Work in my lab addresses the dynamic interactions between viruses and host cells when their genomes are in conflict. My lab pioneered the study of cellular damage sensing machinery as an intrinsic defense to virus infection. We have studied the DNA damage responses with a range of human DNA viruses and identified distinct ways that they manipulate signaling networks and DNA repair processes. Studying DNA damage as part of the cellular response to infection has opened up a new area in the biology of virus-host interactions. It has also provided a platform for interrogating cellular pathways involved in recognition and processing of DNA damage. This work revealed that the MRN complex is the mammalian sensor of DNA breaks and viral genomes, and that it is required for efficient activation of ATM/ATR damage signaling.
Stracker, TH, Carson, CT and Weitzman, MD. (2002) Adenovirus oncoproteins inactivate the Mre11-Rad50-NBS1 DNA repair complex. Nature, 418, 348-352.
Carson, CT, Schwartz, RA, Stracker, TH, Lilley, CE, Lee, DV and Weitzman, MD (2003). The Mre11 complex is required for ATM activation and the G2/M checkpoint. EMBO J, 22,6610-6620.
Lilley, CE, Carson, CT, Muotri, AR, Gage, FH and Weitzman, MD (2005). DNA repair proteins affect the HSV-1 lifecycle. Proc Natl Acad Sci USA, 102, 5844-5849.
Lilley, CE, Chaurushiya, MS, Boutell, C, Everett, RD, and Weitzman, MD (2011). The intrinsic antiviral defense to incoming HSV-1 genomes includes specific DNA repair proteins and is counteracted by the viral protein ICP0. PLoS Pathog 7:e1002084. PMC3116817
Chaurushiya, MS, Lilley, CE, Aslanian, A, Meisenhelder, J, Scott, DC, Landry, S, Ticau, S, Boutell, C, Yates, JR, Schulman, BA, Hunter, T and Weitzman, MD (2012). Viral E3 ubiquitin-mediated degradation of a cellular E3: viral mimicry of a cellular phosphorylation mark targets the RNF8 FHA domain. Mol Cell 46, 79-90. PMC3648639
I have had a long-standing interest in viral and host proteins that bind DNA and chromatin. As a postdoc I used biochemical approaches to identify a recognition sequence for the Rep protein of AAV within the site-specific integration site on chromosome 19 (AAVS1). I demonstrated that Rep proteins can mediate interaction between cellular and viral DNA to promote targeted integration. We have recently employed proteomic approaches to identify proteins associated with viral DNA genomes during infection, as well as the modifications that occur to chromatin on the host genome. We have analyzed histone post-translational modifications during virus infection and shown how these are altered by viruses. We recently discovered that the histone-like protein VII encoded by Adenovirus for packaging of its genome, can also affect the composition of cellular chromatin by retaining danger signals to overcome immune signaling. We are now interested in looking at how viruses impact genome and nuclear architecture and the effects this has on gene expression.
Weitzman, MD, Kyöstiö, SRM, Kotin, RM and Owens, RA (1994). Rep proteins of adeno-associated virus (AAV) mediate a complex formation between AAV DNA and the AAV integration site on human chromosome 19. Proc Natl Acad Sci USA, 91, 5808-5812.
Kulej, K, Avgousti, DC, Weitzman, MD and Garcia, BA (2015). Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics. Methods 90, 8-20.
Avgousti, DC, Herrmann, C, Sekulic, N, Kulej, K, Petrescu, J, Molden, RC, Pancholi, NJ, Reyes, ED, Seeholzer, SH, Black, BE, Garcia, BA and Weitzman, MD (2016). A core viral protein binds host nucleosomes to sequester immune danger signals. Nature 535, 173-177. PMC4950998
Kulej, K, Avgousti, DC, Sidoli, S, Herrman C, Della Fera, AN, Kim ET, Garcia, BA and Weitzman, MD (2017). Time-resolved global and chromatin proteomics during Herpes Simplex Virus Type 1 (HSV-1) infection. Mol Cell Proteomics 16, S92-S107.
Reyes, RD, Kulej, K, Akhtar, LN, Avgousti, DC, Pancholi, NJ, Kim, ET, Bricker, D, Koniski, S, Seeholzer, SH, Isaacs, SN, Garcia, BA, and Weitzman, MD. Identifying host factors associated with DNA replicated during virus infection. (in press).
My lab is interested in cellular responses that restrict virus replication. APOBEC3 proteins belong to a family of cytidine deaminases that provide a line of defense against retroviruses and endogenous mobile retroelements. We were the first to show that human APOBEC3A (A3A) is a catalytically active cytidine deaminase, with a preference for ssDNA. We demonstrated that A3A is a potent inhibitor of endogenous retroelements such as LINE1, and also blocks replication of single-stranded parvoviruses such as AAV and MVM. We have also shown how the SAMHD1 protein limits replication of the DNA virus HSV-1. We discovered ways that cellular DNA repair proteins can act as species-specific barriers through their interaction with viral proteins.
