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Article ; Online: Global analysis of the yeast knockout phenome.

Turco, Gina / Chang, Christie / Wang, Rebecca Y / Kim, Griffin / Stoops, Emily H / Richardson, Brianna / Sochat, Vanessa / Rust, Jennifer / Oughtred, Rose / Thayer, Nathaniel / Kang, Fan / Livstone, Michael S / Heinicke, Sven / Schroeder, Mark / Dolinski, Kara J / Botstein, David / Baryshnikova, Anastasia

Science advances

2023 Volume 9, Issue 21, Page(s) eadg5702

Abstract: Genome-wide phenotypic screens in the budding ... ...

Abstract	Genome-wide phenotypic screens in the budding yeast
MeSH term(s)	Humans ; Saccharomyces cerevisiae/genetics
Language	English
Publishing date	2023-05-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adg5702
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Article ; Online: Collaboration between the essential Esa1 acetyltransferase and the Rpd3 deacetylase is mediated by H4K12 histone acetylation in Saccharomyces cerevisiae.

Chang, Christie S / Pillus, Lorraine

Genetics

2009 Volume 183, Issue 1, Page(s) 149–160

Abstract: Histone modifications that regulate chromatin-dependent processes are catalyzed by multisubunit complexes. These can function in both targeting activities to specific genes and in regulating genomewide levels of modifications. In Saccharomyces cerevisiae, ...

Abstract	Histone modifications that regulate chromatin-dependent processes are catalyzed by multisubunit complexes. These can function in both targeting activities to specific genes and in regulating genomewide levels of modifications. In Saccharomyces cerevisiae, Esa1 and Rpd3 have opposing enzymatic activities and are catalytic subunits of multiple chromatin modifying complexes with key roles in processes such as transcriptional regulation and DNA repair. Esa1 is an essential histone acetyltransferase that belongs to the highly conserved MYST family. This study presents evidence that the yeast histone deacetylase gene, RPD3, when deleted, suppressed esa1 conditional mutant phenotypes. Deletion of RPD3 reversed rDNA and telomeric silencing defects and restored global H4 acetylation levels, in addition to rescuing the growth defect of a temperature-sensitive esa1 mutant. This functional genetic interaction between ESA1 and RPD3 was mediated through the Rpd3L complex. The suppression of esa1's growth defect by disruption of Rpd3L was dependent on lysine 12 of histone H4. We propose a model whereby Esa1 and Rpd3L act coordinately to control the acetylation of H4 lysine 12 to regulate transcription, thereby emphasizing the importance of dynamic acetylation and deacetylation of this particular histone residue in maintaining cell viability.
MeSH term(s)	Acetylation ; Cell Proliferation ; Gene Deletion ; Gene Expression Regulation, Fungal/genetics ; Genetic Complementation Test ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Histone Acetyltransferases/physiology ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; Histone Deacetylases/physiology ; Histones/metabolism ; Histones/physiology ; Lysine/metabolism ; Models, Biological ; Protein Binding ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Suppression, Genetic
Chemical Substances	Histones ; Saccharomyces cerevisiae Proteins ; Esa1 protein, S cerevisiae (EC 2.3.1.48) ; Histone Acetyltransferases (EC 2.3.1.48) ; RPD3 protein, S cerevisiae (EC 3.5.1.-) ; Histone Deacetylases (EC 3.5.1.98) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2009-07-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.109.103846
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Article ; Audio / Video: Collaboration Between the Essential Esa1 Acetyltransferase and the Rpd3 Deacetylase Is Mediated by H4K12 Histone Acetylation in Saccharomyces cerevisiae

Chang, Christie S / Pillus, Lorraine

Genetics. 2009 Sept., v. 183, no. 1

2009

Keywords	Saccharomyces cerevisiae ; yeasts ; histones ; acetylation ; acyltransferases ; esterases ; enzyme activity ; mutants ; phenotype ; transcription (genetics) ; chromatin ; gene expression
Language	English
Dates of publication	2009-09
Size	p. 149–160.
Document type	Article ; Audio / Video
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
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Article ; Online: Suppression analysis of esa1 mutants in Saccharomyces cerevisiae links NAB3 to transcriptional silencing and nucleolar functions.

