Whetstine Lab

Research topics include: histone demethylase; chromatin; C. elegans; transcription; epigenetics; JMJC; HDAC


Johnathan R. Whetstine, PhD
Associate Professor of Medicine
Harvard Medical School

Research Summary

The Whetstine laboratory is interested in understanding how the chromatin microenvironment regulates gene expression while maintaining a stable genome. Our ultimate goal is to harness this mechanistic understanding to identify novel therapeutic opportunities and to block chemotherapeutic resistance.

We integrate biochemistry, genetics, genomics and computation to elucidate chromatin modulators involved in these processes. We have initiated these types of studies by focusing on a specific class of chromatin regulators, the JmjC-containing histone demethylases. Since the discovery of these chromatin regulators, my laboratory has started screening tumors for genomic anomalies (copy changes and mutations) in this class of enzyme and examining their molecular roles at a biochemical, molecular and in vivo level. These combined approaches will determine whether tumors with alterations in JmjC enzymes provide an opportunity to modify conventional chemotherapy and identify novel molecular diagnostics.

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Group Members

Johnathan R. Whetstine, PhD
Principal Investigator

Group Members

  • Joshua C. Black, PhD  
  • Sweta Mishra, PhD 
  • Sedona Murphy
  • Capucine Van Rechem, PhD



Research Projects

Histone methylation and acetylation dynamics: impact on development and cancer pathology

Events within the nucleus are governed by a number of processes, but increasing information emphasizes the relationship between post-translational modifications (PTMs) on the histones within the chromatin and proper developmental patterning and pathologies like cancer. The N-terminal tails of histones are subject to a plethora of PTMs including phosphorylation, ubiquitination, acetylation and methylation. Each modification can affect chromatin architecture, but the sum of these modifications may be the ultimate determinant of the chromatin state and biological outcome. Research has shown that multiple lysine (K) residues on the tails of histone H3 and H4 are sites for methylation. The site and degree of methylation (mono-, di-, or tri-) are linked to transcriptional activation and repression, cell cycle progression, and DNA damage response. Many biological processes like heterochromatin formation and X-inactivation are regulated by histone methylation; therefore, aberrant methylation can result in human diseases such as cancer. For this reason, organisms have developed enzymes that are responsible for both adding and removing the methyl mark. Our group studies the impact that histone-modifying proteins have on development, behavior and cancer pathology.

My laboratory is focused on understanding the mechanistic impact that methylation dynamics has in human cell culture and model systems (e.g., C. elegans and zebrafish). In particular, we are investigating the impact that the histone 3 lysine 9/36 tri-demethylases have on differentiation, neural behavior and tumorigenesis by understanding their roles in transcriptional and post transcriptional regulation of the coding and noncoding regions of the genome, in cell cycle progression through regulating chromatin structure, and in the stability of the genome.

We are also interrogating the mechanisms associated with regulating histone demethylase function. For example, we have demonstrated that KDM4A is modulated throughout the cell cycle by the SCF E3 ubiquitin ligase complex, which is an important regulator of demethylase levels and function during the cell cycle and hypoxia. We have demonstrated that JMJD2A/KDM4A is amplified in a number of tumors, correlates with poor outcome in ovarian cancer patients and regulates the site-specific copy gain of regions implicated in chemotherapy resistance. Through the use of proteomics and genomics, we have been able to identify important associated proteins regulating these KDM4A driven events at regions being directly modulated. Furthermore, we have identified physiological signals that promote KDM4A stabilization and site-specific copy gain of drug resistant regions in the genome from fish to man. Therefore, we are investigating the impact that other cellular input signals have on copy number through the modulation of chromatin regulators.

The laboratory will interrogate the functional role of histone demethylases by using genomic (ChIP-seq, microarrays, and RNA-seq), proteomic (MS-MS complexes and PTMs), cytological (live imaging and deconvolution confocal microscopy) and genetic (C. elegans, human cell lines, and zebrafish) approaches (Figure 1).

Using these strategies, we have uncovered roles for the C. elegans JMJD-2 enzyme in genomic stability and DNA replication (Figure 2). We have extended these studies to demonstrate a conserved role for human JMJD2A/KDM4A in DNA replication and demonstrated that ubiquitin plays a key role in this regulation.

Furthermore, we uncovered a conserved role for chromatin states and KDM4A in modulating rereplication at specific sites in the genome. The rereplication promotes site-specific copy gains of drug resistant regions. This series of discoveries identified the first enzyme, physiological condition and chromatin states that modulate copy gain and selection of drug resistant regions across cancer types.

