Bio

Honors & Awards


  • DARE (Diversifying Academia, Recruiting Excellence) Doctoral Fellowship, Stanford University (2010-2012)
  • Carl Storm Underrepresented Minority Fellowship, Gordon Research Conferences (2009)
  • Research Supplements to Promote Diversity in Health-Related Research, National Institutes of Health (2007-2009)
  • Sally Casanova California Pre-Doctoral Scholarship, California State University (2005)
  • Minority Biomedical Research Support (MBRS) Research Initiative for Scientific Enhancement (RISE), National Institutes of Health (2004-2006)
  • Post-baccalaureate Research Education Program (PREP) Scholarship, National Institutes of Health (2004)
  • University of California Leadership Certificate, University of California, Santa Barbara (2003)

Professional Education


  • Doctor of Philosophy, Stanford University, BIOL-PHD (2012)
  • Master of Science, San Francisco State University, Microbiology (2006)
  • Bachelor of Science, University of California Santa Barbara, Microbiology (2003)

Stanford Advisors


Research & Scholarship

Lab Affiliations


Teaching

Graduate and Fellowship Programs


  • Biology (School of Humanities and Sciences) (Phd Program)

Publications

Journal Articles


  • Nuclear phosphatidylinositol-5-phosphate regulates ING2 stability at discrete chromatin targets in response to DNA damage SCIENTIFIC REPORTS Bua, D. J., Martin, G. M., Binda, O., Gozani, O. 2013; 3

    Abstract

    ING2 (inhibitor of growth family member 2) is a component of a chromatin-regulatory complex that represses gene expression and is implicated in cellular processes that promote tumor suppression. However, few direct genomic targets of ING2 have been identified and the mechanism(s) by which ING2 selectively regulates genes remains unknown. Here we provide evidence that direct association of ING2 with the nuclear phosphoinositide phosphatidylinositol-5-phosphate (PtdIns(5)P) regulates a subset of ING2 targets in response to DNA damage. At these target genes, the binding event between ING2 and PtdIns(5)P is required for ING2 promoter occupancy and ING2-associated gene repression. Moreover, depletion of PtdIns(5)P attenuates ING2-mediated regulation of these targets in the presence of DNA damage. Taken together, these findings support a model in which PtdIns(5)P functions as a sub-nuclear trafficking factor that stabilizes ING2 at discrete genomic sites.

    View details for DOI 10.1038/srep02137

    View details for Web of Science ID 000321287400008

    View details for PubMedID 23823870

  • Structure-activity relationships of methyl-lysine reader antagonists MEDCHEMCOMM Herold, J. M., James, L. I., Korboukh, V. K., Gao, C., Coil, K. E., Bua, D. J., Norris, J. L., Kireev, D. B., Brown, P. J., Jin, J., Janzen, W. P., Gozani, O., Frye, S. V. 2012; 3 (1): 45-51

    View details for DOI 10.1039/c1md00195g

    View details for Web of Science ID 000299975300007

  • SIRT6 is required for maintenance of telomere position effect in human cells NATURE COMMUNICATIONS Tennen, R. I., Bua, D. J., Wright, W. E., Chua, K. F. 2011; 2

    Abstract

    In Saccharomyces cerevisiae, the repressive chromatin environment at telomeres gives rise to telomere position effect (TPE), the epigenetic silencing of telomere-proximal genes. Chromatin-modifying factors that control TPE in yeast have been extensively studied, and, among these, the lifespan regulator and silencing protein Sir2 has a pivotal role. In contrast, the factors that generate and maintain silent telomeric chromatin in human cells remain largely unknown. Here we show that the Sir2 family member SIRT6 is required for maintenance of TPE in human cells. RNAi-mediated depletion of SIRT6 abrogates silencing of both an integrated telomeric transgene and an endogenous telomere-proximal gene. Moreover, enhanced telomeric silencing in response to telomere elongation is associated with increased repressive chromatin marks, and this heterochromatic milieu is lost in SIRT6-deficient cells. Together, these findings establish a new role for SIRT6 in regulating an ageing-associated epigenetic silencing process and provide new mechanistic insight into chromatin silencing at telomeres.