Chang, Christie S / Clarke, Astrid / Pillus, Lorraine

G3 (Bethesda, Md.)

2012 Volume 2, Issue 10, Page(s) 1223–1232

Abstract: The acetyltransferase Esa1 is essential in the yeast Saccharomyces cerevisiae and plays a critical role in multiple cellular processes. The most well-defined targets for Esa1 are lysine residues on histones. However, an increasing number of nonhistone ... ...

Abstract	The acetyltransferase Esa1 is essential in the yeast Saccharomyces cerevisiae and plays a critical role in multiple cellular processes. The most well-defined targets for Esa1 are lysine residues on histones. However, an increasing number of nonhistone proteins have recently been identified as substrates of Esa1. In this study, four genes (LYS20, LEU2, VAP1, and NAB3) were identified in a genetic screen as high-copy suppressors of the conditional temperature-sensitive lethality of an esa1 mutant. When expressed from a high-copy plasmid, each of these suppressors rescued the temperature-sensitivity of an esa1 mutant. Only NAB3 overexpression also rescued the rDNA-silencing defects of an esa1 mutant. Strengthening the connections between NAB3 and ESA1, mutants of nab3 displayed several phenotypes similar to those of esa1 mutants, including increased sensitivity to the topoisomerase I inhibitor camptothecin and defects in rDNA silencing and cell-cycle progression. In addition, nuclear localization of Nab3 was altered in the esa1 mutant. Finally, posttranslational acetylation of Nab3 was detected in vivo and found to be influenced by ESA1.
MeSH term(s)	Acetylation ; Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; Gene Dosage ; Gene Expression Regulation, Fungal ; Gene Silencing ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Histones/metabolism ; Mutation ; Nuclear Proteins/genetics ; Phenotype ; Protein Processing, Post-Translational ; Protein Transport ; RNA-Binding Proteins/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Suppression, Genetic ; Transcription, Genetic
Chemical Substances	Histones ; NAB3 protein, S cerevisiae ; Nuclear Proteins ; RNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Esa1 protein, S cerevisiae (EC 2.3.1.48) ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2012-10-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.112.003558
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Article ; Online: The Set3 Complex Antagonizes the MYST Acetyltransferase Esa1 in the DNA Damage Response

Torres-Machorro, Ana Lilia / Clark, Lauren G. / Chang, Christie S. / Pillus, Lorraine

Molecular and Cellular Biology. 2015 Nov. 1, v. 35, no. 21 p.3714-3725

2015

Abstract: Acetylation is a dynamic posttranslational modification that contributes to chromatin-regulated processes, including DNA replication, repair, recombination, and gene expression. Acetylation is controlled by complexes containing opposing lysine and ... ...

Abstract	Acetylation is a dynamic posttranslational modification that contributes to chromatin-regulated processes, including DNA replication, repair, recombination, and gene expression. Acetylation is controlled by complexes containing opposing lysine and histone acetyltransferase (KAT and HAT) and deacetylase (KDAC and HDAC) activities. The essential MYST family Esa1 KAT acetylates core histones and many nonhistone substrates. Phenotypes of esa1 mutants include transcriptional silencing and activation defects, impaired growth at high temperatures, and sensitivity to DNA damage. The KDAC Rpd3 was previously identified as an activity opposing Esa1, as its deletion suppresses growth and silencing defects of esa1 mutants. However, loss of Rpd3 does not suppress esa1 DNA damage sensitivity. In this work, we identified Hos2 as a KDAC counteracting ESA1 in the damage response. Deletion of HOS2 resulted in changes of esa1's transcriptional response upon damage. Further, loss of HOS2 or components of the Set3 complex (Set3C) in which it acts specifically suppressed damage sensitivity and restored esa1 histone H4 acetylation. This rescue was mediated via loss of either Set3C integrity or of its binding to dimethylated histone H3K4. Our results thus add new insight into the interactions of an essential MYST acetyltransferase with diverse deacetylases to respond specifically to environmental and physiological challenges.
Keywords	DNA damage ; DNA replication ; acetylation ; cell biology ; gene expression ; histone acetyltransferase ; histones ; lysine ; post-translational modification ; transcription (genetics)
Language	English
Dates of publication	2015-1101
Size	p. 3714-3725.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00298-15
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Article ; Online: The Set3 Complex Antagonizes the MYST Acetyltransferase Esa1 in the DNA Damage Response.