Chen, H, Lilley, CE, Yu, Q, Lee, DV, Chou, J, Narvaiza, I, Landau, NR and Weitzman, MD (2006). APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. Curr Bio 16, 480-485.
Narvaiza, I, Linfesty, DC, Greener, BN, Hakata, Y, Pintel, DJ, Logue, E, Landau, NR, and Weitzman, MD (2009). Deaminase-independent inhibition of parvoviruses by the APOBEC3A cytidine deaminase. PLoS Pathog 5, e1000439. PMC2678267
Richardson, SR, Narvaiza, I, Planegger, RA, Weitzman, MD and Moran, JV (2014). APOBEC3A deaminates transiently exposed single-strand DNA that arises during LINE-1 retrotransposition. eLife 3, e02008. PMC4003774
Kim, ET, White, TE, Brandariz-Nunez, A, Diaz-Griffero, F, and Weitzman, MD (2013). SAMHD1 restricts herpes simplex virus type 1 (HSV-1) in macrophages by limiting DNA replication. J Virol 87, 12949-12956. PMC3838123
Lou, DI, Kim, ET, Shan, S, Meyerson, NR, Pancholi, NJ, Mohni, KM, Enard, D, Petrov, DA, Weller, SK, Weitzman, MD*, and Sawyer, SL (2016). An intrinsically disordered region of the DNA repair protein Nbs1 is a species-specific barrier to Herpes Simplex Virus 1 in primates. Cell Host & Microbe 20, 178-188. (*Co-corresponding author)
Proteins that mutate viral genetic material must also be carefully regulated to prevent deleterious effects on the host genome. While studying antiviral functions for A3A we discovered that the enzyme can also act on the cellular genome, inducing DNA breaks and cell cycle arrest. We suggested therefore that APOBEC proteins cause genomic instability and contribute to malignancy, and we are now studying how they are regulated to prevent inappropriate mutations. This body of work demonstrates how studying virus-host interactions can lead to insights into fundamental processes that impact cellular genomic integrity. We have recently found A3A upregulated in a subset of human leukemias and demonstrated how this provides vulnerability for targeted cancer therapies.
Landry, S, Narvaiza, I, Linfesty, DC and Weitzman, MD (2011). APOBEC3A can activate the DNA damage response and cause cell cycle arrest. EMBO Reports 12, 444-450. PMC3090015
Narvaiza, I, Landry, S, and Weitzman, MD (2012). APOBEC3 proteins and genome stability: The high cost of a good defense? Invited Extraview in Cell Cycle 11, 33-38.
Green, AM, Landry, S, Budagyan, K, Avgousti, D, Shalhout, S, Bhagwat, AS and Weitzman, MD (2016). APOBEC3A damages the cellular genome during DNA replication. Cell Cycle 15, 998-1008. PMC4889253
Green, AM, Budagyan, K, Hayer, KE, Reed, MA, Savani, MR, Wertheim, GB and Weitzman, MD (2017). Cytosine deaminase APOBEC3A sensitizes leukemia cells to inhibition of the DNA replication checkpoint. Cancer Research (in press)
Research Interests
Our lab aims to understand host responses to virus infection, and the cellular environment encountered and manipulated by viruses. We study multiple viruses in an integrated experimental approach that combines biochemistry, molecular biology, genetics and cell biology. We have chosen viral models that provide tractable systems to investigate the dynamic interplay between viral genetic material and host defense strategies. We have used proteomic approaches to probe the dynamic interactions that take place on viral and cellular genomes during infection, and have uncovered ways that viruses manipulate histones and chromatin as they take control of cellular processes. The pathways illuminated are key to fighting diseases of viral infection, provide insights into fundamental processes that maintain genome instability, and have implications for the development of efficient viral vectors for gene therapy.
1. Centromere structural biochemistry. The work in my lab in this area is focused on understanding the physical nature of the epigenetic information generated by the incorporation of the histone H3 variant, CENP-A into chromatin. How do the DNA and proteins work together to form a chromatin domain that is distinguished from the rest of the chromosome as the site to build a mitotic kinetochore and as the site for persistent centromere maintenance through cell divisions? Our crystal structure of CENP-A, described in Sekulic et al., 2010 was the first of this protein from any species, in any context, and represents a landmark study in the centromere field. We also combined a battery of biophysical approaches alongside cell-based functional assays to identify CENP-C as an essential collaborator in maintaining centromere identity in Falk et al., 2015. In addition, we reconstituted the core centromeric nucleosome complex (CCNC) that includes both CENP-C and CENP-N and defined their independent modes of binding and roles of each in maintaining centromere identity in Guo et al., 2017. In the course of these studies, we found that CENP-C surprisingly alters the shape and the dynamics of the CENP-A nucleosome when it binds, revealing a novel mode of regulation that nucleosome-binding proteins can bring to bear on chromatin.
