains DY150 (wild type), DY7815 (spt16-11), DY13178 (asf1 spt16-11), DY12554 (pob3-Q308K), DY12869 (asf1), DY13168 (asf1 pob3-Q308K), DY7379 (pob3-L78R), and DY13156 (asf1 pob3-L78R) were grown in plates with or without 25 mM hydroxyurea. C. Overexpression of ASF1 is toxic in FACT mutants. Strains DY150 (wild type), DY7815 (spt16-11), DY10308 (pob3-Q308K), and DY7379 (pob3-L78R) were transformed with either the pRS426 (YEp-URA3) vector or multicopy YEp-ASF1, and serial dilutions were grown on plates lacking uracil at the indicated temperature.

Fig 5. FACT binds to URS2 before Asf1

ChIPs were performed with synchronized cells in A, B, D, and E. A. FACT binds to URS2 at 20 min in wild type (DY6669; GALp::CDC20). B. Asf1 binds to URS2 at 30 min in wild type (DY13010; GALp::CDC20 ASF1-Myc). C. Using asynchronous cells, Asf1-Myc binds to HO URS2 in wild type (DY12997), but Asf1-Myc binding is lost in swi5 (DY13145), swi2 (DY13176), gcn5 (DY13164), gal11 (DY13162), pob3 (DY13150), and swi6 (DY13147) mutants. DY150 was used as the untagged control. D. FACT binds to URS2 in an asf1 mutant (DY12914; GALp::CDC20 asf1). E. FACT binding to URS2 in wild type (DY6669; GALp::CDC20), gcn5 (DY6650; GALp::CDC20 gcn5), gal11 (DY7419; GALp::CDC20 gal11), swi6 (DY13373; GALp::CDC20 swi6), swi5 (DY6570; GALp::CDC20 swi5), and swi2 (DY9718; GALp::CDC20 swi2) strains. F. FACT interacts with Swi6. Extracts prepared from strains DY150 (no tag), DY8341 (SWI4-Myc[18]) (150 kd), DY8353 (SWI6-Myc[18]) (117 kd), DY5832 (SWI5-Myc[8]) (92 kd), and DY12997 (ASF1-Myc[13]) (51 kd), were immunoprecipitated with anti-Myc antibody and analyzed on western blots, along with controls corresponding to 10% of the input before immunoprecipitation, and the blots were probed with anti-Myc, anti-Spt16, and anti-Pob3 antibodies. Error bars in ChIP assays reflect the standard deviation of three replicate PCRs.

Fig 6. Swi5 and Swi/Snf are required for nucleosome eviction at URS1 and FACT and Asf1 for eviction at URS2

Histone H3 ChIP was performed using the following synchronized cells and PCR primers for URS1 centered at −1293, URS2 at −666, at TATA at −55: A. DY6669 (GALp::CDC20), B. DY6570 (GALp::CDC20 swi5), C. DY9718 (GALp::CDC20 swi2), D. DY6650 (GALp::CDC20 gcn5), E. DY7419 (GALp::CDC20 gal11). F. DY11246 (GALp::CDC20 pob3), G. DY12914 (GALp::CDC20 asf1), and H. DY13373 (GALp::CDC20 swi6). I. The wild type, pob3 and asf1 H3 ChIPs were probed with URS2 primers centered at −729. J. The wild type, pob3 and asf1 H3 ChIPs were probed with URS2 primers centered at −349. Error bars in ChIP assays reflect the standard deviation of three replicate PCRs.

Fig 7. Model of events at the HO promoter during the cell cycle

Times are minutes after release from GALp::CDC20 arrest.