Chromatin Structure Modulation in Saccharomyces cerevisiae by Centromere and Promoter Factor 1

Abstract

CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and in the promoters of numerous genes, including those encoding enzymes of the methionine biosynthetic pathway. Strains lacking CPF1 are methionine auxotrophs, and it has been proposed that CPF1 might positively influence transcription at the MET25 and MET16 genes by modulating promoter chromatin structure. We test this hypothesis and show that the regions surrounding the CDEI motifs in the MET25 and MET16 promoters are maintained in a nucleosome-free state and that this requires the entire CPF1 protein. However, the chromatin structure around the CDEI motifs does not change on derepression of transcription and does not correlate with the methionine phenotype of the cell. An intact CDEI motif but not CPF1 is required for transcriptional activation from a region of the MET25 upstream activation sequence. Our results suggest that CPF1 functions to modulate chromatin structure around the CDEI motif but that these changes at the MET25 and MET16 promoters do not explain how CPF1 functions to maintain methionine-independent growth. The presence of CPF1-dependent chromatin structures at these promoters leads to a weak repression of transcription.

Metabolism of sulfur amino acids in Saccharomyces cerevisiae.

“…A nearly identical result was obtained for the MET25 promoter (109). Furthermore, important modifications of the overall chromatin structure were not observed upstream of MET16 and MET25 upon transcriptional activation (109). Thus, Cbf1p does not seem to function in modifying the phasing of the nucleosomes.…”

“…However, cells that lack Cbf1p exhibited changes in the chromatin structure upstream of MET16, which were limited to the immediate nucleotides adjacent to TCACGTG (189). A nearly identical result was obtained for the MET25 promoter (109). Furthermore, important modifications of the overall chromatin structure were not observed upstream of MET16 and MET25 upon transcriptional activation (109).…”

“…Furthermore, when methionine prototrophic rever-tants were selected from cells expressing the Cbf1p-AP4 hybrid protein, they all contained an amino acid change in the basic AP4 portion of the hybrid (58). Despite these observations, Mellor and coworkers proposed that Cbf1p might function in a non-DNA bound form during transcriptional activation of the MET genes while a DNA bound form acted at centromeres (109,172). This conclusion arose mainly from the analysis of one Cbf1p derivative (a Glu231Ala replacement), which failed to bind in vitro to the CACGTG sequence but did not cause methionine auxotrophy when expressed in yeast (172).…”

ChromWave: Deciphering the DNA-encoded competition between transcription factors and nucleosomes with deep neural networks

“…A class of abundant and essential TFs including Abf1, Rap1, Reb1, and Cbf1 drive promoter nucleosome exclusion around TSSs (Kent et al ., 1994; Yarragudi et al ., 2004; Badis et al ., 2008; Hartley and Madhani, 2009; Tsankov et al ., 2010, 2011; Ganapathi et al ., 2011). In order to assess whether ChromWave successfully models the competition between TFs and nucleosomes, we examined ChromWave’s first convolutional layer to search for learned DNA sequence patterns that are important in predicting nucleosome and TF occupancies.…”