Epigenetic regulatory mechanisms are critical for multicellular development and normal function, as epigenetic deregulation underlies human diseases ranging from cancers to intellectual disabilities. My lab will integrate epigenomics with new methods in single-molecule imaging and proteomics, to discover the biophysical principles that underlie epigenetic regulatory systems.

Honors & Awards

  • Charles B. Carrington Memorial Award, Department of Pathology, Stanford University School of Medicine (2016)
  • Holly and Gerald N. Wogan Award for Scientific Research Excellence, Aspen Cancer Conference (2016)
  • AACR NextGen Star, American Association for Cancer Research (2015)
  • NIH Pathway to Independence Award (K99/R00), NIH/NCI (2014)
  • Postdoctoral Fellow, American Cancer Society (2012)
  • Ruth L. Kirschstein National Research Service Award, The Eunice Kennedy Shriver National Institute of Child Health & Human Development (2012)

Professional Education

  • Postdoctoral Fellow, Stanford University School of Medicine
  • Doctor of Philosophy, University of California Berkeley (2009)

Stanford Advisors

Research & Scholarship

Current Research and Scholarly Interests

My research involves the development of experimental and analytical approaches to investigate the biophysical mechanisms underlying epigenetic systems. We will focus on single-molecule imaging, and use other quantitative techniques from epigenomics and proteomics, to reveal in quantitative, predictive terms how epigenetic regulators function and how their dysfunction contributes to the earliest stages of cancer and other disorders.


2013-14 Courses


All Publications

  • The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harbor perspectives in medicine Hodges, C., Kirkland, J. G., Crabtree, G. R. 2016; 6 (8)


    During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ?20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.

    View details for DOI 10.1101/cshperspect.a026930

    View details for PubMedID 27413115

  • Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nature genetics Stanton, B. Z., Hodges, C., Calarco, J. P., Braun, S. M., Ku, W. L., Kadoch, C., Zhao, K., Crabtree, G. R. 2016


    Trithorax-group proteins and their mammalian homologs, including those in BAF (mSWI/SNF) complexes, are known to oppose the activity of Polycomb repressive complexes (PRCs). This opposition underlies the tumor-suppressive role of BAF subunits and is expected to contribute to neurodevelopmental disorders. However, the mechanisms underlying opposition to Polycomb silencing are poorly understood. Here we report that recurrent disease-associated mutations in BAF subunits induce genome-wide increases in PRC deposition and activity. We show that point mutations in SMARCA4 (also known as BRG1) mapping to the ATPase domain cause loss of direct binding between BAF and PRC1 that occurs independently of chromatin. Release of this direct interaction is ATP dependent, consistent with a transient eviction mechanism. Using a new chemical-induced proximity assay, we find that BAF directly evicts Polycomb factors within minutes of its occupancy, thereby establishing a new mechanism for the widespread BAF-PRC opposition underlying development and disease.

    View details for DOI 10.1038/ng.3735

    View details for PubMedID 27941795

  • Dynamics of inherently bounded histone modification domains PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hodges, C., Crabtree, G. R. 2012; 109 (33): 13296-13301


    A central goal of chromatin biology is to reveal how posttranslational histone marks modulate gene expression; however, relatively little is known about the spatial or temporal dynamics of these marks. We previously showed that a dynamic model of histone mark nucleation, propagation, and turnover fits the mean enrichment profiles from 99% of noncentromeric histone H3 lysine 9 trimethylation (H3K9me3) domains in mouse embryonic stem cells without the need for boundary or insulator elements. Here we report the full details of this "inherently bounded" model of histone modification dynamics and describe several dynamic features of the model using H3K9me3 as a paradigm. By analyzing the kinetic and structural constraints that drive formation of inherently bounded domains, we find that such domains are optimized when the rates of marking and turnover are comparable. Additionally, we find that to establish such domains, propagation of the histone marks must occur primarily through local contacts.

    View details for DOI 10.1073/pnas.1211172109

    View details for Web of Science ID 000307807000039

    View details for PubMedID 22847427

  • Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II SCIENCE Hodges, C., Bintu, L., Lubkowska, L., Kashlev, M., Bustamante, C. 2009; 325 (5940): 626-628


    RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.