Torres-Machorro, Ana Lilia / Clark, Lauren G / Chang, Christie S / Pillus, Lorraine

Molecular and cellular biology

2015 Volume 35, Issue 21, Page(s) 3714–3725

Abstract	Acetylation is a dynamic posttranslational modification that contributes to chromatin-regulated processes, including DNA replication, repair, recombination, and gene expression. Acetylation is controlled by complexes containing opposing lysine and histone acetyltransferase (KAT and HAT) and deacetylase (KDAC and HDAC) activities. The essential MYST family Esa1 KAT acetylates core histones and many nonhistone substrates. Phenotypes of esa1 mutants include transcriptional silencing and activation defects, impaired growth at high temperatures, and sensitivity to DNA damage. The KDAC Rpd3 was previously identified as an activity opposing Esa1, as its deletion suppresses growth and silencing defects of esa1 mutants. However, loss of Rpd3 does not suppress esa1 DNA damage sensitivity. In this work, we identified Hos2 as a KDAC counteracting ESA1 in the damage response. Deletion of HOS2 resulted in changes of esa1's transcriptional response upon damage. Further, loss of HOS2 or components of the Set3 complex (Set3C) in which it acts specifically suppressed damage sensitivity and restored esa1 histone H4 acetylation. This rescue was mediated via loss of either Set3C integrity or of its binding to dimethylated histone H3K4. Our results thus add new insight into the interactions of an essential MYST acetyltransferase with diverse deacetylases to respond specifically to environmental and physiological challenges.
MeSH term(s)	Acetylation ; DNA Damage ; Gene Deletion ; Gene Expression Regulation, Fungal ; Histone Acetyltransferases/genetics ; Histone Acetyltransferases/metabolism ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; Histones/genetics ; Histones/metabolism ; Models, Molecular ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Histones ; Saccharomyces cerevisiae Proteins ; Esa1 protein, S cerevisiae (EC 2.3.1.48) ; Histone Acetyltransferases (EC 2.3.1.48) ; HOS2 protein, S cerevisiae (EC 3.5.1.-) ; Set3 protein, S cerevisiae (EC 3.5.1.-) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00298-15
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Article: A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Lee, Young-Suk / Krishnan, Arjun / Oughtred, Rose / Rust, Jennifer / Chang, Christie S / Ryu, Joseph / Kristensen, Vessela N / Dolinski, Kara / Theesfeld, Chandra L / Troyanskaya, Olga G

Cell systems

2019 Volume 8, Issue 2, Page(s) 152–162.e6

Abstract: A key challenge for the diagnosis and treatment of complex human diseases is identifying their molecular basis. Here, we developed a unified computational framework, ... ...

Abstract	A key challenge for the diagnosis and treatment of complex human diseases is identifying their molecular basis. Here, we developed a unified computational framework, URSA
MeSH term(s)	Gene Expression Profiling/methods ; Genomics/methods ; Humans ; Machine Learning/standards ; Transcriptome/genetics
Language	English
Publishing date	2019-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2018.12.010
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Article ; Online: The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.

