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Article ; Online: Elucidating the structure and function of the nucleus-The NIH Common Fund 4D Nucleome program.

Roy, Ananda L / Conroy, Richard S / Taylor, Veronica G / Mietz, Judy / Fingerman, Ian M / Pazin, Michael J / Smith, Phillip / Hutter, Carolyn M / Singer, Dinah S / Wilder, Elizabeth L

Molecular cell

2023 Volume 83, Issue 3, Page(s) 335–342

Abstract: Genomic architecture appears to play crucial roles in health and a variety of diseases. How nuclear structures reorganize over different timescales is elusive, partly because the tools needed to probe and perturb them are not as advanced as needed by the ...

Abstract	Genomic architecture appears to play crucial roles in health and a variety of diseases. How nuclear structures reorganize over different timescales is elusive, partly because the tools needed to probe and perturb them are not as advanced as needed by the field. To fill this gap, the National Institutes of Health Common Fund started a program in 2015, called the 4D Nucleome (4DN), with the goal of developing and ultimately applying technologies to interrogate the structure and function of nuclear organization in space and time.
MeSH term(s)	United States ; Cell Nucleus/genetics ; Genome ; Genomics
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Intramural
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.12.025
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Article ; Online: Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells.

Goyal, Yogesh / Busch, Gianna T / Pillai, Maalavika / Li, Jingxin / Boe, Ryan H / Grody, Emanuelle I / Chelvanambi, Manoj / Dardani, Ian P / Emert, Benjamin / Bodkin, Nicholas / Braun, Jonas / Fingerman, Dylan / Kaur, Amanpreet / Jain, Naveen / Ravindran, Pavithran T / Mellis, Ian A / Kiani, Karun / Alicea, Gretchen M / Fane, Mitchell E /

Ahmed, Syeda Subia / Li, Haiyin / Chen, Yeqing / Chai, Cedric / Kaster, Jessica / Witt, Russell G / Lazcano, Rossana / Ingram, Davis R / Johnson, Sarah B / Wani, Khalida / Dunagin, Margaret C / Lazar, Alexander J / Weeraratna, Ashani T / Wargo, Jennifer A / Herlyn, Meenhard / Raj, Arjun

Nature

2023 Volume 620, Issue 7974, Page(s) 651–659

Abstract: Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those ... ...

Abstract	Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells
MeSH term(s)	Humans ; Clone Cells/drug effects ; Clone Cells/metabolism ; Clone Cells/pathology ; DNA Barcoding, Taxonomic ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology ; RNA-Seq ; Single-Cell Gene Expression Analysis ; Tumor Cells, Cultured ; Antineoplastic Agents/pharmacology
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2023-07-19
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06342-8
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Article ; Online: Biological functions of DEAD/DEAH-box RNA helicases in health and disease.

Andrisani, Ourania / Liu, Qian / Kehn, Patricia / Leitner, Wolfgang W / Moon, Kyung / Vazquez-Maldonado, Nancy / Fingerman, Ian / Gale, Michael

Nature immunology

2022 Volume 23, Issue 3, Page(s) 354–357

MeSH term(s)	DEAD-box RNA Helicases/genetics ; RNA ; RNA Helicases/genetics
Chemical Substances	RNA (63231-63-0) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/s41590-022-01149-7
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Article ; Online: Controlling histone methylation via trans-histone pathways.

Fingerman, Ian M / Du, Hai-Ning / Briggs, Scott D

Epigenetics

2008 Volume 3, Issue 5, Page(s) 237–242

MeSH term(s)	Chromatin/metabolism ; Histones/metabolism ; Lysine/metabolism ; Methylation ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/metabolism ; Ubiquitination
Chemical Substances	Chromatin ; Histones ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2008-09-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ISSN	1559-2308
ISSN (online)	1559-2308
DOI	10.4161/epi.3.5.6869
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Article: p53-mediated transcriptional activation: from test tube to cell.

Fingerman, Ian M / Briggs, Scott D

Cell

2004 Volume 117, Issue 6, Page(s) 690–691

Abstract: Posttranslational modifications of histones have been strongly correlated with transcriptional regulation. In this issue of Cell, comprehensively examined the nature of arginine methyltransferases and histone modifications in p53-mediated transcription. ...

Abstract	Posttranslational modifications of histones have been strongly correlated with transcriptional regulation. In this issue of Cell, comprehensively examined the nature of arginine methyltransferases and histone modifications in p53-mediated transcription.
MeSH term(s)	Animals ; Genes, Regulator/genetics ; Histones/genetics ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational/genetics ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; Transcriptional Activation/genetics ; Transcriptional Activation/physiology ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism
Chemical Substances	Histones ; Tumor Suppressor Protein p53 ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; coactivator-associated arginine methyltransferase 1 (EC 2.1.1.319)
Language	English
Publishing date	2004-06-11
Publishing country	United States
Document type	Journal Article ; Review ; Comment
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2004.05.021
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Article: In vitro histone methyltransferase assay.