Allu, P.K., Dawicki-McKenna, J.M., Van Eeuwen, T., Slavin, M., Braitbard, M., Xu, C., Kalisman, N., Murakami, K., and B.E. Black*. 2019. Structure of the human core centromeric nucleosome complex. Curr. Biol., 29:2625-2639. (*corresponding author) [PMCID: PMC6702948]
Guo, L.Y., P.K. Allu, L. Zandarashvili, K.L. McKinley, N. Sekulic, J.M. Dawicki-McKenna, D. Fachinetti, G.A. Logsdon, R.M. Jamiolkowski, D.W. Cleveland, I.M. Cheeseman, and B.E. Black*. 2017. Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome structural transition. Nat. Commun., 8:15775. (*corresponding author) [PMCID: PMC5472775]
Falk, S.J.†, L.Y. Guo†, N. Sekulic†, E.M. Smoak†, T. Mani, G.A. Logsdon, K. Gupta, L.E.T. Jansen, G.D. Van Duyne, S.A. Vinogradov, M.A. Lampson, and B.E. Black*. 2015. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science, 348:699-703. (*corresponding author; †contributed equally) [PMCID: PMC4610723]
Sekulic, N., E.A. Bassett, D.J. Rogers, and B.E. Black*. 2010. The structure of (CENP-A—H4)2 reveals physical features that mark centromeres. Nature, 467:347-351. (*corresponding author) [PMCID: PMC2946842]
Black, B.E., D.R. Foltz, S. Chakravarthy, K. Luger, V.L. Woods Jr., and D.W. Cleveland. 2004. Structural determinants for generating centromeric chromatin. Nature 430:578-582.
2. Aurora B-mediated mitotic error correction. While studying patient-derived cells harboring neocentromeres, my team made the observation that the Aurora B kinase is highly enriched at chromosomes that have spindle attachment errors. This appears to be quite a fundamental observation. We find this to be a common feature of healthy, diploid cells, but one that is absent from the aneuploid, tumor-derived cells typically used for mammalian mitosis research. Further investigation revealed dynamic modulation of Aurora B levels at each centromere in a chromosome autonomous fashion that greatly expands the dynamic range of this kinase in phosphorylating kinetochore substrates. It appears that this feedback leads to highly efficient mitotic error correction; a discovery that greatly impact understanding of Aurora B function.
Zaystev, A.V., D. Sagura-Peña, M. Godzi, A. Calderon, E.R. Ballister, R. Stamatov, A.M. Mayo, L. Peterson, B.E. Black, F.L. Ataullakhanov, M.A. Lampson, E.L. Grishchuk. 2016. Bistability of a coupled Aurora B kinase-phosphatase system in cell division. Elife, 5:e10644. [PMCID: PMC4798973]
Salimian, K.J., E.R. Ballister, E.M. Smoak, S. Wood, T. Panchenko, M.A. Lampson*, and B.E. Black*. 2011. Feedback control in sensing chromosome biorientation by the Aurora B kinase. Curr. Biol., 21:1158-1165. (*corresponding authors) [PMCID: PMC3156581]
Bassett, E.A., S. Wood, K.J. Salimian, S. Ajith, D.R. Foltz, and B.E. Black*. 2010. Epigenetic centromere specification directs Aurora B accumulation but is insufficient to efficiently correct mitotic errors. J. Cell Biol., 190:177-185. (*corresponding author) [PMCID: PMC2930274]
3. Centromere chromatin assembly. Given the importance of CENP-A in defining the properties of centromeric nucleosomes, one key question in chromatin biology and epigenetics is that of how histone variants (including CENP-A) are delivered to – and incorporated into – the correct nucleosomes at appropriate locations, and how they are ‘sorted’ from each other by so-called histone chaperones. Starting with the discovery of the cis-acting element within CENP-A that targets it to centromeres (which I called the CENP-A targeting domain, CATD), I have contributed highly to the understanding of these processes. My group identified the precise mode of recognition of CENP-A by HJURP using a very effective combination of cell-based functional assays, conventional biochemistry, and high-resolution biophysical approaches. Using these data, we formulated a new model for centromere assembly in which HJURP stabilizes the histone fold domains of both CENP-A and its partner histone H4 for a substantial portion of the cell cycle prior to mediating chromatin assembly at the centromere. More recently we devised a ChIP-seq-based strategy to probe centromeric chromatin architecture at very high-resolution with a study (Hasson et al., 2013; 3b, below) that resolved a longstanding conflict regarding the nature of human centromeric nucleosomes assembled by HJURP. We’ve also used a new approach to establish a new functional centromere at an ectopic locus to understand the relationship between the elements that direct new CENP-A chromatin assembly and the first steps in centromere establishment. These findings led to our landmark development of new types of human artificial chromosomes (HACs) that improve the technology and bring mammalian synthetic chromosomes one step closer to reality in Logsdon et al., 2019.
