Antagonistic Controls of Chromatin and mRNA Start Site Selection by Tup Family Corepressors and the CCAAT-Binding Factor

Abstract

The Tup family corepressors contribute to critical cellular responses, such as the stress response and differentiation, presumably by inducing repressive chromatin, though the precise repression mechanism remains to be elucidated. E ukaryotic chromosomal DNA is packaged in a highly organized and condensed chromatin structure. Many DNA-associated reactions, including DNA damage repair, replication, recombination, and transcription, are regulated by the chromatin structure (1, 2). The chromatin structure is modulated by two distinct classes of regulators, histone modification enzymes and ATP-dependent chromatin remodeling factors (3, 4). Such regulatory components are recruited by two types of cis-acting regulatory factors, transcriptional activators and repressors. Transcriptional activators and repressors bind to cis-acting elements to activate and repress transcription, respectively, by affecting the chromatin structure and regulating RNA polymerase II accumulation in the promoter region (5-7). These transcriptional regulators also interact with coactivators and corepressors to regulate gene expression (8, 9). The Tup family transcriptional corepressors are conserved between yeast and humans and regulate gene expression during the stress response and cellular differentiation (10, 11). Saccharomyces cerevisiae Tup1 represses some genes regulated by cell type, glucose, oxidative stress, DNA damage, and other cellular stress responses (12, 13). Tup1 represses the expression of genes via distinct mechanisms: by establishing a repressive chromatin structure around the target gene promoter, by recruiting histone deacetylases, and by directly interfering with the general transcription machinery (14-18). Two Tup1 orthologs in Schizosaccharomyces pombe, Tup11 and Tup12 (Tup11/12), regulate multiple stress-responsive genes, including the fbp1 ϩ and cta3 ϩ genes, to provide stress specificity (19,20). However, the precise molecular mechanisms of Tup1 family proteins in gene repression have not been fully uncovered.The fbp1 ϩ gene encodes fructose-1,6-bisphosphatase and is robustly induced upon glucose starvation (21,22). fbp1 ϩ expression is strictly repressed by Tup11/12 and activated by the transcriptional activators Atf1, Rst2, and Php5 (23-26). Atf1, a bZIP protein, is regulated through phosphorylation by the mitogen-activated protein kinase pathway (27-29), while Rst2, a C 2 H 2 Zn finger-type protein, is under the regulation of the protein kinase A pathway (23, 30). Php5, a component of the S. pombe CCAATbinding factor (CBF; also known as NF-Y) that possesses a histone hold domain, forms a complex with Php2/Php3 and contributes to cyc1 ϩ transcription (31, 32). In addition, two cis-acting elements required for fbp1 ϩ transcription have been identified (33). Upstream activation sequence 1 (UAS1) contains a cyclic AMP response element (CRE) and is the binding site for Atf1 and its binding partner, Pcr1 (34), while UAS2 resembles the S. cerevisiae stress response element (STRE) and serves as the binding site for Rst2 (...

Interplay between chromatin modulators and histone acetylation regulates the formation of accessible chromatin in the upstream regulatory region of fission yeast <i>fbp1</i>

“…Moreover, the CCATT box binding factor (CBF), which includes Php5 that possesses a histone-fold domain, is required for fbp1 activation (Janoo et al, 2001). CBF binds to the UAS1-UAS2 region with a peak at UAS2 in glucose-starved cells (Asada et al, 2015). The Tup11/12 global co-repressors also bind to the fbp1 upstream region and regulate transcription to ensure a stress-specific response through chromatin regulation (Hirota et al, 2004(Hirota et al, , 2006.…”

Histone Chaperone Asf1 Is Required for the Establishment of Repressive Chromatin in Schizosaccharomyces pombe fbp1 Gene Repression

“…We previously demonstrated the critical role played by Tup11/12 in stress-specific chromatin regulation upstream from fbp1 and other genes (41). The role played by Tup11/12 in the determination of the transcription start site has been recently reported (25). These results suggest that the fission yeast Tup1 orthologs Tup11/12 might not act as simple corepressors but serve as transcriptional regulators via chromatin modulation.…”

“…First, Tup11/12 repress chromatin relaxation in the region upstream from the fbp1 promoter. Second, Tup11/12 interfere with the stable binding of RNA polymerase II (RNAPII) at the TATA box (25,26). We also demonstrated that Tup11/12 repress the binding of Rst2 to the fbp1 upstream binding site (16).…”

“…Northern blot and ChIP analyses were performed as described previously (8). ChIP analysis was performed as described previously (25) using anti-Atf1 antibody (Abcam), anti-DYKDDDDK antibody (Wako; 018-22383), anti-H3 antibody (abcam; ab1791), antiacetylated histone H3 antibody (Millipore; 06-599), and anti-trimethylated histone H3K4 antibody (abcam; ab8580).…”

Phospho-mimicking Atf1 mutants bypass the transcription activating function of the MAP kinase Sty1 of fission yeast

“…Regarding the interaction of unphosphorylated Atf1 with transcriptional repressors under basal conditions, the co-repressors Tup11 and Tup12 have been reported to restrain the expression of the gluconeogenesis gene fbp1 (Asada, et al 2015, Takemata, et al 2016. Atf1 has also been described to recruit repressive activities at the mating locus through the binding to several hetereochromatin assembly factors such as Clr3, Clr4, Clr6 and Swi6 (Jia, et al 2004, Kim, et al 2004, Yamada, et al 2005.…”