    View details for DOI 10.1126/science.1172926

    View details for Web of Science ID 000268493000054

    View details for PubMedID 19644123

  • A General Non-Radioactive ATPase Assay for Chromatin Remodeling Complexes. Current protocols in chemical biology Stanton, B. Z., Hodges, C., Crabtree, G. R., Zhao, K. 2017; 9 (1): 1?10


    Chromatin remodeling complexes couple the energy released from ATP hydrolysis to facilitate transcription, recombination, and repair mechanisms essential for a wide variety of biologic responses. While recombinant expression of the regulatory subunits of these enzymes is possible, measuring catalytic (ATPase) activity of the intact complexes recovered from normal or mutant cells is critical for understanding their mechanisms. SWI/SNF-like remodeling complexes can be megadaltons in size and include many regulatory subunits, making reconstitution of purified subunits challenging for recapitulating in vivo function. The protocol in this article defines the first highly quantitative ATPase assay for intact remodeling complexes that does not require radiation or reconstitution of recombinantly expressed subunits. This protocol is specifically useful for defining the catalytic role of active-site mutations in the context of other regulatory subunits and quantitatively rank-ordering inactivating catalytic-site mutations. 2017 by John Wiley & Sons, Inc.

    View details for DOI 10.1002/cpch.16

    View details for PubMedID 28253434

  • TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nature structural & molecular biology Miller, E. L., Hargreaves, D. C., Kadoch, C., Chang, C. Y., Calarco, J. P., Hodges, C., Buenrostro, J. D., Cui, K., Greenleaf, W. J., Zhao, K., Crabtree, G. R. 2017


    The resolution and formation of facultative heterochromatin are essential for development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood owing to the difficulty of studying heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription. This indicates that changes in DNA topology that take place through (de-)catenation rather than the release of torsional stress through swiveling are necessary for heterochromatin resolution. TOP2 and BAF cooperate to recruit pluripotency factors, which explains some of the instructive roles of BAF complexes. Unexpectedly, we found that TOP2 also plays a role in the re-formation of facultative heterochromatin; this finding suggests that facultative heterochromatin and accessible chromatin exist at different states of catenation or other topologies, which might be critical to their structures.

    View details for DOI 10.1038/nsmb.3384

    View details for PubMedID 28250416

  • Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nature genetics Kadoch, C., Hargreaves, D. C., Hodges, C., Elias, L., Ho, L., Ranish, J., Crabtree, G. R. 2013; 45 (6): 592-601


    Subunits of mammalian SWI/SNF (mSWI/SNF or BAF) complexes have recently been implicated as tumor suppressors in human malignancies. To understand the full extent of their involvement, we conducted a proteomic analysis of endogenous mSWI/SNF complexes, which identified several new dedicated, stable subunits not found in yeast SWI/SNF complexes, including BCL7A, BCL7B and BCL7C, BCL11A and BCL11B, BRD9 and SS18. Incorporating these new members, we determined mSWI/SNF subunit mutation frequency in exome and whole-genome sequencing studies of primary human tumors. Notably, mSWI/SNF subunits are mutated in 19.6% of all human tumors reported in 44 studies. Our analysis suggests that specific subunits protect against cancer in specific tissues. In addition, mutations affecting more than one subunit, defined here as compound heterozygosity, are prevalent in certain cancers. Our studies demonstrate that mSWI/SNF is the most frequently mutated chromatin-regulatory complex (CRC) in human cancer, exhibiting a broad mutation pattern, similar to that of TP53. Thus, proper functioning of polymorphic BAF complexes may constitute a major mechanism of tumor suppression.

    View details for DOI 10.1038/ng.2628

    View details for PubMedID 23644491

  • Dynamics and Memory of Heterochromatin in Living Cells CELL Hathaway, N. A., Bell, O., Hodges, C., Miller, E. L., Neel, D. S., Crabtree, G. R. 2012; 149 (7): 1447-1460