Logsdon, G.L., C.W. Gambogi, M.A. Liskovykh, E.J. Barrey, V. Larionov, K.H. Miga, P. Heun, and B.E. Black*. 2019. Human artificial chromosomes that bypass centromeric DNA. Cell, 178:624-639. (*corresponding author) [PMCID: PMC6657561]
Logsdon, G.L., E. Barrey, E.A. Bassett, J.E. DeNizio, L.Y. Guo, T. Panchenko, J.M. Dawicki-McKenna, P. Heun, and B.E. Black*. 2015. Both tails and the centromere targeting domain of CENP-A are required for centromere establishment. J. Cell Biol., 208:521-531. (*corresponding author) [PMCID: PMC4347640]
Hasson, D. †, T. Panchenko†, K.J. Salimian†, M.U. Salman, N. Sekulic, A. Alonso, P.E. Warburton, and B.E. Black*. 2013. The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat. Struct. Mol. Biol., 20:687-695. (*corresponding author; †contributed equally and listed in alphabetical order) [PMCID: PMC3760417]
Bassett, E.A., J. DeNizio, M.C. Barnhart-Dailey, T. Panchenko, N. Sekulic, D.J. Rogers, D.R. Foltz, and B.E. Black*. 2012. HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/ histone H4 for centromere assembly. Dev. Cell, 22: 749-762. (*corresponding author) [PMCID: PMC3353549]
Black, B.E.*, and D.W. Cleveland*. 2011. Epigenetic centromere propagation and the nature of CENP-A nucleosomes. Cell, 144:471-479. (*corresponding authors) [PMCID: PMC3061232]
4. Hydrogen/deuterium exchange-mass spectrometry (HXMS) with chromatin proteins. My group has emerged as the world leader in applying HXMS to chromatin-associated proteins. This powerful approach probes structure and dynamics in solution, and is a strong complement to more conventional structural biology techniques. We have used it successfully to gain insight into a diverse set of chromatin assembly complexes and natively unstructured nucleosomal DNA binding proteins, gaining insight into complexes that have been recalcitrant to other standard approaches (e.g. crystallography and NMR). Along the way we have advanced HXMS technology and dispelled the earlier misconceptions that the approach is low-resolution (it is not, and we have achieved near amino acid resolution of HX behavior on several proteins) and merely a probe of what happens on the surfaces of proteins (it is not, and we have gained important insight into the core of individual proteins and proteins within large multi-subunit complexes).
Zandarashvili, L.†, M.F. Langelier†, U.K. Velagapudi, M.A. Hancock, J.D. Steffen, R. Billur, Z.M. Hannan, A.J. Wicks, D.B. Krastev, S.J. Pettitt, C.J. Lord, T.T. Talele, J.M. Pascal*, and B.E. Black*. 2020. Structural basis for allosteric PARP-1 retention on DNA breaks. Science, 368:eaax6367. (*corresponding authors; †contributed equally) [PMCID: PMC7347020]
Langelier, M.F., L. Zandarashvili, P.M. Aguiar, B.E. Black*, and J.M. Pascal*. 2018. NAD+ analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains. Nat. Commun., 9:844. (*corresponding authors) [PMCID: PMC5829251]
Dawicki-McKenna, J.M.†, M.F. Langelier†, J.E. DeNizio, A.A. Riccio, C.D. Cao, K.R. Karch, M. McCauley, J.D. Steffen, B.E. Black*, and J.M. Pascal*. 2015. PARP-1 activation requires local unfolding of an autoinhibitory domain. Mol. Cell, 60:755-768. (*corresponding author; †contributed equally) [PMCID: PMC4712911]
DeNizio, J., S.J. Elsässer, and B.E. Black*. 2014. DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues. Nucleic Acids Res., 42:4318-4331. (*corresponding author) [PMCID: PMC3985662]
Hansen, J.C.*, B.B. Wexler, D.J. Rogers, K.C. Hite, T. Panchenko, S. Ajith, and B.E. Black*. 2011. DNA binding restricts the intrinsic conformational flexibility of Methyl CpG Binding Protein 2 (MeCP2). J. Biol. Chem., 286:18938-18948. (*corresponding authors) [PMCID: PMC3099709]
5. Centromere inheritance through the mammalian germline. This is a relatively recent research direction in my group, and we are already making headway into understanding how the epigenetic centromere mark represented by nucleosomes containing CENP-A is successfully transmitted through the male and female germlines. Both male and female germlines present major challenges to the centromere, and we are using mouse as a model system to understand how this faithfully occurs.