Fingerman, Ian M / Du, Hai-Ning / Briggs, Scott D

CSH protocols

2008 Volume 2008, Page(s) pdb.prot4939

Abstract: INTRODUCTIONHistone methyltransferases catalyze the addition of one or more methyl groups to a specific lysine or arginine residue within histones. Currently, there is a great deal of interest in histone methyltransferases, because mutations and ... ...

Abstract	INTRODUCTIONHistone methyltransferases catalyze the addition of one or more methyl groups to a specific lysine or arginine residue within histones. Currently, there is a great deal of interest in histone methyltransferases, because mutations and misregulation of the genes encoding these proteins have been linked to various cancers and other diseases. Many genes encoding putative histone methyltransferases have been identified in eukaryotes, but the proteins they encode have not been functionally characterized. This protocol describes an in vitro assay for histone methyltransferase activity that uses bacterial cell extracts in which expression of a methyltransferase of interest is induced. In many cases, purification of the enzyme is unnecessary, making this experiment ideal for pilot studies. Bacterial cell extract containing the methyltransferase of interest is incubated with S-adenosyl-L-[methyl-(3)H]-methionine and various histone substrates, many of which are commercially available. Incorporation of the methyl-(3)H can be measured easily by scintillation counting. The labeled substrate is visualized by SDS-polyacrylamide gel electrophoresis (PAGE) followed by fluorography. This allows the substrate specificity and activity of a histone methyltransferase of interest to be readily characterized.
Language	English
Publishing date	2008-02-01
Publishing country	United States
Document type	Journal Article
DOI	10.1101/pdb.prot4939
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Article: Histone H3 K36 methylation is mediated by a trans-histone methylation pathway involving an interaction between Set2 and histone H4.

Du, Hai-Ning / Fingerman, Ian M / Briggs, Scott D

Genes & development

2008 Volume 22, Issue 20, Page(s) 2786–2798

Abstract: Set2-mediated H3 K36 methylation is an important histone modification on chromatin during transcription elongation. Although Set2 associates with the phosphorylated C-terminal domain (CTD) of RNA polymerase II (RNAPII), the mechanism of Set2 binding to ... ...

Abstract	Set2-mediated H3 K36 methylation is an important histone modification on chromatin during transcription elongation. Although Set2 associates with the phosphorylated C-terminal domain (CTD) of RNA polymerase II (RNAPII), the mechanism of Set2 binding to chromatin and subsequent exertion of its methyltransferase activity is relatively uncharacterized. We identified a critical lysine residue in histone H4 that is needed for interaction with Set2 and proper H3 K36 di- and trimethylation. We also determined that the N terminus of Set2 contains a histone H4 interaction motif that allows Set2 to bind histone H4 and nucleosomes. A Set2 mutant lacking the histone H4 interaction motif is able to bind to the phosphorylated CTD of RNAPII and associate with gene-specific loci but is defective for H3 K36 di- and trimethylation. In addition, this Set2 mutant shows increased H4 acetylation and resistance to 6-Azauracil. Overall, our study defines a new interaction between Set2 and histone H4 that mediates trans-histone regulation of H3 K36 methylation, which is needed for the preventative maintenance and integrity of the genome.
MeSH term(s)	Antimetabolites/pharmacology ; Blotting, Western ; Chromatin/metabolism ; Chromatin Immunoprecipitation ; Gene Expression Regulation, Fungal ; Histones/genetics ; Histones/metabolism ; Immunoblotting ; Immunoprecipitation ; Lysine/chemistry ; Lysine/genetics ; Lysine/metabolism ; Methylation ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Mutation/genetics ; Nucleosomes/metabolism ; Phosphorylation ; Protein Kinases/metabolism ; Protein Processing, Post-Translational ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Uracil/analogs & derivatives ; Uracil/pharmacology
Chemical Substances	Antimetabolites ; CTDK-I protein complex, S cerevisiae ; Chromatin ; Histones ; Nucleosomes ; Saccharomyces cerevisiae Proteins ; Uracil (56HH86ZVCT) ; Methyltransferases (EC 2.1.1.-) ; Set2 protein, S cerevisiae (EC 2.1.1.-) ; Protein Kinases (EC 2.7.-) ; RNA Polymerase II (EC 2.7.7.-) ; azauracil (I14TWN70LR) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2008-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.1700008
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Article: A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway.

Fingerman, Ian M / Li, Hui-Chun / Briggs, Scott D

Genes & development

2007 Volume 21, Issue 16, Page(s) 2018–2029

Abstract: Saccharomyces cerevisiae cells lacking Dot1 exhibit a complete loss of H3K79 methylation and defects in heterochromatin-mediated silencing. To further understand the mechanism of Dot1-mediated methylation, the substrate requirement of Dot1 was determined. ...

