Genetics and Epigenetic Control of Genome Function in Brain Development and Disease
: Epigenetics, Neuroepigenetics, DNA methylation, Chromatin Organization, Genomic Editing, CRISPR, MeCP2, CDKL5, Neurexin, Rett Syndrome, Autism, Major Depression
Description of Research
A fundamental question in Genetics and Neuroscience is how the brain executes genetic programs while maintaining the ability to adapt to the environment. The underlying molecular mechanisms are not well understood, but epigenetic regulation, mediated by DNA methylation and chromatin organization, provides an intricate platform bridging genetics and the environment, and allows for the integration of intrinsic and environmental signals into the genome and subsequent translation of the genome into stable yet adaptive functions in the brain. Impaired epigenetic regulation has been implicated in many neurodevelopmental and neuropsychiatric disorders.
The Zhou laboratory is interested in understanding the epigenetic mechanisms that integrate environmental factors with genetic code to govern brain development and function, elucidating the pathophysiology of specific neurodevelopmental disorders with known genetic causes such as Rett syndrome and CDKL5 deficiency, and illuminating the pathogenesis of selective neuropsychiatric disorders with complex genetic traits such as autism and major depression. We use a variety of cutting-edge genomic technologies, together with cellular and physiological assays in genetically modified mice, to pursue our interests. We aim to ultimately translate our findings into therapeutic development to improve the treatment for neurodevelopmental and neuropsychiatric disorders.
1) Defining the stress-induced epigenetic code underlying depressive-like behaviors
The genetic underpinnings of neuropsychiatric disorders are highly complex, involving multifaceted interactions between risk genes and the environment. It is known that environmental factors such as adverse early life events or chronic traumatic experience confer significantly greater susceptibility to psychiatric conditions later in life. However, the pathogenic mechanisms by which environmental factors interact with genetic programs in the nervous system to trigger psychiatric illness remain poorly understood. Thus, we have developed novel genetically modified mice, and plan to employ the next-generation sequencing and single cell sequencing technologies to identify the stress-induced epigenetic modifications from neuronal cell types of interest, to employ CRISPR-mediated genomic and epigenomic editing techniques to evaluate the causal relationship between stress-induced epigenetic changes and maladaptive behaviors, and to elucidate the key signaling pathways that mediate gene-environment interactions in the brain.
2) Elucidating the molecular basis of Rett Syndrome
Rett Syndrome (RTT) is a neurodevelopmental disorder characterized by developmental regression, motor dysfunction, and cognitive deficits. The majority of RTT cases are associated with mutations on an X-linked gene encoding MeCP2, a methyl-CpG binding protein involved in organizing chromatin and modulating gene expression. To understand the molecular pathogenesis of RTT, we have developed mouse models recapitulating RTT-associated mutations. We found that mice with RTT-associated missense mutations, such as R106W, T158M and T158A, develop RTT-like phenotypes and show deficits in neural circuitry. These mutations decrease the binding of MeCP2 to methylated DNA and concomitantly reduce MeCP2 protein stability, leading to gene expression and cellular morphological changes in a neuronal cell type-specific manner (Ref). We aim to define the role of methyl-DNA binding of MeCP2 in protein stability, delineate the cellular origin of impaired neural circuitry, and elucidate the mechanisms by which MeCP2 modulates neuronal cell-type specific function.
3) Understanding the pathogenic mechanisms of CDKL5 deficiency
CDKL5 deficiency is a disorder caused by genetic defects in the the X-linked gene encoding cyclin-dependent kinase-like 5 (CDKL5). Patients with CDKL5 dysfunction show early onset intractable seizures and severe neurodevelopmental impairment, and are frequently diagnosed with a number of disorders including Infantile Spasms, West Syndrome, Lennox-Gastaut, atypical Rett Syndrome, and autism. To gain insight into the pathogenic mechanisms underlying CDKL5-related disorders, we have developed mouse models in which the CDKL5 gene is ablated or modified. We found that loss of functional CDKL5 disrupts multiple signal transduction pathways, impairs hippocampal event-related potentials, and leads to autistic-like phenotypes in mice. We plan to identify the molecular targets of CDKL5, dissect the signaling cascades responsible for cardinal autistic-like phenotypes, and investigate the neural mechanisms by which CDKL5 dysfunction leads to early onset seizures and cognitive deficits.
4) Exploring the coding and decoding of the methylome in neurons
Cytosine methylation (5mC), mostly at CpG dinucleotides in mammals, is a central epigenetic mark essential for development. While we can now profile genome-wide DNA methylation at single-base resolution (sequencing methylome), how the methylome is established and maintained, and how the cell interprets the methylome to affect gene expression and chromatin structure remain poorly understood. Moreover, recent studies have challenged the stability of the methylome in postmitotic neurons and have coupled changes in DNA methylation at specific loci to adaptive behaviors. We are interested in understanding how DNA methylation is coded and decoded genome-wide but with locus-specificity in neurons. Given the high abundance of hydroxymethylcytosine (5hmC) in the brain, we set up to address the functional significance of 5mC and 5hmC in neural development, the role of the methylome in the establishment of neuronal identity, and the molecular mechanisms by which the methylome modulates genome function in the brain.