Das, A., A. Iwata-Otsubo, A. Destouni, J.M. Dawicki-McKenna, K.G. Boese, B.E. Black*, and M.A. Lampson*. 2022. Epigenetic, genetic and maternal effects enable stable centromere inheritance. Nat. Cell Biol., 24:748-756. (*corresponding authors) [PMCID: PMC9107508]
Lampson, M.A.*, and B.E. Black*. 2017. Cellular and molecular mechanisms of centromere drive. Cold Spring Harb. Symp. Quant. Biol., 82:249-257. (*corresponding authors) [PMCID: PMC6041145]
Iwata-Otsubo, A. †, J.M. Dawicki-McKenna†, T. Akera, S.J. Falk, L. Chmátal, K. Yang, B.A. Sullivan, R.M. Schultz, M.A. Lampson*, and B.E. Black*. 2017. Expanded satellite repeats amplify a discrete CENP-A nucleosome assembly site on chromosomes that drive in female meiosis. Curr. Biol., 27:2365-2373. (*corresponding authors; †contributed equally) [PMCID: PMC5567862]
Smoak, E.M., P. Stein, R.M. Schultz, M.A. Lampson*, and B.E. Black*. 2016. Long-term retention of CENP-A nucleosomes in mammalian oocytes underpins transgenerational inheritance of centromere identity. Curr. Biol., 26:1110-1116. (*corresponding authors) [PMCID: PMC4846481]
Research Interest
The Black Lab is answering the most pressing questions in chromosome biology, such as:
- How does genetic inheritance actually work?
- How was epigenetic information transmitted to us from our parents?
- Can building new artificial chromosomes help us understand how natural chromosomes work?
- How are the key enzymes protecting the integrity of our genome specifically and potently activated by potential catastrophes like DNA breaks or chromosome misattachment to the mitotic spindle?
We have generated custom Oligopaint probes to precisely target population-defined domains known as TADs in single cells and, using high- and super-resolution microscopy, found evidence for extensive heterogeneity across individual alleles. As this has implications for gene regulation, we discovered that the expression of genes at TAD boundaries are particularly sensitive to reduced cohesin levels in pathological cohesin dysfunction such as in cohesinopathies like Cornelia De Lange Syndrome. We further found that cohesin promotes stochastic boundary bypass between domains for proper expression of boundary-proximal genes. More recently, we found that co-depletion of NIPBL and WAPL, two opposing regulators of cohesin, rescues chromatin misfolding and gene misexpression, consistent with a model in which cohesin levels are balanced by its activity on chromatin.
Research Interest
Our laboratory studies the spatial organization of the genome. We use a combination of cellular, molecular, genetic, and computational tools to elucidate how the structure and position of chromosomes within the nucleus is established and inherited across cell divisions, and how dysfunctional organization contributes to genome instability and disease. We also develop and utilize new technologies that use fluorescent in situ hybridization (FISH) to interrogate chromosome structure at single-cell resolution.
1. My laboratory has pioneered the structure-function analysis of histone acetyltransferases (HATs) and continues to make seminal contributions in this area. Specifically, my laboratory determined the first crystal structure of a type A HAT and characterized its mechanism of catalysis, and the first to describe the mode of histone substrate binding by a HAT. My laboratory has extended our studies to the broader family of N- acetyltransferases including the non-histone lysine acetyltransferases (KATs) and the N-amino acetyltransferases (NATs). We have uncovered important molecular signatures that distinguish HATs, KATs and NATs. My laboratory has also contributed to the development of acetyltransferase inhibitors. The vast majority of the human proteome is acetylated in a functionally important manner and alterations occur in human diseases. This suggests that protein acetylation may rival protein phosphorylation as a biologically important protein modification and that KATs and NATs represent important therapeutic targets.
