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TitleA high-resolution protein architecture of the budding yeast genome
Date2021
AbstractThe genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is ill defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq) to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons, and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex (PIC). Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs and cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.
MetadataClick here for full metadata
Data DOIdoi:10.26208/rykf-6050

Researchers
Rossi, M. J.
Penn State Department of Biochemistry and Molecular Biology
Kuntala, P. K.
Penn State Department of Biochemistry and Molecular Biology
Lai, W. K. M.
Penn State Department of Biochemistry and Molecular Biology
Yamada, N.
Penn State Department of Biochemistry and Molecular Biology
Badjatia, N.
Penn State Department of Biochemistry and Molecular Biology
Mittal, C.
Penn State Department of Biochemistry and Molecular Biology
Kuzu, G.
Penn State Department of Biochemistry and Molecular Biology
Bocklund, K.
Penn State Department of Biochemistry and Molecular Biology
Farrell, N. P.
Penn State Department of Biochemistry and Molecular Biology
Blanda, T.R.
Penn State Department of Biochemistry and Molecular Biology
Mairose, J. D.
Penn State Department of Biochemistry and Molecular Biology
Basting, A. V.
Penn State Department of Biochemistry and Molecular Biology
Mistretta, K. S.
Penn State Department of Biochemistry and Molecular Biology
Rocco, D. J.
Penn State Department of Biochemistry and Molecular Biology
Perkinson, E. S.
Penn State Department of Biochemistry and Molecular Biology
Kellogg, G. D.
Penn State Department of Biochemistry and Molecular Biology
Mahony, S.
Penn State Department of Biochemistry and Molecular Biology
Pugh, B. F.
Penn State Department of Biochemistry and Molecular Biology

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