A Role for FACT in Repopulation of Nucleosomes at Inducible Genes

Abstract

Xenobiotic drugs induce Pleiotropic Drug Resistance (PDR) genes via the orthologous Pdr1/Pdr3 transcription activators. We previously identified the Mediator transcription co-activator complex as a key target of Pdr1 orthologs and demonstrated that Pdr1 interacts directly with the Gal11/Med15 subunit of the Mediator complex. Based on an interaction between Pdr1 and the FACT complex, we show that strains with spt16 or pob3 mutations are sensitive to xenobiotic drugs and display diminished PDR gene induction. Although FACT acts during the activation of some genes by assisting in the nucleosomes eviction at promoters, PDR promoters already contain nucleosome-depleted regions (NDRs) before induction. To determine the function of FACT at PDR genes, we examined the kinetics of RNA accumulation and changes in nucleosome occupancy following exposure to a xenobiotic drug in wild type and FACT mutant yeast strains. In the presence of normal FACT, PDR genes are transcribed within 5 minutes of xenobiotic stimulation and transcription returns to basal levels by 30–40 min. Nucleosomes are constitutively depleted in the promoter regions, are lost from the open reading frames during transcription, and the ORFs are wholly repopulated with nucleosomes as transcription ceases. While FACT mutations cause minor delays in activation of PDR genes, much more pronounced and significant defects in nucleosome repopulation in the ORFs are observed in FACT mutants upon transcription termination. FACT therefore has a major role in nucleosome redeposition following cessation of transcription at the PDR genes, the opposite of its better-known function in nucleosome disassembly.

Histone chaperone networks shaping chromatin function

“…Displacement of a H2A–H2B dimer can be facilitated by FACT 36 , and the resultant hexasome can be maintained by FACT 36 or Nap1 (REFS 52,186). The loss of either chaperone leads to the depletion of histones in transcribed regions 187–189 . The re-establishment of chromatin structure after the passage of RNA polymerase II prevents the initiation of transcription from cryptic promoters 190,191 , and a substantial number of histone chaperones, including SPT2, SPT6, Rtt106, FACT, Vps75, Asf1 and HIRA 2,185,192 , are implicated in this process (reviewed in REF.…”

Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae

“…This could explain the increased nucleosome turnover observed in highly transcribed regions upon acute depletion of FACT (Jamai et al 2009), as nucleosomes destabilized during transcription could not be restored to the canonical state and would therefore need to be replaced. Consistent with this view, FACT can stabilize nucleosomes in vitro (Hsieh et al 2013;Chang et al 2014) and it is needed to restore nucleosome occupancy after transcription (Biswas et al 2007;Fleming et al 2008;Kaplan et al 2008;Ransom et al 2009;Hainer et al 2011Hainer et al , 2012Voth et al 2014;Feng et al 2016). However, FACT also has an established role in ejecting nucleosomes from promoters during transcriptional activation (Biswas et al 2006;Ransom et al 2009;Takahata et al 2009a,b;Shakya et al 2015).…”

Large-scale ATP-independent nucleosome unfolding by a histone chaperone

“…Consistent with roles in both forming and bypassing nucleosomes, FACT participates in a range of processes including DNA transcription, replication, and repair 13–15 . Notably, FACT is needed for efficient removal of nucleosomes during induction of transcription 16,17 , it facilitates nucleosome recovery during elongation and nucleosome repopulation during repression of transcription 18–20 and it promotes transcription through chromatin by RNA polymerase II in vitro 21,22 , highlighting the importance of both its stabilization and destabilization activities.…”