Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

Abstract

SUMMARY A canonical nucleosome architecture around promoters establishes the context in which proteins regulate gene expression. Whether gene regulatory proteins that interact with nucleosomes are selective for individual nucleosome positions across the genome is not known. Here we examine in Saccharomyces several protein-nucleosome interactions, including those that 1) bind histones (Bdf1/SWR1 and Srm1), 2) bind specific DNA sequences (Rap1 and Reb1), and 3) potentially collide with nucleosomes during transcription (RNA polymerase II). We find that the Bdf1/SWR1 complex forms a di-nucleosome complex that is selective for the +1 and +2 nucleosomes of active genes. Rap1 selectively binds to its cognate site on the rotationally exposed first and second helical turn of DNA inside either border of the −1 nucleosome, whereas Reb1 is selective for a single NFR-proximal border of the −1 nucleosome. We find that a transcribing RNA polymerase creates a delocalized state of resident nucleosomes. These findings suggest that nucleosomes around promoter regions have position-specific functions, and that some gene regulators have position-specific nucleosomal interactions.

Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription

“…We speculate that the yeast Taf4/Taf12 heterodimer, with at least two independent activator-binding sites (for Rap1 and possibly other transactivators), collectively fulfills the roles of the metazoan Taf homology domain. Such distribution of function among multiple yeast proteins has been seen in the case of the TFIID-associated protein Bdf1, which supplies bromodomain functions absent from yeast Taf1 but present in metazoan Taf1, resulting in comparable conservation of overall TFIID function from yeast to man (33).…”

“…RPG transcription is coordinately regulated and highly sensitive to diverse environmental stimuli (31). Repressor activator protein 1 (Rap1)-binding sites are found within the majority of RPG enhancers, and Rap1 is the only transactivator absolutely required for RPG transcription, although Rap1 does collaborate with additional transcription factors such as Fhl1/Ifh1/Crf1, Sfp1, Hmo1, and the NuA4 coactivator to modulate RPG expression (21,24,30,(32)(33)(34). In contrast to the other factors noted above (35-37), Rap1 enhancer occupancy does not change significantly with transcription rates.…”

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

“…To determine the relative contribution of each histone PTM in targeting the NuA3 complex, we reasoned that histone PTMs that promote the interaction of NuA3 with chromatin would colocalize with Sas3. To this end, we mapped NuA3-bound nucleosomes at high resolution in vivo using a MNase-based ChIP-seq approach, which has previously been used to map chromatin remodelers (Koerber et al 2009;Floer et al 2010;Yen et al 2012;Ramachandran et al 2015). We immunoprecipitated HA-tagged Sas3, in parallel with an untagged control, from cross-linked MNase-digested chromatin and performed paired-end sequencing.…”

Stable and dynamic nucleosome states during a meiotic developmental process

“…The concentration of H3K9ac at the +1 nucleosome, H3K4me3 at +1,2,3, H3K36me3 at all genic positions except +1,2, and H3K79me3 at all genic locations, results in a specific marking system in which the first four nucleosomes downstream of the TSS may be distinguished from each other. This may be important for events surrounding transcription initiation and early elongation, where nucleosome-binding regulatory proteins selectively interact with nucleosomes in a position-specific manner (Koerber et al 2009). However, there is no evidence that the widespread occurrence of marks as detected here is linked to an equivalent widespread binding of cognate factors, and so additional regulatory determinants are likely involved.…”