Experimental Techniques and Themes:
Generation of mouse models using CRISPR or ES cell-based homologous recombination; Epigenetic remodeling using adapted CRISPR-editing systems; Mouse behavioral assessment and characterization; Examination of in vivo neuronal connectivity with confocal microscopy; Analysis of neural circuit function with electrophysiology; Studies of genomics using next-generation and single cell-based high throughput sequencing; Biochemical characterization of signaling transduction pathways; and More
Current Lab Members
Yolanda (Yue) Cui, Research Specialist
Deborah Kwon, Postdoctoral Associate
Andrew Edmondson, Postdoctoral Fellow
Barbara Terzic, NGG Graduate Student
Daniel Connolly, MD/PhD Student in NGG
Jonathan Nofziger, Research Specialist
Erin Nugent, Research Specialist
Nicolas Sarmiento, Undergraduate Research Assistant
Christine Liu, Undergraduate Research Assistant
Dasha Zaitzeva, Undergraduate Research Assistant
Judy Wang (NGG 2010-2014), now Account Executive at Signals Analytics; Brian Johnson (CAMB 2010-2016), now Postdoc Fellow at Stanford University; Kathleen Wood (CAMB 2011-2016), now Clinical Genomic Scientist at Children's Hospital of Philadelphia; Maria Fasolino (NGG 2013-2017), now Postdoc Fellow at the University of Pennsylvania; Sheng Tang (NGG MD/PhD 2015-2018), now Medical student at the University of Pennsylvania Perelman School of Medicine
Darren Goffin (2009-2014), now Assistant Professor and Lecturer at the University of York; Le Zhang (2010-2011), now Associate Research Scientist at Yale University; Erina Hara (2011-2012), now Project Manager at Columbia University Irving Medical Center; Janine Lamonica (2012-2018), now Senior Research Investigator and Project Lead in the Gene Therapy Program at University of Pennsylvania; Yingtao (Jerry) Zhao (2012-2019), now Assistant professor at the New York Institute of Technology
Research Specialists/Post-Baccalaureate Students
Maria Amorim (2009-2010), Graduate Student at Hospital A.C. Camargo; Megan Allen (2009-2011), Graduate Student at Georgetown University; Nicha Ubol (2011-2012), Nursing Student at Rutgers University; Arith Reyes (2012-2013), Medical Student at the Washington University In St. Louis; Hallene Guo (2014-2015), Medical Student at the University of Maryland; Jun Yeop Lee (2013-2015); Medical Student at Mount Sinai Icahn School of Medicine; Jie Zhou (2018-2019), Graduate Student at the University of Connecticut; George Gardner (2018-2019), Medical Subscriber at the Hospital of the University of Pennsylvania
Arith Reyes (2009-2012); Suzie Hong (2010-2013); Naomi Hachen (2010); Bryan Cam (2011-2012); Serena Zhou (2011-2012); Diana Nwokoye (2013); Olivia Rabe (2013); Hallene Guo (2013-2014); Daniel Bu (2013-2016); Katarina Pance (2016-2017); Zhou Zhou (2017); Hansoo Chang (2017); Katherine Sizov (2016-2018)
Connolly D and Zhou Z*: Genomic Insights into MeCP2 Function: A Role for the Maintenance of Chromatin Architecture. Current Opinion in Neurobiology 2019 Notes: Special Issue on "Neural Epigenetics", 2019.
Lamonica JM and Zhou Z*: Disentangling chromatin architecture to gain insights into the etiology of brain disorders. Current Opinion in Genetics and Development 2019 Notes: Special Issue on "Genome Architecture and Expression", 2019.
Tang S#, Terzic B#, Wang I-T, Sarmieto N, Sizov K, Cui Y, Takano H, Marsh ED, Zhou Z* and Coulter DA* (*co-corresponding author): Altered NMDAR Signaling Underlies Autistic-like Features in Mouse Models of CDKL5 Deficiency Disorder. Nature Communications 10: 2655. doi: 10.1038/s41467-019-10689-w. 2019.
Zhao YT, Kwon DY, Johnson BS, Fasolino M, Lamonica JM, Kim YJ, Zhao BS, He C, Vahedi G, Kim TH and Zhou Z*: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains. Genome Research 28(7): 933-942, 2018.
Johnson BS#, Zhao Y#, Fasolino M#, Lamonica JM, Kim YJ, Georgakilas G, Wood KH, Bu D, Cui Y, Goffin D, Vahedi G, Kim TH and Zhou Z*: Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Nature Medicine 23(10): 1203-1214, 2017.
Tang S, Wang I-T, Yue C, Takano H, Terzic B, Pance K, Lee JY, Cui Y, Coulter DA* and Zhou Z* (*co-corresponding author): Loss of CDKL5 in glutamatergic neurons disrupts hippocampal microcircuitry and leads to memory impairment in mice. Journal of Neuroscience 37(31): 7420-7437, 2017.
Kwon DY, Zhao YT, Lamonica JM and Zhou Z*: Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC. Nature Communications 8: 15315. doi: 10.1038/ncomms15315, 2017.
Lamonica JM, Kwon DY, Goffin D, Fenik P, Johnson BS, Cui Y, Guo H, Veasey S and Zhou Z*: Elevating expression of MeCP2 T158M rescues DNA binding and Rett syndrome–like phenotypes. Journal of Clinical Investigation 127(5): 1889-1904, 2017.
Goffin D, Brodkin ES, Blendy JA, Siegel SJ and Zhou Z*: Cellular origins of auditory event-related potential deficits in Rett syndrome. Nature Neuroscience 17(6): 804-806, 2014.
Goffin D, Allen M#, Zhang L#, Amorim M#, Wang IT#, Reyes A, Mercado-Berton A, Ong C, Cohen S, Hu L, Blendy JA, Carlson G, Siegel S, Greenberg ME and Zhou Z*: Rett syndrome mutation MeCP2 T158A disrupts DNA binding, protein stability and ERP responses. Nature Neuroscience 15(2): 274-283, 2012.
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Last updated: 06/20/2019
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