Professional Education

  • Doctor of Philosophy, University of Toronto (2012)
  • Bachelor of Science, University of Toronto (2006)

Stanford Advisors

Research & Scholarship

Lab Affiliations


All Publications

  • Histone Recognition by Human Malignant Brain Tumor Domains JOURNAL OF MOLECULAR BIOLOGY Nady, N., Krichevsky, L., Zhong, N., Duan, S., Tempel, W., Amaya, M. F., Ravichandran, M., Arrowsmith, C. H. 2012; 423 (5): 702-718


    Histone methylation has emerged as an important covalent modification involved in a variety of biological processes, especially regulation of transcription and chromatin dynamics. Lysine methylation is found in three distinct states (monomethylation, dimethylation and trimethylation), which are recognized by specific protein domains. The malignant brain tumor (MBT) domain is one such module found in several chromatin regulatory complexes including Polycomb repressive complex 1. Here, we present a comprehensive characterization of the human MBT family with emphasis on histone binding specificity. SPOT-blot peptide arrays were used to screen for the methyllysine-containing histone peptides that bind to MBT domains found in nine human proteins. Selected interactions were quantified using fluorescence polarization assays. We show that all MBT proteins recognize only monomethyllysine and/or dimethyllysine marks and provide evidence that some MBT domains recognize a defined consensus sequence while others bind in a promiscuous, non-sequence-specific manner. Furthermore, using structure-based mutants, we identify a triad of residues in the methyllysine binding pocket that imparts discrimination between monomethyllysine and dimethyllysine. This study represents a comprehensive analysis of MBT substrate specificity, establishing a foundation for the rational design of selective MBT domain inhibitors that may enable elucidation of their role in human biology and disease.

    View details for DOI 10.1016/j.jmb.2012.08.022

    View details for Web of Science ID 000310666400005

    View details for PubMedID 22954662

  • Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation NATURE STRUCTURAL & MOLECULAR BIOLOGY Rothbart, S. B., Krajewski, K., Nady, N., Tempel, W., Xue, S., Badeaux, A. I., Barsyte-Lovejoy, D., Martinez, J. Y., Bedford, M. T., Fuchs, S. M., Arrowsmith, C. H., Strahl, B. D. 2012; 19 (11): 1155-?


    A fundamental challenge in mammalian biology has been the elucidation of mechanisms linking DNA methylation and histone post-translational modifications. Human UHRF1 (ubiquitin-like PHD and RING finger domain-containing 1) has multiple domains that bind chromatin, and it is implicated genetically in the maintenance of DNA methylation. However, molecular mechanisms underlying DNA methylation regulation by UHRF1 are poorly defined. Here we show that UHRF1 association with methylated histone H3 Lys9 (H3K9) is required for DNA methylation maintenance. We further show that UHRF1 association with H3K9 methylation is insensitive to adjacent H3 S10 phosphorylation--a known mitotic 'phospho-methyl switch'. Notably, we demonstrate that UHRF1 mitotic chromatin association is necessary for DNA methylation maintenance through regulation of the stability of DNA methyltransferase-1. Collectively, our results define a previously unknown link between H3K9 methylation and the faithful epigenetic inheritance of DNA methylation, establishing a notable mitotic role for UHRF1 in this process.

    View details for DOI 10.1038/nsmb.2391

    View details for Web of Science ID 000310788800015

    View details for PubMedID 23022729

  • Recognition of Multivalent Histone States Associated with Heterochromatin by UHRF1 Protein JOURNAL OF BIOLOGICAL CHEMISTRY Nady, N., Lemak, A., Walker, J. R., Avvakumov, G. V., Kareta, M. S., Achour, M., Xue, S., Duan, S., Allali-Hassani, A., Zuo, X., Wang, Y., Bronner, C., Chedin, F., Arrowsmith, C. H., Dhe-Paganon, S. 2011; 286 (27): 24300-24311


    Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance DNA methylation at hemimethylated CpG sites, which are specifically recognized through its SRA domain and also interacts with histone H3 trimethylated on lysine 9 (H3K9me3) in an unspecified manner. Here we show that UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). Solution NMR and crystallographic data reveal the TTD simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first Tudor subdomain and unmodified H3K4 within a groove between the tandem subdomains. The subdomains undergo a conformational adjustment upon peptide binding, distinct from previously reported mechanisms for dual histone mark recognition. Mutant UHRF1 protein deficient for H3K4me0/K9me3 binding shows altered localization to heterochromatic chromocenters and fails to reduce expression of a target gene, p16(INK4A), when overexpressed. Our results demonstrate a novel recognition mechanism for the combinatorial readout of histone modification states associated with gene silencing and add to the growing evidence for coordination of, and cross-talk between, the modification states of H3K4 and H3K9 in regulation of gene expression.