a. Deng, S., McTiernan, N., Wei, X., Arnesen, T. and Marmorstein, R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK, (2020) Nature Comm., 11: 14584-14587. PMID32042062: PMCID: PMC7010799
b. Deng, S., Pan, B., Gottlieb, L. and Marmorstein, R. Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. (2020) eLife. 9: e57491. PMID32885784
Deng, S., Gottlieb, L., Pan, B., Supplee, J., Wei, Xuepeng, Petersson, E.J. and Marmorstein, R., Molecular mechanism of N-terminal acetylation by the ternary NatC complex. (2021) Structure, S0969-2126. PMID34019809
Gottlieb, L., Guo, L., Shorter, J. and Marmorstein, R. N-alpha-acetylation of Huntingtin protein increases its propensity to aggregate. (2021) J. Biol. Chem., 31: 101363-. PMID34732320
2. My laboratory is studying the molecular basis for how chromatin is assembled and maintain by histone chaperone complexes. We have focused on the binding and histone deposition of H3/H4 complexes by the ASF1 and VPS75 proteins and the multi-subunit HIRA complex, which specifically deposits the histone H3 variant, H3.3, in a replication independent manner. Histone H3.3 is deposited at active genes, after DNA repair and in certain forms of heterochromatin in non-proliferating senescent cells, and recurrent H3.3 mutations are found in pediatric glioblastoma and dysregulation of H3.3-specific activities in tumor growth and leukemia exemplifies the necessity for proper regulation of H3.3-specific deposition pathways. Together with the Peter Adams laboratory we have pioneered a molecular understanding of the HIRA complex highlighting the particular importance of the HIRA and Ubn1 subunits of H3.3-specific activities.
a. Ricketts, M.D., Frederick, B., Hoff. H., Tang, Y., Schultz, D.C. Rai, T.S., Vizioli, M.G. Adams, P.D. and Marmorstein, R. Ubinuclein-1 confers histone H3.3-specific binding specificity by the HIRA histone chaperone complex. (2015) Nature Commun. 6:7711-. PMID: 26159857: PMCID: PMC4509171
b. Haigney, A., Ricketts, M. D. and Marmorstein, R. Dissecting the Molecular Roles of Histone Chaperones in Histone Acetylation by Type B Histone Acetyltransferases (HAT-B), (2015) J. Biol. Chem., 290:30648-30657. PMID: 26522166: PMCID: PMC4683284
c. Ray-Gallet, D., Ricketts, M.D., Sato, Y., Gupta, K., Boyarchuk, E., Senda, T., Marmorstein, R., and Almouzni, G. Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit. (2018) Nat. Commun. 9:3103. PMID:30082790: PMCID: PMC6078998
d. Ricketts, M.D., Dasgupta, N., Fan, J., Han, J., Gerace, M., Tang, Y., Black, B.E., Adams, P.D. and Marmorstein, R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4 and DNA binding activity. (2019) J. Biol. Chem., 294: 9239-9259. PMID:31040182; PMCID: PMC6556585
3. My laboratory has leveraged our expertise in biochemistry and X-ray crystallography with small molecule screening for structure-based Inhibitor development for therapy of melanoma and other cancers. There is a particular interest in melanoma and the laboratory had developed inhibitors to several important oncogenic kinases in melanoma including BRAF, PI3K, PAK1 and S6K1. The laboratory has also targeted the oncoproteins E7 and E6 from human papillomavirus (HPV), the causative agent of a number of epithelial cancers, and a significant portion of head and neck cancers. These studies have important implications for therapy.
a. Qin, J., Rajaratnam, R., Feng, L., Salami, J., Barber-Rotenberg, J.S., Domsic, J., Reyes-Uribe, P., Liu, H., Dang, W., Berger, S.L., Villanueva, J., Meggers, E. and Marmorstein, R. Development of organometallic S6K1 inhibitors. (2015) J. Med. Chem. 58:305-314. PMID: 25356520; PMCID: PMC4289024
b. Grasso, M., Estrada, M.A., Ventocilla, C., Samanta, M., Maksimoska, J., Villanueva, J., Winkler, J.D. and Marmorstein, R. Chemically linked vemurafenib inhibitors promote an inactive BRAFV600E conformation. (2016) ACS Chem. Biol. 11: 2876-2888. PMID: 27571413: PMCID: PMC5108658
c. Emtage, R.P., Schoeberger, M.J. Fergusion, K.M., and Marmorstein, R. Intramolecular autoinhibition of Checkpoint Kinase 1 is mediated by conserved basic motifs of the C-terminal Kinase Associated-1 domain. (2017) J. Biol. Chem. 292:19024-19033. PMID:28972186: PMCID: PMC5704483
d. Grasso, M., Estrada, M.A., Berrios, K.N., Winkler, J.D. and Marmorstein, R. N-(7-Cyano-6-(4-fluro-3-(2-(3-(trifluoromethyl)phenyl)acetamido)phenoxy)benzo[d]thiazol-2-yl)cyclopropanecarboxamide (TAK632) promotes inhibition of BRAF through the induction of inhibited dimers. (2018) J. Med. Chem. 61:5034-5046. PMID: 29727562: PMCID: PMC6540792
4. My laboratory has more recently studied the connection between metabolism with cancer signaling and chromatin regulation, with a particular focus on the acetyl-CoA metabolism and metabolite acylation enzymes such as ATP citrate lyase (ACLY). Our studies uncovered the molecular mechanism of ACLY and provided a molecular scaffold for the structure-based development of ACLY inhibitors for therapy of cancer and metabolic and cardiovascular disorders.