Therefore, combining model systems with human cell culture models as well as integrating multiple approaches, we are poised to uncovered mechanisms impacting genome stability and drug resistant gene selection across tumors.

Research Positions

Postdoctoral Fellow (1)

My laboratory is focused on understanding the impact that both methylation and acetylation dynamics has in both human cell culture and C. elegans. In particular, the laboratory is investigating the impact that the histone 3 lysine 9/36 tri-demethylases [JMJD2A-D; Whetstine et al., (2007) Cell 125: 467-81] have on tumorigenesis, transcriptional regulation, and genomic integrity. The laboratory will interrogate the role of these enzymes by using genomic, proteomic, cytological and genetic approaches. Similar approaches allowed an important link to be established for histone deacetylase 1 (HDAC-1) and the regulation of extra-cellular matrix biology in both human and C. elegans, which has direct implications in cancer chemotherapy [Whetstine et al., (2005) Mol. Cell 18:483-90]. The laboratory will continue to investigate the functional overlap or unique pathways that the C. elegans class I histone deacetylases regulate by using the same type of approaches. Overall, the laboratory will integrate a number of approaches and systems to determine the important biological pathways regulated by histone demethylases and histone deacetylases. The laboratory is looking for highly motivated, tenacious scientists that are enthusiastic, team players and love science. The laboratory is looking for researchers with documented proficiency in any of the following areas (basic molecular biology, protein biochemistry, genomics, epigenetics, C. elegans, cytology, development biology, DNA damage and repair) but interested in learning new approaches or systems to answer the exciting questions before us. Requirements: For these positions a PhD and/or MD is required. These positions require enthusiastic, self motivated, independent thinkers with strong interpersonal skills, and the ability to communicate with laboratory members, national and international collaborators.


Center for Cancer Research
149 13th Street, Room 7-213
Charlestown, MA 02129
E-mail: jwhetstine@hms.harvard.edu


View a list of publications by researchers at the Whetstine Laboratory

Selected Publications

Black JC, Atabakhsh E, Kim J, Biette KB, Van Rechem C, Ladd B, Burrowes Pd, Donado C, Mattoo H, Kleinstiver BP, Song B, Andriani G, Joung JK, Iliopoulos O, Montagna C, Pillai S, Getz G, Whetstine JR. Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Genes and Development. 29, 1018-1031, 2015.

Van Rechem C, Black JC, Greninger P, Zhao Y, Donado C, Burrowes Pd, Ladd, B, Christiani DC, Benes CH, Whetstine JR.  A Coding Single Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors. Cancer Discov. 5, 245-254, 2015.

Van Rechem C, Black JC, Boukhali M, Aryee MJ, Graslund S, Haas W, Benes CH, Whetstine JR. Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis. Cancer Discov. 5, 255-263, 2015.

Black JC, Manning AL, Van Rechem C, Kim J, Ladd B, Cho J, Pineda CM, Murphy N, Daniels DL, Montagna C, Lewis PW, Glass K, Allis CD, Dyson NJ, Getz G, Whetstine JR. KDM4A Lysine Demethylase Induces Site- Specific Copy Gain and Rereplication of Regions Amplified in Tumors. Cell. 154, 541-555, 2013.

Black JC, Van Rechem C, Whetstine JR. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol Cell. 48(4):491-507, 2012 November.

Black JC, Allen A, Van Rechem C, Forbes E, Longworth M, Tschöp K, Rinehart C, Quiton J, Walsh R, Smallwood A, Dyson NJ, Whetstine JR. Conserved antagonism between JMJD2A/KDM4A and HP1 during cell cycle progression. Mol Cell. 40(5):736-48, 2010 Dec 10.


Video: Drug-resistant lung cancer research funded by the American Lung Association. In this video, Dr. Johnathan Whetstine, Associate Professor of Medicine at Harvard Medical School and Dr. Sweta Mishra, a Postdoctoral Research Fellow discuss their work at Massachusetts General Hospital Cancer Center with drug-resistant lung cancer research and the American Lung Association Research Awards Nationwide. Read more here.


Video: Making strides Against Breast Cancer Kick off breakfast, August 2nd, 2016. Making Strides Against Breast Cancer supporters help the American Cancer Society share in hope,courage, and caring to make the world free from the pain and suffering of breast cancer.


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