ArticleNature2021
A high-resolution protein architecture of the budding yeast genome.
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Article in Nature, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers.
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160citing papers in PubMed
17.0field-weighted citation impact, top 1% of its field
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Who cites it
160 citing papers in PubMed, 271 citations in OpenAlex.
- Genetic landscape of an in vivo protein interactome.Nature genetics · 2026Article
- Single-molecule imaging reveals DNA shape read-out by the INO80 chromatin remodeler.Nature communications · 2026Article
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Nucleosomes and IDRs suppress promiscuous GCN4 binding on minichromosomes.Nature structural & molecular biology · 2026Article
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- Sequence-dependent binding modes of INO80 control +1 nucleosome positioning.bioRxiv : the preprint server for biology · 2026Article
- Cohesin facilitates nucleosome invasion by transcription factors.Science advances · 2026Article
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions.Nature communications · 2026Article
- Induced DNA double strand breaks by genotoxic drugs occur at active transcription H3K36 tri-methylation sites.Communications biology · 2026Article
- Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.The EMBO journal · 2026Article
- mChIP-seq for Multiplex and Multifactorial Epigenomic Profiling Uncovers Cancer-specific Histone Features in Cellular and Circulating Nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae.Scientific reports · 2026Article
- Dbf4-dependent kinase finetunes Ino80 function at chromosome replication origins.Nature communications · 2026Article
- Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries.Science (New York, N.Y.) · 2026Article
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- Multiple strategies to resolve the conflict between replication and transcription in mammalian cells.Nucleic acids research · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.Nature cell biology · 2026Article
100 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors at 1 institution in 1 country.
Matthew J RossiCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Prashant K KuntalaCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
William K M LaiCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Naomi YamadaCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Nitika BadjatiaCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Chitvan MittalCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Guray KuzuCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Kylie BocklundCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Nina P FarrellCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Thomas R BlandaCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Joshua D MairoseCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Ann V BastingCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Katelyn S MistrettaCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
David J RoccoCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Emily S PerkinsonCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Gretta D KelloggCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.ORCID http://orcid.org/0000-0002-9171-8696
Shaun MahonyCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
B Franklin PughCenter for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. fp265@cornell.edu.ORCID http://orcid.org/0000-0001-8341-4476
Pennsylvania State University · US
Funding
REGULATION OF TBP DIMERSR01GM059055 · NIGMS · PENNSYLVANIA STATE UNIVERSITY-UNIV PARK · PI PUGH, B FRANKLIN · 2000 to 2020
$6.6MHigh Resolution Mapping of Function Elements in the Yeast GenomeR01HG004160 · NHGRI · PENNSYLVANIA STATE UNIVERSITY, THE · PI PUGH, B FRANKLIN · 2007 to 2022
$5.3MPromoter Regulation in Response to Environmental StressR01ES013768 · NIEHS · PENNSYLVANIA STATE UNIVERSITY, THE · PI PUGH, B FRANKLIN · 2007 to 2019
$4.9MHigh Resolution Mapping of Functional Elements in the Yeast GenomeR56HG004160 · NHGRI · PENNSYLVANIA STATE UNIVERSITY, THE · PI PUGH, B FRANKLIN · 2017 to 2017
$300kNHGRI NIH HHS R01 HG004160NHGRI NIH HHS R56 HG004160NIEHS NIH HHS R01 ES013768NIGMS NIH HHS R01 GM059055
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)
Indexed as
CoenzymesFungal ProteinsGenome, FungalMultiprotein ComplexesPromoter Regions, GeneticRNA Polymerase IRNA Polymerase IIRNA Polymerase IIISaccharomyces cerevisiaeTATA-Box Binding ProteinTranscription FactorsTranscription Factor TFIIBTranscription Factor TFIIDCoenzymesFungal ProteinsMultiprotein ComplexesRNA Polymerase IRNA Polymerase IIRNA Polymerase IIITATA-Box Binding ProteinTranscription FactorsTranscription Factor TFIIBTranscription Factor TFIID
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.