    Posttranslational histone modifications are important for gene regulation, yet the mode of propagation and the contribution to heritable gene expression states remains controversial. To address these questions, we developed a chromatin in vivo assay (CiA) system employing chemically induced proximity to initiate and terminate chromatin modifications in living cells. We selectively recruited HP1? to induce H3K9me3-dependent gene silencing and describe the kinetics and extent of chromatin modifications at the Oct4 locus in fibroblasts and pluripotent cells. H3K9me3 propagated symmetrically and continuously at average rates of ~0.18 nucleosomes/hr to produce domains of up to 10 kb. After removal of the HP1? stimulus, heterochromatic domains were heritably transmitted, undiminished through multiple cell generations. Our data enabled quantitative modeling of reaction kinetics, which revealed that dynamic competition between histone marking and turnover, determines the boundaries and stability of H3K9me3 domains. This framework predicts the steady-state dynamics and spatial features of the majority of euchromatic H3K9me3 domains over the genome.

    View details for DOI 10.1016/j.cell.2012.03.052

    View details for Web of Science ID 000305753800012

    View details for PubMedID 22704655

  • The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes NATURE STRUCTURAL & MOLECULAR BIOLOGY Bintu, L., Kopaczynska, M., Hodges, C., Lubkowska, L., Kashlev, M., Bustamante, C. 2011; 18 (12): 1394-1399


    Upon transcription, histones can either detach from DNA or transfer behind the polymerase through a process believed to involve template looping. The details governing nucleosomal fate during transcription are not well understood. Our atomic force microscopy images of yeast RNA polymerase II-nucleosome complexes confirm the presence of looped transcriptional intermediates and provide mechanistic insight into the histone-transfer process through the distribution of transcribed nucleosome positions. Notably, we find that a fraction of the transcribed nucleosomes are remodeled to hexasomes, and this fraction depends on the transcription elongation rate. A simple model involving the kinetic competition between transcription elongation, histone transfer and histone-histone dissociation quantitatively explains our observations and unifies them with results obtained from other polymerases. Factors affecting the relative magnitude of these processes provide the physical basis for nucleosomal fate during transcription and, therefore, for the regulation of gene expression.

    View details for DOI 10.1038/nsmb.2164

    View details for Web of Science ID 000298011600028

    View details for PubMedID 22081017

  • ClpX(P) Generates Mechanical Force to Unfold and Translocate Its Protein Substrates CELL Maillard, R. A., Chistol, G., Sen, M., Righini, M., Tan, J., Kaiser, C. M., Hodges, C., Martin, A., Bustamante, C. 2011; 145 (3): 459-469


    AAA(+) unfoldases denature and translocate polypeptides into associated peptidases. We report direct observations of mechanical, force-induced protein unfolding by the ClpX unfoldase from E. coli, alone, and in complex with the ClpP peptidase. ClpX hydrolyzes ATP to generate mechanical force and translocate polypeptides through its central pore. Threading is interrupted by pauses that are found to be off the main translocation pathway. ClpX's translocation velocity is force dependent, reaching a maximum of 80 aa/s near-zero force and vanishing at around 20 pN. ClpX takes 1, 2, or 3 nm steps, suggesting a fundamental step-size of 1 nm and a certain degree of intersubunit coordination. When ClpX encounters a folded protein, it either overcomes this mechanical barrier or slips on the polypeptide before making another unfolding attempt. Binding of ClpP decreases the slip probability and enhances the unfolding efficiency of ClpX. Under the action of ClpXP, GFP unravels cooperatively via a transient intermediate.

    View details for DOI 10.1016/j.cell.2011.04.010

    View details for Web of Science ID 000290022900014

    View details for PubMedID 21529717

  • Following translation by single ribosomes one codon at a time NATURE Wen, J., Lancaster, L., Hodges, C., Zeri, A., Yoshimura, S. H., Noller, H. F., Bustamante, C., Tinoco, I. 2008; 452 (7187): 598-603


    We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation--and-pause cycles. The distribution of pause lengths, with a median of 2.8 s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases--one codon-and occurs in less than 0.1 s. Analysis of the times required for translocation reveals, surprisingly, that there are three substeps in each step. Pause lengths, and thus the overall rate of translation, depend on the secondary structure of the mRNA; the applied force destabilizes secondary structure and decreases pause durations, but does not affect translocation times. Translocation and RNA unwinding are strictly coupled ribosomal functions.

    View details for DOI 10.1038/nature06716

    View details for Web of Science ID 000254567200038

    View details for PubMedID 18327250

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