Gene expression of the human genome in response to physiological and environmental stimuli is dictated by chemical modifications of the DNA and the DNA-packing histones, as well as transcription factors. This highly complex biological system that operates with a large number and different combinations of epigenetic modifications has defied our full investigation of its basic mechanisms with existing tools. A prime example is the biology of stem cell in which a balance between self-renewal and differentiation lies at the heart of how its chromatin structure enacts different transcriptional programs to instruct pluripotent cell behavior. Yamanaka's reprogramming of somatic cells to induced pluripotent stem cells using four transcription factors Oct3/4, Sox2, Klf4 and c-Myc (OSKM) highlights the ultimate control of cell fate by gene transcription. However, the questions on how the OSKM factors transform the cell's epigenome and how their own expression are controlled during stem cell self-renewal and differentiation are yet to be answered. The functional effects of epigenetic modifications are realized by the binding of epigenome readers such as the acetyl-lysine binding bromodomain and the methyl-lysine binding chromodomain that are present in transcription and chromatin regulators. Unlike RNA interference or gene knockout that entails the removal of an entire protein along with all its interactions, a small-molecule inhibitor (chemical probe) could remove a single interaction in a multi-domain protein in its endogenous form, thus providing a much finer tool for the temporal perturbation of the complex biological system. In this multidisciplinary research project, we will develop high affinity and selective chemical probes for a selected group of bromodomains and chromodomains that function in stem cell biology, either individually (i.e. single-target probes) or as a group in a biological pathway (i.e. multi-target probes). Our study uses a coherent set of structural/chemical biology and chromatin/stem cell biology methods being developed by our key investigators with multidisciplinary expertise. We will also develop an Epigenome Reader KnowledgeBase to aid target profiling, design, production and validation of new chemical probes. To attain these goals, we will achieve the following three specific aims: (1) Target profiling of epigenome readers based on their epigenetic functions;(2) Probe development using target structure-guided strategy;and (3) Probe validation in a functional context of gene transcriptional regulation in stem cell biology.

Public Health Relevance

This study aims to develop new transformative research tools and technologies to tackle the most challenging problems in the current biomedical research, particularly stem cell biology. Therefore, the outcome will empower the research community to determine the fundamental molecular basis of human biology of health and disease.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Pazin, Michael J
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Icahn School of Medicine at Mount Sinai
Schools of Medicine
New York
United States
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Gacias, Mar; Gerona-Navarro, Guillermo; Plotnikov, Alexander N et al. (2014) Selective chemical modulation of gene transcription favors oligodendrocyte lineage progression. Chem Biol 21:841-54
Zeng, Lei; Kuti, Miklos; Mujtaba, Shiraz et al. (2014) Structural insights into FRS2? PTB domain recognition by neurotrophin receptor TrkB. Proteins 82:1534-41
Plotnikov, Alexander N; Yang, Shuai; Zhou, Thomas Jiachi et al. (2014) Structural insights into acetylated-histone H4 recognition by the bromodomain-PHD finger module of human transcriptional coactivator CBP. Structure 22:353-60
Meslamani, Jamel; Smith, Steven G; Sanchez, Roberto et al. (2014) ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. Bioinformatics 30:1481-3
Sanchez, Roberto; Meslamani, Jamel; Zhou, Ming-Ming (2014) The bromodomain: from epigenome reader to druggable target. Biochim Biophys Acta 1839:676-85
Smith, Steven G; Sanchez, Roberto; Zhou, Ming-Ming (2014) Privileged diazepine compounds and their emergence as bromodomain inhibitors. Chem Biol 21:573-83
Shi, Jian; Wang, Yifan; Zeng, Lei et al. (2014) Disrupting the interaction of BRD4 with diacetylated Twist suppresses tumorigenesis in basal-like breast cancer. Cancer Cell 25:210-25
Di Micco, Raffaella; Fontanals-Cirera, Barbara; Low, Vivien et al. (2014) Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes. Cell Rep 9:234-47
Marmorstein, Ronen; Zhou, Ming-Ming (2014) Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol 6:a018762
Lin, Yingjie; Yoo, Seungyeul; Sanchez, Roberto (2012) SiteComp: a server for ligand binding site analysis in protein structures. Bioinformatics 28:1172-3

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