Title: A truncated proteoform of H2AX supersedes the DNA damage response & the epigenetics of aging
Abstract: Histones are commonly hypermodified with multiple posttranslational modifications (PTMs) co-occurring on single molecules. Thus, histone reading, writing, erasing, and clipping occur within the context of preexisting hypermodified substrates. Many mechanisms of chromatin regulation rely on multiple modifications functioning in concert. However, multiple PTMs also occur in trans, on separate copies of the same histone family within the same nucleosome. Additionally, the same PTM on different variants may also carry distinct meaning. Further complicating our understanding, each method presents different experimental ambiguities in defining the precise configuration of PTMs, proteoforms (PTM combinations), and nucleoforms (nucleosomes with defined proteoforms). We recently introduced the Needed Nomenclature for Nucleosomes: N3 to enable effective communication that clearly distinguishes various combinatorial configurations of histone posttranslational modifications (PTMs). This allows for clearly defined specificity, while also describing experimental ambiguity. This enables more effective description and discussion of the language of covalent histone modification. We present examples from our recent work.
We have established quantitative differences of histone proteoforms in multiple tissues and cell lines basally, with age, and in response to multiple stresses. Tissues exhibit dramatically different histone proteoforms from cultured cells. In all mouse tissues, histone variant H3.3 increases with age from around 10% to 95% of total H3. Approximately 90% of H3.3 proteoforms contain two or more PTMs. Specific combinations of H3.3 modification also change with age. AAV expression of transcription factor EB (TFEB) in the mouse cortex results in a male-specific 30 percent lifespan extension. The H3.3 specific single molecule combination of K27me2 and K36me2, which increases with normal aging by 6 percentage points from 2 months to 25 months, is rescued in this age extension model. Further analysis has revealed a Y-chromosome-located histone demethylase gene KDM6C as a TFEB target gene and its enhanced expression is likely responsible for clearance of this conflicted bivalent epigenetic mark.
Phosphorylation of the histone variant H2AX at serine 139 (γH2AX) by ATM/ATR kinases is a central marker of the DNA damage response (DDR), widely used to detect DNA double-strand breaks (DSBs). However, the molecular basis for tissue- and context-specific variation in γH2AX signaling remains poorly defined. Here we identify a post-translational truncation of H2AX, mediated by lysine demethylase 4A (KDM4A), which removes two C-terminal amino acids critical for ATM/ATR-dependent phosphorylation. This truncation renders H2AX refractory to γH2AX formation, effectively bypassing canonical DDR signaling. We find that truncated H2AX accumulates in select cell lines, primary cells, patient-derived tumors, and normal tissues. Genetic knockdown or pharmacologic inhibition of KDM4A reduces H2AX truncation, restores γH2AX induction, and enhances DNA repair capacity. Conversely, KDM4A overexpression—frequently observed in malignancies—promotes H2AX truncation, impairs γH2AX signaling, and exacerbates DNA damage accumulation. These findings uncover a previously unrecognized regulatory axis in genome surveillance, implicating H2AX truncation as a mechanism of checkpoint evasion and repair deficiency. Our results provide mechanistic insight into the link between KDM4A activity and genome instability and suggest new opportunities for prognostic stratification and therapeutic intervention in cancer.
Bio:
University of California, Berkeley B.S. 05/1997 Chemistry
University of California, Davis Ph.D. 03/2007 Chemistry
Princeton University Postdoctoral 04/2012 Molecular Biology
A. Personal Statement
I study mechanisms of chromatin and genome biology with quantitative top down proteomics. The methods I have pioneered discriminate single protein molecules as they exist physiologically. Where prevailing methods measure an ensemble average of protein attributes, I measure the single-molecule combinations of these attributes. Where prevailing methods quantify several ensemble attributes on a relative scale, I quantitate how these attributes combine as single molecule instances on an absolute scale and with exceptional precision. With these approaches we study chromatin mechanisms with access to 1) the quantitative abundance of histone PTMs on an absolute and relative scale; 2) the abundance and function of sequence variants; 3) single molecule combinations of PTMs that coexist on single protein molecules, on specific variants; 4) the specificity of histone modifying enzymes to substrate pre-existing PTMs and between histone variants; 5) how histone variants and PTMs co-exist at the level of single nucleosomes. Our primary lines of inquiry using these established technological innovations are primarily within neurobiology and aging in mouse models. We observe changes to histone proteoforms along multiple axes, such as aging, development, and spatially within the mouse brain. We then use genetic or pharmacological manipulation to test hypotheses that establish functional links or detailed mechanisms. The long-term goal of my research endeavor is to develop a more rigorous and complete understanding of transcription regulation that is informed by quantitative proteoform-level insights. Thus, I possess a unique knowledge, perspective, and expertise in chromatin biology and quantitative top down proteomics that enables this grant.
