A needed nomenclature for nucleosomes

Michael-Christopher Keogh¹, Genevieve Almouzni², Andrew J Andrews³, Karim-Jean Armache⁴, Cheryl H Arrowsmith⁵, Sung Hee Baek⁶, Mark T Bedford⁷, Emily Bernstein⁸, Jacques Côté⁹, Yael David¹⁰, John M Denu¹¹, Beat Fierz¹², Benjamin A Garcia¹³, Karen C Glass¹⁴, Or Gozani¹⁵, Kristian Helin¹⁶, Steven Henikoff¹⁷, Ole N Jensen¹⁸, Steven Z Josefowicz¹⁹, Neil L Kelleher²⁰, Tatiana G Kutateladze²¹, Herbert H Lindner²², Chao Lu²³, Karolin Luger²⁴, Parag Mallick²⁵, Catherine A Musselman²⁶, Tom W Muir²⁷, Ljiljana Paša-Tolić²⁸, Robert Schneider²⁹, Xiaobing Shi³⁰, Yang Shi³¹, Simone Sidoli³², Lloyd M Smith³³, Jessica K Tyler³⁴, Cynthia Wolberger³⁵, Jerry L Workman³⁶, Brian D Strahl³⁷, Nicolas L Young³⁸

Affiliations

¹ EpiCypher Inc, Durham, NC 27709, USA.
² Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France.
³ University of North Carolina at Wilmington, Wilmington, NC 28403, USA.
⁴ Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
⁵ Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
⁶ Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
⁷ Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Centre, Houston, TX 77230, USA.
⁸ Department of Dermatology, Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁹ St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Québec G1J 0J9, Canada.
¹⁰ Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
¹¹ Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹² SB ISIC LCBM, École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland.
¹³ Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
¹⁴ Department of Pharmacology and University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.
¹⁵ Department of Biology, Stanford University, Stanford, CA 94305, USA.
¹⁶ Institute of Cancer Research, London SW3 6JB, UK.
¹⁷ Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
¹⁸ Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.
¹⁹ Immunology and Microbial Pathogenesis Program and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
²⁰ Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA.
²¹ Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
²² Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
²³ Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
²⁴ Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.
²⁵ Canary Center for Cancer Early Detection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
²⁶ Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
²⁷ Department of Chemistry, Princeton University, Princeton, Princeton, NJ 08544, USA.
²⁸ Pacific Northwest National Laboratory, Richland, WA 99352, USA.
²⁹ Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
³⁰ Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
³¹ Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.
³² Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
³³ Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
³⁴ Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
³⁵ Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
³⁶ Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
³⁷ Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
³⁸ Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: nicolas.young@bcm.edu.

PMID: 41043390
DOI: 10.1016/j.molcel.2025.08.029

Review

A needed nomenclature for nucleosomes

Michael-Christopher Keogh et al. Mol Cell. 2025.

. 2025 Oct 2;85(19):3554-3561.

doi: 10.1016/j.molcel.2025.08.029.

Authors

Affiliations

¹ EpiCypher Inc, Durham, NC 27709, USA.
² Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France.
³ University of North Carolina at Wilmington, Wilmington, NC 28403, USA.
⁴ Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
⁵ Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
⁶ Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
⁷ Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Centre, Houston, TX 77230, USA.
⁸ Department of Dermatology, Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁹ St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Québec G1J 0J9, Canada.
¹⁰ Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
¹¹ Wisconsin Institute of Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹² SB ISIC LCBM, École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland.
¹³ Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
¹⁴ Department of Pharmacology and University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.
¹⁵ Department of Biology, Stanford University, Stanford, CA 94305, USA.
¹⁶ Institute of Cancer Research, London SW3 6JB, UK.
¹⁷ Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
¹⁸ Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark.
¹⁹ Immunology and Microbial Pathogenesis Program and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
²⁰ Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA.
²¹ Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
²² Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
²³ Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
²⁴ Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.
²⁵ Canary Center for Cancer Early Detection, School of Medicine, Stanford University, Stanford, CA 94305, USA.
²⁶ Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
²⁷ Department of Chemistry, Princeton University, Princeton, Princeton, NJ 08544, USA.
²⁸ Pacific Northwest National Laboratory, Richland, WA 99352, USA.
²⁹ Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
³⁰ Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
³¹ Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.
³² Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
³³ Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
³⁴ Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
³⁵ Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
³⁶ Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
³⁷ Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
³⁸ Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: nicolas.young@bcm.edu.

PMID: 41043390
DOI: 10.1016/j.molcel.2025.08.029

Abstract

Histone post-translational modifications (PTMs) are crucial to eukaryotic genome regulation, with a range of reported functions and mechanisms of action. Though often studied individually, it has long been recognized that the modifications function by combinatorial synergy or antagonism. Interplay may involve PTMs on the same histone, within the same nucleosome (containing a histone octamer), or between nucleosomes in higher-order chromatin. Given this, the field must distinguish ever greater complexity, and the context in which it is studied, with brevity and precision. The proteoform was introduced to define individual forms of a protein by sequence and PTMs, followed by the nucleoform to describe the particular gathering of histones within an individual nucleosome. There is now a need to define specific forms of these entities in prose while providing space for experimental nuance. To this end, we introduce a nomenclature that can express discrete PTMs, proteoforms, nucleoforms, or situations where defined PTMs exist in an uncertain context. Though specifically designed for the chromatin field, adaptions of the framework could be used to describe-and thus dissect-how proteoforms are configured in functionally distinct complexes across biology.

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Conflict of interest statement

Declaration of interests M.-C.K., M.T.B., O.G., and B.D.S. are board members of EpiCypher Inc., a commercial developer of reagents and platforms for chromatin studies.

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A needed nomenclature for nucleosomes

Affiliations

A needed nomenclature for nucleosomes

Authors

Affiliations

Abstract

Conflict of interest statement

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LinkOut - more resources

Full Text Sources

Miscellaneous