a. Bazilevsky, G.A., Affronti, H.C., Wei, X., Campbell, S.L., Wellen, K.E. and Marmorstein. R. ATP-citrate lyase multimerization is required for coenzyme-A substrate binding and catalysis, (2019) J. Biol. Chem. 294:7529-7268. PMID: 30877197; PMCID: PMC6509486
b. Wei, X., Schultz, K., Bazilevsky, G.A., Vogt, A. and Marmorstein R. Molecular basis of acetyl-CoA production by ATP-citrate lyase. (2020) Nature Structural & Molecular Biology 27:33-41. PMID: 31873304
Wei, X. and Marmorstein, R., Reply to: Acetyl-CoA is produced by the citrate synthetase homology module of ATP-citrate lyase. (2021) Nat. Struct. Mol. Biol., 28: 639-641. PMID34294921
Wei, X., Kixmoeller, K., Baltrusaitis, E., Yang, X. and Marmorstein, R. Allosteric role of a structural NADP+ molecule in glucose-6-phosphate dehydrogenase activity, (2022) Proc. Nat. Acad. Sci. USA, 119(29): e2119695119
Research Interest
The Marmorstein laboratory studies the molecular mechanisms of (1) epigenetic regulation (2) protein post- and co-translational modification with a particular focus on protein acetylation, and (3) enzyme signaling in cancer and metabolism. The laboratory uses a broad range of biochemical, biophysical and structural research tools (X-ray crystallography and cryo-EM) to determine macromolecular structure and mechanism of action. The laboratory also uses high-throughput small molecule screening and structure-based design strategies to develop protein-specific small-molecule probes to interrogate protein function and for preclinical studies.
The Cremins Lab focuses on higher-order genome folding and how chromatin works through long-range, spatial mechanisms to govern neural specification and synaptic plasticity in healthy and diseased neural circuits. We have developed molecular and computational technologies to create kilobase-resolution maps of chromatin folding and have built synthetic architectural proteins to engineer loops with light, together catalyzing new understanding of the genome’s structure-function relationship. We applied our technologies to discover that topologically associating domains (TADs), nested subTADs, and loops undergo marked reconfiguration during neural lineage commitment, somatic cell reprogramming, neuronal activity stimulation, and in models of repeat expansion disorders. We have demonstrated that loops induced by neural circuit activation, engineered through synthetic architectural proteins, and miswired in fragile X syndrome (FXS) are tightly connected to transcription, thus providing early insight into the genome’s structure-function relationship. Moreover, we have also demonstrated that cohesin-mediated loop extrusion can position the location of human replication origins which fire in early S phase, revealing a role for genome structure beyond gene expression in DNA replication. Recently, we have discovered that nearly all unstable short tandem repeat tracts in trinucleotide expansion disorders are localized to the boundaries between TADs, suggesting they are hotspots for pathological instability. We have identified that Mb-scale H3K9me3 domains decorating autosomes and the X chromosome in FXS are exquisitely sensitive to the length of the CGG STR tract. H3K9me3 domains spatially connect via inter-chromosomal interactions to silence synaptic genes and stabilize STRs prone to instability on autosomes. Together, our work uncovers a link between subMegabase-scale genome folding and genome function in the mammalian brain, thus providing the foundation upon which we will dissect the functional role for chromatin mechanisms in governing defects in synaptic plasticity and long-term memory in currently intractable and poorly understood neurological disorders.
Research Interest
The Cremins lab aims to understand how chromatin works through long-range physical folding mechanisms to encode neuronal specification and long-term synaptic plasticity in healthy and diseased neural circuits. We pursue a multi-disciplinary approach integrating data across biological scales in the brain, including molecular Chromosome-Conformation-Capture sequencing technologies, single-cell imaging, optogenetics, genome engineering, induced pluripotent stem cell differentiation to neurons/organoids, and in vitro and in vivo electrophysiological measurements.
Our long-term scientific goal is to dissect the fundamental mechanisms by which chromatin architecture causally governs genome function and, ultimately, long-term synaptic plasticity and neural circuit features in healthy mammalian brains as well as during the onset and progression of neurodegenerative and neurodevelopmental disease states
Our long-term mentorship goal is to develop a diverse cohort of next-generation scientific thinkers and leaders cross-trained in molecular and computational approaches. We seek to create a positive, high-energy environment with open and honest communication to empower individuals to discover and refine their purpose and grow into the best versions of themselves.