Ongoing and recently completed projects that I would like to highlight include:
R44AG091990
Co-investigator
09/20/2025 – 09/19/2027
Development Of Novel Epigenetic Biomarkers And Detection Reagents For Aging
1 P01 AG066606-01
PI: Zheng, Hui
Roles: Co-Project Lead, Project 1 & Core Leader, Core B
6/01/2021-3/31/2026
Lysosomal Metabolism and Signaling in Aging and Alzheimer’s Disease
1R01GM139295-01
Young (PI)
9/1/2020-6/30/2026
Neutron encoded activity-based probes
1R01NS136375
West (PI)
Role: Co-investigator
6/1/2024 – 4/30/2029
Mechanisms of chromatin dysregulation in neurodevelopmental disorders
1R01CA276663-01
Davis (PI) Role: co-investigator
9/1/2022 – 8/31/2027
Developmental control of chromatin states in cancer
University of North Carolina, Creativity Hubs Pilot Award
Brian Strahl (PI), Role: coinvestigator
Co-investigator
11/11/2020 – 5/10/2024
The Chemical Epigenomics Hub, Creativity Hubs Pilot Award
American Society for Mass Spectrometry Research Award,
Young (PI)
7/1/2019 – present
Isotopologue Encoded Activity-Based Probes for Cellular Pharmacological Profiling
Citations:
1. Young NL, Dere R. Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans. 2021 Jan 25:BST20191219. PMID: 33492339.
2. Kanishk Jain Matthew R Marunde Jonathan M Burg Susan L Gloor Faith M Joseph Karl F Poncha Zachary B Gillespie Keli L Rodriguez Irina K Popova Nathan W Hall Anup Vaidya Sarah A Howard Hailey F Taylor Laylo Mukhsinova Ugochi C Onuoha Emily F Patteson Spencer W Cooke Bethany C Taylor Ellen N Weinzapfel Marcus A Cheek Matthew J Meiners Geoffrey C Fox Kevin EW Namitz Martis W Cowles Krzysztof Krajewski Zu-Wen Sun Michael S Cosgrove Nicolas L Young Michael-C Keogh Brian D Strahl (2023) An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability eLife 12:e82596.
3. Holt MV, Wang T, Young NL “High-Throughput Quantitative Top-Down Proteomics: Histone H4.”, J Am Soc Mass Spectrom. 2019 Dec;30(12):2548-2560. PMID: 31741267
B. Positions, Scientific Appointments, and Honors
Positions and Scientific Appointments
2021-Present Associate Professor, Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX
2021-Present Associate Professor (Secondary Appointment), Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
2021-Present Associate Professor, (Secondary Appointment), Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX
2020-Present Member, Dan L. Duncan Comprehensive Cancer Center
2020 Ad Hoc Reviewer, NIH Drug Discovery and Molecular Pharmacology Study Section (DMP)
2016-2021 Assistant Professor, Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX
2016-2021 Assistant Professor (Secondary Appointment), Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
2012 – 2015 Director of Biological Applications, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL
2008 – 2012 NIH Postdoctoral Fellow (National Cancer Institute), Molecular Biology Department, Princeton University, Princeton, NJ
2002 – 2007 Graduate Student, University of California, Davis, CA
2002 – 2008 Staff Scientist, Biosecurity and Nanoscience Laboratory, Lawrence Livermore National Laboratory, Livermore, CA
1999 – 2002 Mass Spectrometrist, Bay Bioanalytical Laboratory, Hercules, CA
Honors
2025 Guest Editor, Mass Spectrometry Reviews Special Issue: “Top Down Proteomics”
2020 Robert J. Cotter New Investigator Award, US Human Proteome Organization
2019-2020 Guest Editor, Methods [Elsevier], Special Issue: “Quantitative, Innovative, and High Throughput Methods for the Analysis of Chromatin”
2019 Research Award, American Society for Mass Spectrometry
2018 Organizer, 34th Asilomar Conference on Mass Spectrometry “Quantitative Analysis of Posttranslational Modifications by Mass Spectrometry”
2018-2019 Coordinator, ASMS Interest Group on Top-Down Proteomics
2018-2019 Organizer/Session Chair, Top Down Proteomics Workshop, ASMS
2018-2019 Organizer, Top Down Proteomics Interest Group, ASMS
2013 Founding Organizer/Session Chair, Top Down Proteomics Workshop
2012-2014 Leader, Pilot Project #1, The Consortium for Top Down Proteomics
2010-2012 Postdoctoral Fellowship, National Institutes of Health (NRSA F32 1F32CA139893)
2009-2010 Postdoctoral Training Grant, National Institutes of Health (T32 5T3CA09528)
2004-2008 Q Security Clearance, US Department of Energy
2002 Chair, Bay Area Mass Spectrometry Society
2002-2006 Graduate Scholarship, Department of Energy Advanced Study Program Scholar
2001 Program Chair & Chair Elect, Bay Area Mass Spectrometry Society
1988 Young Scholar, National Science Foundation”
Faculty Host: Lloyd Smith