Neural stem cells (NSCs) hold promise for the treatment of neurological disorders, and understanding the molecular mechanisms of NSC neurogenesis and gliogenesis is key to unlocking their therapeutic potential. The adult brain - including that of humans - harbors a population of NSCs in the subventricular zone (SVZ). How NSCs 'forget'the epigenetic memory of their stem cell identity and 'learn'the developmental programs for neurogenesis and gliogenesis is poorly understood. Mll1 (Mixed lineage leukemia-1), a chromatin-remodeling factor related to Drosophila Trithorax, can regulate cellular identity by mediating the application or removal of specific chromatin modifications. We previously showed that Mll1 is required for the genesis of neurons - but not glial cells - from postnatal SVZ NSCs (Nature 2009, 458:529- 33). Emerging studies indicate that distinct chromatin signatures at DNA regulatory elements called enhancers determine the transcriptional activity of specific gene promoters, but little is known about how the chromatin-state at enhancers is regulated. In Preliminary Studies, we show that MLL1 promotes the expression of neurogenic genes Dlx2 and Dlx5 by regulating intergenic enhancer elements (manuscript submitted to Nature Cell Bio). Our chromatin analysis supports a model in which MLL1 maintains enhancers in a 'poised'state to facilitate rapid gene activation during neuronal differentiation. Furthermore, we found that MLL1 is required for the localization of JMJD3, a histone demethylase capable of removing repressive trimethylation of histone 3 at lysine 27 (H3K27me3) at poised enhancer elements. To investigate the role of JMJD3 in adult neurogenesis, we studied JMJD3-loss of function in vivo and in vitro with conditional knockout and shRNA-mediate knockdown. Indeed, JMJD3-deficient SVZ NSCs were defective for neurogenesis, but not gliogenesis. Based on these new data, we hypothesize that MLL1 coordinates neuronal differentiation from multipotent NSCs by targeting specific enhancer elements, enabling their rapid activation by the action of JMJD3. In this application, we propose Specific Aims that test this regulatory model, which has broad implications for development in general, and further determine the role of MLL1 in neural development.

Public Health Relevance

Neural stem cells (NSCs) hold promise for the treatment of neurological disorders, and understanding the molecular mechanisms by which NSCs differentiate into neurons and glia is key to unlocking their therapeutic potential. Our goal is to determine the molecular mechanisms that regulate NSC biology. For NSCs to make neurons, daughter cells need to express certain sets of genes while repressing others. Such lineage-specific gene expression is in regulated by chromatin structure - the packaged state of DNA. Recent work in my lab demonstrated that the MLL1 chromatin remodeling factor is required for neuronal differentiation from NSCs. We plan to use cell biology and molecular approaches to investigate how MLL1 and related factors coordinate the production of neurons from NSCs. Data from these proposed studies may advance the development of cell-based therapies for service-related injuries as well as neurodegenerative diseases in our Veteran population.

National Institute of Health (NIH)
Veterans Affairs (VA)
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Cellular and Molecular Medicine (CAMM)
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Veterans Affairs Medical Center San Francisco
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Delgado, Ryan N; Lim, Daniel A (2017) Maintenance of Positional Identity of Neural Progenitors in the Embryonic and Postnatal Telencephalon. Front Mol Neurosci 10:373
Liu, S John; Horlbeck, Max A; Cho, Seung Woo et al. (2017) CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355:
Müller, Sören; Liu, Siyuan John; Di Lullo, Elizabeth et al. (2016) Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol 12:889
Ramos, Alexander D; Attenello, Frank J; Lim, Daniel A (2016) Uncovering the roles of long noncoding RNAs in neural development and glioma progression. Neurosci Lett 625:70-9
Liu, Siyuan John; Nowakowski, Tomasz J; Pollen, Alex A et al. (2016) Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol 17:67
Diaz, Aaron; Liu, Siyuan J; Sandoval, Carmen et al. (2016) SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics 32:2219-20
Rolston, John D; Ramos, Alexander D; Heath, Susan et al. (2015) Thalamotomy-Like Effects From Partial Removal of a Ventral Intermediate Nucleus Deep Brain Stimulator Lead in a Patient With Essential Tremor: Case Report. Neurosurgery 77:E831-6; discussion E836-7
Delgado, Ryan N; Lim, Daniel A (2015) Embryonic Nkx2.1-expressing neural precursor cells contribute to the regional heterogeneity of adult V-SVZ neural stem cells. Dev Biol 407:265-74
Ramos, Alexander D; Andersen, Rebecca E; Liu, Siyuan John et al. (2015) The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell 16:439-447
Park, Dae Hwi; Hong, Sung Jun; Salinas, Ryan D et al. (2014) Activation of neuronal gene expression by the JMJD3 demethylase is required for postnatal and adult brain neurogenesis. Cell Rep 8:1290-9

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