    View details for DOI 10.1038/ncomms1443

    View details for Web of Science ID 000294806500026

    View details for PubMedID 21847107

  • Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9 Regulation of lysine methyltransferases by physical interaction with their substrates EPIGENETICS Binda, O., Leroy, G., Bua, D. J., Garcia, B. A., Gozani, O., Richard, S. 2010; 5 (8): 767-775

    Abstract

    Chromatin is broadly compartmentalized in two defined states: euchromatin and heterochromatin. Generally, euchromatin is trimethylated on histone H3 lysine 4 (H3K4(me3)) while heterochromatin contains the H3K9(me3) marks. The H3K9(me3) modification is added by lysine methyltransferases (KMTs) such as SETDB1. Herein, we show that SETDB1 interacts with its substrate H3, but only in the absence of the euchromatic mark H3K4(me3). In addition, we show that SETDB1 fails to methylate substrates containing the H3K4(me3) mark. Likewise, the functionally related H3K9 KMTs G9A, GLP, and SUV39H1 also fail to bind and to methylate H3K4(me3) substrates. Accordingly, we provide in vivo evidence that H3K9(me2)-enriched histones are devoid of H3K4(me2/3) and that histones depleted of H3K4(me2/3) have elevated H3K9(me2/3). The correlation between the loss of interaction of these KMTs with H3K4 (me3) and concomitant methylation impairment leads to the postulate that, at least these four KMTs, require stable interaction with their respective substrates for optimal activity. Thus, novel substrates could be discovered via the identification of KMT interacting proteins. Indeed, we find that SETDB1 binds to and methylates a novel substrate, the inhibitor of growth protein ING2, while SUV39H1 binds to and methylates the heterochromatin protein HP1?. Thus, our observations suggest a mechanism of post-translational regulation of lysine methylation and propose a potential mechanism for the segregation of the biologically opposing marks, H3K4(me3) and H3K9(me3). Furthermore, the correlation between H3-KMTs interaction and substrate methylation highlights that the identification of novel KMT substrates may be facilitated by the identification of interaction partners.

    View details for DOI 10.4161/epi.5.8.13278

    View details for Web of Science ID 000284263500013

    View details for PubMedID 21124070

  • Epigenome Microarray Platform for Proteome-Wide Dissection of Chromatin-Signaling Networks PLOS ONE Bua, D. J., Kuo, A. J., Cheung, P., Liu, C. L., Migliori, V., Espejo, A., Casadio, F., Bassi, C., Amati, B., Bedford, M. T., Guccione, E., Gozani, O. 2009; 4 (8)

    Abstract

    Knowledge of protein domains that function as the biological effectors for diverse post-translational modifications of histones is critical for understanding how nuclear and epigenetic programs are established. Indeed, mutations of chromatin effector domains found within several proteins are associated with multiple human pathologies, including cancer and immunodeficiency syndromes. To date, relatively few effector domains have been identified in comparison to the number of modifications present on histone and non-histone proteins. Here we describe the generation and application of human modified peptide microarrays as a platform for high-throughput discovery of chromatin effectors and for epitope-specificity analysis of antibodies commonly utilized in chromatin research. Screening with a library containing a majority of the Royal Family domains present in the human proteome led to the discovery of TDRD7, JMJ2C, and MPP8 as three new modified histone-binding proteins. Thus, we propose that peptide microarray methodologies are a powerful new tool for elucidating molecular interactions at chromatin.

    View details for DOI 10.1371/journal.pone.0006789

    View details for Web of Science ID 000269335000031

    View details for PubMedID 19956676

  • The Return of the INGs, Histone Mark Sensors and Phospholipid Signaling Effectors CURRENT DRUG TARGETS Bua, D. J., Binda, O. 2009; 10 (5): 418-431

