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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

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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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
Database	NAL-Catalogue (AGRICOLA)

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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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
Database	NAL-Catalogue (AGRICOLA)

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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.

Islamaj Dogan, Rezarta / Kim, Sun / Chatr-Aryamontri, Andrew / Chang, Christie S / Oughtred, Rose / Rust, Jennifer / Wilbur, W John / Comeau, Donald C / Dolinski, Kara / Tyers, Mike

Database : the journal of biological databases and curation

2017 Volume 2017

Abstract: A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. ... ...

Abstract	A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein-protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future uses of the BioC-BioGRID corpus are detailed in this report.Database URL: http://bioc.sourceforge.net/BioC-BioGRID.html.
MeSH term(s)	Data Curation/methods ; Data Mining/methods ; Databases, Genetic ; Proteins/genetics ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2017-01-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baw147
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BioGRID: A Resource for Studying Biological Interactions in Yeast.

Cold Spring Harbor protocols

2016 Volume 2016, Issue 1, Page(s) pdb.top080754

Abstract: The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental ... ...

Abstract	The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species--including yeast, nematode, fly, zebrafish, mouse, and human--with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology. BioGRID has achieved comprehensive curation coverage of the entire literature for these two major yeast models, which is actively maintained through monthly curation updates. As of September 2015, BioGRID houses approximately 335,400 biological interactions for budding yeast and approximately 67,800 interactions for fission yeast. BioGRID also supports an integrated posttranslational modification (PTM) viewer that incorporates more than 20,100 yeast phosphorylation sites curated through its sister database, the PhosphoGRID.
MeSH term(s)	Animals ; Databases, Genetic/statistics & numerical data ; Gene Regulatory Networks ; Humans ; Protein Interaction Mapping ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins ; Yeasts/genetics ; Yeasts/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2016-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1559-6095
ISSN (online)	1559-6095
DOI	10.1101/pdb.top080754
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.

Cold Spring Harbor protocols

2016 Volume 2016, Issue 1, Page(s) pdb.prot088880

Abstract: The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida albicans SC5314, as well as for several other ... ...

Abstract	The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida albicans SC5314, as well as for several other model organisms and humans. This protocol describes how to use the BioGRID website to query genetic or protein interactions for any gene of interest, how to visualize the associated interactions using an embedded interactive network viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set.
MeSH term(s)	Animals ; Databases, Genetic ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Regulatory Networks ; Internet ; Protein Interaction Mapping ; Yeasts/metabolism
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2016-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1559-6095
ISSN (online)	1559-6095
DOI	10.1101/pdb.prot088880
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

Kim, Sun / Islamaj Doğan, Rezarta / Chatr-Aryamontri, Andrew / Chang, Christie S / Oughtred, Rose / Rust, Jennifer / Batista-Navarro, Riza / Carter, Jacob / Ananiadou, Sophia / Matos, Sérgio / Santos, André / Campos, David / Oliveira, José Luís / Singh, Onkar / Jonnagaddala, Jitendra / Dai, Hong-Jie / Su, Emily Chia-Yu / Chang, Yung-Chun / Su, Yu-Chen /

Chu, Chun-Han / Chen, Chien Chin / Hsu, Wen-Lian / Peng, Yifan / Arighi, Cecilia / Wu, Cathy H / Vijay-Shanker, K / Aydın, Ferhat / Hüsünbeyi, Zehra Melce / Özgür, Arzucan / Shin, Soo-Yong / Kwon, Dongseop / Dolinski, Kara / Tyers, Mike / Wilbur, W John / Comeau, Donald C

Database : the journal of biological databases and curation

2016 Volume 2016

Abstract: BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to ...

Abstract	BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein-protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators' feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/.
MeSH term(s)	Data Curation/methods ; Data Mining/methods ; Electronic Data Processing/methods ; Information Dissemination/methods
Language	English
Publishing date	2016-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baw121
Database	MEDical Literature Analysis and Retrieval System OnLINE

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