    View details for DOI 10.1074/jbc.M111.234104

    View details for Web of Science ID 000292294900071

    View details for PubMedID 21489993

  • Recognition and specificity determinants of the human cbx chromodomains. journal of biological chemistry Kaustov, L., Ouyang, H., Amaya, M., Lemak, A., Nady, N., Duan, S., Wasney, G. A., Li, Z., Vedadi, M., Schapira, M., Min, J., Arrowsmith, C. H. 2011; 286 (1): 521-529


    The eight mammalian Cbx proteins are chromodomain-containing proteins involved in regulation of heterochromatin, gene expression, and developmental programs. They are evolutionarily related to the Drosophila HP1 (dHP1) and Pc (dPc) proteins that are key components of chromatin-associated complexes capable of recognizing repressive marks such as trimethylated Lys-9 and Lys-27, respectively, on histone H3. However, the binding specificity and function of the human homologs, Cbx1-8, remain unclear. To this end we employed structural, biophysical, and mutagenic approaches to characterize the molecular determinants of sequence contextual methyllysine binding to human Cbx1-8 proteins. Although all three human HP1 homologs (Cbx1, -3, -5) replicate the structural and binding features of their dHP counterparts, the five Pc homologs (Cbx2, -4, -6, -7, -8) bind with lower affinity to H3K9me3 or H3K27me3 peptides and are unable to distinguish between these two marks. Additionally, peptide permutation arrays revealed a greater sequence tolerance within the Pc family and suggest alternative nonhistone sequences as potential binding targets for this class of chromodomains. Our structures explain the divergence of peptide binding selectivity in the Pc subfamily and highlight previously unrecognized features of the chromodomain that influence binding and specificity.

    View details for DOI 10.1074/jbc.M110.191411

    View details for PubMedID 21047797

  • Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2 NUCLEIC ACIDS RESEARCH Guo, Y., Nady, N., Qi, C., Allali-Hassani, A., Zhu, H., Pan, P., Adams-Cioaba, M. A., Amaya, M. F., Dong, A., Vedadi, M., Schapira, M., Read, R. J., Arrowsmith, C. H., Min, J. 2009; 37 (7): 2204-2210


    The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2-H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl-lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family.

    View details for DOI 10.1093/nar/gkp086

    View details for Web of Science ID 000265741600013

    View details for PubMedID 19233876

  • A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research TRENDS IN BIOCHEMICAL SCIENCES Nady, N., Min, J., Kareta, M. S., Chedin, F., Arrowsmith, C. H. 2008; 33 (7): 305-313


    Post-translational modifications of histones serve as docking sites and signals for effector proteins and chromatin-remodeling enzymes, thereby influencing many fundamental cellular processes. Nevertheless, there are huge gaps in the knowledge of which proteins read and write the 'histone code'. Several techniques have been used to decipher complex histone-modification patterns. However, none is entirely satisfactory owing to the inherent limitations of in vitro studies of histones, such as deficits in the knowledge of the proteins involved, and the associated difficulties in the consistent and quantitative generation of histone marks. An alternative technique that could prove to be a useful tool in the study of the histone code is the use of synthetic peptide arrays (SPOT blot analysis) as a screening approach to characterize macromolecules that interact with specific covalent modifications of histone tails.

    View details for DOI 10.1016/j.tibs.2008.04.014

    View details for Web of Science ID 000258041900004

    View details for PubMedID 18538573



    The bulbocavernosus reflex was investigated electrophysiologically in 14 normal adult male subjects and in 80 patients with neurogenic bladders and/or impotence due to various neurological causes as well as in patients with functional impotence. The glans penis was stimulated superficially by single electrical shocks and the reflex responses were recorded from the bulbocavernosus (BC) and the striated anal sphincter muscles by means of concentric needle EMG electrodes. In all normal subjects, the BC reflex was recorded from the BC muscle as a stable and constant response having a mean latency of 36.1 msec. A response from the external anal sphincter was obtained in only 21% of the subjects investigated. In 13 patients with cauda equina lesions, the BC reflex was either absent or was present with a prolonged latency. Twenty-two patients with polyneuropathy of various causes were also investigated; in these patients the latency of the BC reflex was significantly greater than in the normal controls, but the most abnormal results were obtained in cases of alcoholic polyneuropathy. In the 19 cases of spinal cord disease with spasticity the BC reflex response was very intense, often with after discharges but latency values were within normal limits. In the 16 cases with functional impotence, the BC reflexes were basically normal; but in 3 cases, the threshold of the reflex was significantly raised, and in 1 case a prolonged latency was observed. The value and the practical application of the BC reflex in the BC reflex in the differential diagnosis of bladder dysfunction and of impotence was stressed.

    View details for Web of Science ID A1976BP78100001

    View details for PubMedID 180261