    Abstract

    Since their discovery, the members of the ING (inhibitor of growth) family of tumor suppressors have emerged as essential and core components of chromatin modifying complexes. Recent work has identified the ING family as histone mark sensors that orchestrate cellular responses to genotoxic insults and regulate chromatin homeostasis. Dysregulation of chromatin homeostasis is implicated in tumorigenesis through mechanisms such as silencing of tumor suppressor genes, inappropriate activation of oncogenes, and genomic instability due to failure to repair DNA damage. This review will concentrate on the chromatin signaling aspects of the ING proteins, focusing on how recognition of histone H3 trimethylated at lysine 4 (H3K4me3) by the PHD (plant homeodomain) finger of ING proteins is critical for regulating cellular functions such as gene expression. We will also discuss how H3K4me3-recognition by ING proteins plays a critical role in their tumor suppressive functions. Finally, we will discuss the relevance of the association between one ING protein (ING2) and the nuclear phosphoinositide, phosphatidylinositol-5-phosphate (PtdIns(5)P). Interestingly, the ING2-PtdIns(5)P interaction involves the PHD finger and an adjacent polybasic region. The level of nuclear PtdIns(5)P sharply increases upon genotoxic stress, and this increase positively regulates ING2-mediated responses. Thus, the PHD finger of ING2 integrates phosphoinositide and chromatin signaling networks to prevent unchecked cell growth.

    View details for Web of Science ID 000265680600004

    View details for PubMedID 19442114

  • Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Koh, A. S., Kuo, A. J., Park, S. Y., Cheung, P., Abramson, J., Bua, D., Carney, D., Shoelson, S. E., Gozani, O., Kingston, R. E., Benoist, C., Mathis, D. 2008; 105 (41): 15878-15883

    Abstract

    Aire induces ectopic expression of peripheral tissue antigens (PTAs) in thymic medullary epithelial cells, which promotes immunological tolerance. Beginning with a broad screen of histone peptides, we demonstrate that the mechanism by which this single factor controls the transcription of thousands of genes involves recognition of the amino-terminal tail of histone H3, but not of other histones, by one of Aire's plant homeodomain (PHD) fingers. Certain posttranslational modifications of H3 tails, notably dimethylation or trimethylation at H3K4, abrogated binding by Aire, whereas others were tolerated. Similar PHD finger-H3 tail-binding properties were recently reported for BRAF-histone deacetylase complex 80 and DNA methyltransferase 3L; sequence alignment, molecular modeling, and biochemical analyses showed these factors and Aire to have structure-function relationships in common. In addition, certain PHD1 mutations underlying the polyendocrine disorder autoimmune polyendocrinopathy-candidiases-ectodermaldystrophy compromised Aire recognition of H3. In vitro binding assays demonstrated direct physical interaction between Aire and nucleosomes, which was in part buttressed by its affinity to DNA. In vivo Aire interactions with chromosomal regions depleted of H3K4me3 were dependent on its H3 tail-binding activity, and this binding was necessary but not sufficient for the up-regulation of genes encoding PTAs. Thus, Aire's activity as a histone-binding module mediates the thymic display of PTAs that promotes self-tolerance and prevents organ-specific autoimmunity.

    View details for DOI 10.1073/pnas.0808470105

    View details for Web of Science ID 000260240900044

    View details for PubMedID 18840680

Presentations


  • Genomic analyses of the tumor suppressor protein ING2 in response to stress

    Poster

    Time Period

    10/27/2011

    Presented To

    Society for Advancement of Chicanos and Native Americans in Science (SACNAS) National Conference

    Location

    san jose, california

  • Epigenome peptide microarrays facilitate molecular dissection of chromatin signaling networks

    Short Talk

    Time Period

    4/1/2009

    Presented To

    Gordon Research Conference: Signal Transduction within the Nucleus

    Location

    Ventura, CA

  • Genetic Interactions Between Lagging Strand DNA Replication Machinery and Cdc24p in Fission Yeast

    Poster

    Time Period

    8/26/2005

    Presented To

    Cold Spring Harbor Laboratory

    Location

    cold spring harbor, new york

  • Interactions between Cdc24 and lagging strand DNA synthesis machinery: Cdc17 (DNA ligase I homolog) and Rad2 (FEN-1) homolog in Schizosaccharomyces pombe

    Talk

    Time Period

    12/1/2005

    Presented To

    27th Annual Asilomar Chromatin and Chromosomes Conference

    Location

    asilomar, california

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