Abstract	Saccharomyces cerevisiae cells lacking Dot1 exhibit a complete loss of H3K79 methylation and defects in heterochromatin-mediated silencing. To further understand the mechanism of Dot1-mediated methylation, the substrate requirement of Dot1 was determined. This analysis found that Dot1 requires histone H4 for in vitro methyltransferase activity and the histone H4 tail for Dot1-mediated methylation in yeast. Mutational analyses demonstrated that the basic patch residues (R(17)H(18)R(19)) of the histone H4 N-terminal tail are required for Dot1 methyltransferase activity in vitro as well as Dot1-mediated histone H3K79 methylation in vivo. In vitro binding assays show that Dot1 can interact with the H4 N-terminal tail via the basic patch residues. Furthermore, an acidic patch at the C terminus of Dot1 is required for histone H4 tail binding in vitro, histone H3K79 di- and trimethylation in vivo, and proper telomere silencing. Our data suggest a novel trans-histone regulatory pathway whereby charged residues of one histone are required for the modification of another histone. These findings not only provide key insights into the mechanism of Dot1 histone methylation but also illustrate how chromatin-modifying enzymes engage their nucleosomal substrates in vivo.
MeSH term(s)	Amino Acids, Basic/chemistry ; Animals ; Binding Sites/genetics ; Cell Line ; Chickens ; Electrochemistry ; Gene Silencing ; Histone-Lysine N-Methyltransferase ; Histones/chemistry ; Histones/genetics ; Histones/metabolism ; Humans ; In Vitro Techniques ; Methylation ; Methyltransferases/metabolism ; Models, Biological ; Nuclear Proteins/metabolism ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/metabolism ; Substrate Specificity ; Telomere/genetics ; Telomere/metabolism
Chemical Substances	Amino Acids, Basic ; Histones ; Nuclear Proteins ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; Silent Information Regulator Proteins, Saccharomyces cerevisiae ; Methyltransferases (EC 2.1.1.-) ; Dot1 protein, S cerevisiae (EC 2.1.1.43) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43)
Language	English
Publishing date	2007-08-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.1560607
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Article ; Online: NCBI Epigenomics: what's new for 2013.

Fingerman, Ian M / Zhang, Xuan / Ratzat, Walter / Husain, Nora / Cohen, Robert F / Schuler, Gregory D

Nucleic acids research

2012 Volume 41, Issue Database issue, Page(s) D221–5

Abstract: The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this ... ...

Abstract	The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.
MeSH term(s)	Animals ; Databases, Genetic ; Epigenomics ; Humans ; Internet ; Mice
Language	English
Publishing date	2012-11-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gks1171
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Article ; Online: Charge-based interaction conserved within histone H3 lysine 4 (H3K4) methyltransferase complexes is needed for protein stability, histone methylation, and gene expression.

Mersman, Douglas P / Du, Hai-Ning / Fingerman, Ian M / South, Paul F / Briggs, Scott D

The Journal of biological chemistry

2011 Volume 287, Issue 4, Page(s) 2652–2665

Abstract: Histone H3 lysine 4 (H3K4) methyltransferases are conserved from yeast to humans, assemble in multisubunit complexes, and are needed to regulate gene expression. The yeast H3K4 methyltransferase complex, Set1 complex or complex of proteins associated ... ...

Abstract	Histone H3 lysine 4 (H3K4) methyltransferases are conserved from yeast to humans, assemble in multisubunit complexes, and are needed to regulate gene expression. The yeast H3K4 methyltransferase complex, Set1 complex or complex of proteins associated with Set1 (COMPASS), consists of Set1 and conserved Set1-associated proteins: Swd1, Swd2, Swd3, Spp1, Bre2, Sdc1, and Shg1. The removal of the WD40 domain-containing subunits Swd1 and Swd3 leads to a loss of Set1 protein and consequently a complete loss of H3K4 methylation. However, until now, how these WD40 domain-containing proteins interact with Set1 and contribute to the stability of Set1 and H3K4 methylation has not been determined. In this study, we identified small basic and acidic patches that mediate protein interactions between the C terminus of Swd1 and the nSET domain of Set1. Absence of either the basic or acidic patches of Set1 and Swd1, respectively, disrupts the interaction between Set1 and Swd1, diminishes Set1 protein levels, and abolishes H3K4 methylation. Moreover, these basic and acidic patches are also important for cell growth, telomere silencing, and gene expression. We also show that the basic and acidic patches of Set1 and Swd1 are conserved in their human counterparts SET1A/B and RBBP5, respectively, and are needed for the protein interaction between SET1A and RBBP5. Therefore, this charge-based interaction is likely important for maintaining the protein stability of the human SET1A/B methyltransferase complexes so that proper H3K4 methylation, cell growth, and gene expression can also occur in mammals.
MeSH term(s)	DNA-Binding Proteins ; Gene Expression Regulation/physiology ; Histone-Lysine N-Methyltransferase/genetics ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/genetics ; Histones/metabolism ; Humans ; Methylation ; Multienzyme Complexes/genetics ; Multienzyme Complexes/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Stability ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	DNA-Binding Proteins ; Histones ; Multienzyme Complexes ; Nuclear Proteins ; RBBP5 protein, human ; Saccharomyces cerevisiae Proteins ; Swd1 protein, S cerevisiae ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; Setd1A protein, human (EC 2.1.1.43)
Language	English
Publishing date	2011-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M111.280867
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