Chromatin structure of the yeast FBP1 gene: Transcription‐dependent changes in the regulatory and coding regions

Abstract

We have studied the chromatin structure of the Saccharomyces cerevisiae FBP1 gene, which codes for fructose‐1,6‐bisphosphatase. A strong, constitutive, DNase I, micrococcal nuclease and S1 nuclease hypersensitive site is present close to the 3′ end of the coding region. In the repressed state, positioned nucleosomes exist around this site, and subtle changes occur in this nucleosomal organization upon derepression. A DNase I hypersensitive region is located within the promoter between positions −540 and −400 and it extends towards the gene in the derepressed state, leading to an alteration of nucleosomal positioning. Psoralen crosslinking of chromatin, which is used for the first time to study the mobility of restriction fragments from an RNA polymerase II gene, revealed that part of the promoter is nucleosome‐free, in accordance with the results of DNase I digestion. A model is presented that, based on the chromatin structure, puts forward the hypothesis that the promoter UAS is located between − 540 and − 340. Finally, psoralen crosslinking, as well as digestions with micrococcal nuclease or restriction endonucleases suggests that most if not all of the copies of the active FBP1 gene are covered by nucleosomes.

AnCF, the CCAAT Binding Complex of Aspergillus nidulans, Is Essential for the Formation of a DNase I-Hypersensitive Site in the 5′ Region of the amdS Gene

“…Adjacent to the DNase I-hypersensitive site an ordered nucleosome array covering the coding region and sequences upstream of the promoter exists under repressing conditions. Upon derepression, the discrete MNase bands become diffuse, indicating that the exact positioning of the nucleosomes is lost and that they can slide along the DNA, a change also observed in other genes and characteristic of the active state (15,36,68,76).…”

Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective invivo in response to acidic activators

“…Transcriptional regulation is mediated by Cha4p through two binding sites, UAS1 CHA (positions −240 to −214) and UAS2 CHA (positions −214 to −161), present in the promoter region. Several loci in yeast show activation‐dependent structural changes (Almer and Hörz, 1986; Fedor and Kornberg, 1989; del Olmo et al ., 1993; Verdone et al ., 1996). The nucleosomal organization of the CHA1 gene was investigated employing micrococcal nuclease (MNase) and DNase I digests of repressed or derepressed SG76 ( CHA4 ) cells.…”

“…In the repressed state a constitutive hypersensitive site exists, comprising the UASs with an ordered nucleosome array covering the coding region and a positioned nucleosome over the TATA box (nuc-1). Upon induction, the discrete band pattern observed for the coding region is lost and becomes diffuse and smeary, a change also observed in other genes in the active state and characteristic of active genes (Wu et al, 1979;Lee and Garrard, 1991;Vincenz et al, 1991;del Olmo et al, 1993). Furthermore, upon activation the nucleosome occluding the TATA box (nuc-1) is remodeled, thereby broadening the hypersensitive site in the promoter region.…”

The Transcriptional Coactivators SAGA, SWI/SNF, and Mediator Make Distinct Contributions to Activation of Glucose-repressed Genes

“…1, A and B). This result was surprising in light of the fact that the Cat8 binding site is in a nucleosome-free region at FBP1 (20). Several activators whose binding sites are similarly accessible bind without the aid of coactivators, such as Pho2/Pho4 at PHO8, Swi5 at HO, and Gal4 at GAL1/GAL10 (21)(22)(23).…”