A high-resolution protein architecture of the budding yeast genome

Matthew J. Rossi, Prashant K. Kuntala, William K. M. Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P. Farrell, Thomas R. Blanda, Joshua D. Mairose, Ann V. Basting, Katelyn S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony and B. Franklin Pugh ()
Additional contact information
Matthew J. Rossi: The Pennsylvania State University
Prashant K. Kuntala: The Pennsylvania State University
William K. M. Lai: The Pennsylvania State University
Naomi Yamada: The Pennsylvania State University
Nitika Badjatia: The Pennsylvania State University
Chitvan Mittal: The Pennsylvania State University
Guray Kuzu: The Pennsylvania State University
Kylie Bocklund: The Pennsylvania State University
Nina P. Farrell: The Pennsylvania State University
Thomas R. Blanda: The Pennsylvania State University
Joshua D. Mairose: The Pennsylvania State University
Ann V. Basting: The Pennsylvania State University
Katelyn S. Mistretta: The Pennsylvania State University
David J. Rocco: The Pennsylvania State University
Emily S. Perkinson: The Pennsylvania State University
Gretta D. Kellogg: The Pennsylvania State University
Shaun Mahony: The Pennsylvania State University
B. Franklin Pugh: The Pennsylvania State University

Nature, 2021, vol. 592, issue 7853, 309-314

Abstract: Abstract The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP–exo/seq)1,2 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. 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 engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (5)

Downloads: (external link)
https://www.nature.com/articles/s41586-021-03314-8 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:592:y:2021:i:7853:d:10.1038_s41586-021-03314-8

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-021-03314-8

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().