We have contributed to the understanding of mechanisms that create and control cell-to-cell variability in gene expression. In particular, our work was amongst the first to use quantitative single molecule RNA detection techniques to describe the phenomenon of transcriptional bursts, in which we found that transcription is a pulsatile process consisting of pulses of activity interspersed with periods when the gene is completely inactive (Raj et al. PLOS Bio 2006, Leveque and Raj Nat Meth 2013a). We also contributed to the mathematical modeling of this field (Raj et al. PLOS Bio 2006). We have now shown how these pulses relate to homeostatic mechanisms that maintain transcript concentration despite changes in cell volume and DNA content (Padovan-Merhar et al. Mol Cell 2015). We have also shown that variability can be used as a tool for dissecting mechanisms of transcriptional control of molecules such as long non-coding RNA (Maamar et al. Genes and Dev. 2013).
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells.PLoS Biol. 2006 Oct;4(10):e309. PubMed PMID: 17048983; PubMed Central PMCID: PMC1563489.
Levesque MJ, Raj A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nat Methods. 2013 Mar;10(3):246-8. doi: 10.1038/nmeth.2372. Epub 2013 Feb 17. Erratum in: Nat Methods. 2013 May;10(5):445. PubMed PMID: 23416756; PubMed Central PMCID: PMC4131260.
Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev. 2013 Jun 1;27(11):1260-71. doi: 10.1101/gad.217018.113. Epub 2013 May 30. PubMed PMID: 23723417; PubMed Central PMCID: PMC3690399.
Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A. Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms. Mol Cell. 2015 Apr 16;58(2):339-52. doi: 10.1016/j.molcel.2015.03.005. Epub 2015 Apr 9. PubMed PMID: 25866248; PubMed Central PMCID: PMC4402149.
We have contributed to the understanding of how cell-to-cell variability can lead to phenotypic consequences. Specifically, we showed that variability in transcription can lead to random cell fate decisions in bacteria (Maamar and Raj et al. Science 2008), and that variability in gene expression can lead to phenotypic variability in metazoan development (Raj and Rifkin et al. Nature 2010). More recently, we have linked gene expression variability to single cell non-genetic resistance mechanisms in melanoma (Shaffer et al. Nature, in press).
Maamar H, Raj A, Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science. 2007 Jul 27;317(5837):526-9. Epub 2007 Jun 14. PubMed PMID: 17569828; PubMed Central PMCID: PMC3828679.
Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 2010 Feb 18;463(7283):913-8. doi: 10.1038/nature08781. PubMed PMID: 20164922; PubMed Central PMCID: PMC2836165.
Shaffer SM, Dunagin M, Torborg S, Torre EA, Emert T, Krepler C, Beqiri M, Sproesser K, Brafford P, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson K, Heryn M, Raj A. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature, in press.
We have contributed to methodological approaches to measuring expression and transcription in single cells via RNA fluorescence in situ hybridization (RNA FISH). First, we developed a method that greatly simplifies the detection of individual RNA molecules by RNA FISH (Raj et al. Nat Meth 2008). We have since pushed the method to high multiplexing in the detection of chromosome structure and gene expression simultaneously (Levesque and Raj, Nat Meth 2013a). We also have enabled the detection of single nucleotide variants on individual RNA molecules (Levesque et al. Nat Meth 2013b), which allows for mutation detection and measurements of allele-specific expression. Further, we have developed an ultra-fast variant of RNA FISH that enables use in diagnostic and point of care settings (Shaffer et al. PLOS ONE 2013).
Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008 Oct;5(10):877-9. doi: 10.1038/nmeth.1253. Epub 2008 Sep 21. PubMed PMID: 18806792; PubMed Central PMCID: PMC3126653.
Levesque MJ, Raj A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nat Methods. 2013 Mar;10(3):246-8. doi: 10.1038/nmeth.2372. Epub 2013 Feb 17. Erratum in: Nat Methods. 2013 May;10(5):445. PubMed PMID: 23416756; PubMed Central PMCID: PMC4131260.
Levesque MJ, Ginart P, Wei Y, Raj A. Visualizing SNVs to quantify allele-specific expression in single cells. Nat Methods. 2013 Sep;10(9):865-7. doi: 10.1038/nmeth.2589. Epub 2013 Aug 4. PubMed PMID: 23913259; PubMed Central PMCID: PMC3771873.
Shaffer SM, Wu MT, Levesque MJ, Raj A. Turbo FISH: a method for rapid single molecule RNA FISH. PLoS One. 2013 Sep 16;8(9):e75120. doi: 10.1371/journal.pone.0075120. eCollection 2013. PubMed PMID: 24066168; PubMed Central PMCID: PMC3774626.
Research Interest
Our lab aims to develop a quantitative understanding of the molecular biology of the cell. Interests include chromosome structure and gene expression, non-coding RNA, and global regulation of gene expression. Applications include genetics, cancer and stem cells.