Oughtred, Rose / Rust, Jennifer / Chang, Christie / Breitkreutz, Bobby-Joe / Stark, Chris / Willems, Andrew / Boucher, Lorrie / Leung, Genie / Kolas, Nadine / Zhang, Frederick / Dolma, Sonam / Coulombe-Huntington, Jasmin / Chatr-Aryamontri, Andrew / Dolinski, Kara / Tyers, Mike

Protein science : a publication of the Protein Society

2020 Volume 30, Issue 1, Page(s) 187–200

Abstract: The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ...

Abstract	The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases.
MeSH term(s)	Animals ; COVID-19/genetics ; COVID-19/virology ; Databases, Factual ; Humans ; Mice ; Protein Interaction Mapping ; Proteins/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; User-Computer Interface
Chemical Substances	Proteins
Keywords	covid19
Language	English
Publishing date	2020-11-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3978
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Article: Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery.

Chen, Steven T / Park, Matthew D / Del Valle, Diane Marie / Buckup, Mark / Tabachnikova, Alexandra / Simons, Nicole W / Mouskas, Konstantinos / Lee, Brian / Geanon, Daniel / D'Souza, Darwin / Dawson, Travis / Marvin, Robert / Nie, Kai / Thompson, Ryan C / Zhao, Zhen / LeBerichel, Jessica / Chang, Christie / Jamal, Hajra / Chaddha, Udit /

Mathews, Kusum / Acquah, Samuel / Brown, Stacey-Ann / Reiss, Michelle / Harkin, Timothy / Feldmann, Marc / Powell, Charles A / Hook, Jaime L / Kim-Schulze, Seunghee / Rahman, Adeeb H / Brown, Brian D / Beckmann, Noam D / Gnjatic, Sacha / Kenigsberg, Ephraim / Charney, Alexander W / Merad, Miriam

bioRxiv : the preprint server for biology

2022

Abstract: Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative ... ...

Abstract	Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoMΦ). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.
Language	English
Publishing date	2022-01-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.01.11.475918
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Article ; Online: A conserved dendritic-cell regulatory program limits antitumour immunity.

Nature

2020 Volume 580, Issue 7802, Page(s) 257–262

Abstract: Checkpoint blockade therapies have improved cancer treatment, but such immunotherapy regimens fail in a large subset of patients. Conventional type 1 dendritic cells (DC1s) control the response to checkpoint blockade in preclinical models and are ... ...

Abstract	Checkpoint blockade therapies have improved cancer treatment, but such immunotherapy regimens fail in a large subset of patients. Conventional type 1 dendritic cells (DC1s) control the response to checkpoint blockade in preclinical models and are associated with better overall survival in patients with cancer, reflecting the specialized ability of these cells to prime the responses of CD8
MeSH term(s)	Animals ; Antigens, Neoplasm/immunology ; B7-H1 Antigen/immunology ; B7-H1 Antigen/metabolism ; CD8-Positive T-Lymphocytes/immunology ; Carcinoma, Non-Small-Cell Lung/immunology ; Carcinoma, Non-Small-Cell Lung/pathology ; Carcinoma, Non-Small-Cell Lung/therapy ; Dendritic Cells/drug effects ; Dendritic Cells/immunology ; Dendritic Cells/metabolism ; Dendritic Cells/pathology ; Humans ; Immunotherapy ; Interferon-gamma/immunology ; Interleukin-12/immunology ; Interleukin-4/antagonists & inhibitors ; Interleukin-4/immunology ; Interleukin-4/metabolism ; Lung Neoplasms/immunology ; Lung Neoplasms/pathology ; Lung Neoplasms/therapy ; Male ; Mice ; Tumor Burden/drug effects ; Tumor Burden/immunology
Chemical Substances	Antigens, Neoplasm ; B7-H1 Antigen ; CD274 protein, human ; Cd274 protein, mouse ; Interleukin-12 (187348-17-0) ; Interleukin-4 (207137-56-2) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2020-03-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2134-y
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