Zhaolan (Joe) Zhou, Ph.D.

Professor, Department of Genetics; Chair, Graduate Program in Genetics and Epigenetics (G&E)

Department of Genetics
University of Pennsylvania School of Medicine
452A Clinical Research Building
415 Curie Blvd
Philadelphia, PA 19104-6145
Fax: 215-573-7760



Research Interest

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 (RTT) and CDKL5 deficiency disorder (CDD), and illuminating the pathogenesis of selective neuropsychiatric disorders with complex genetic traits such as autism and major depressive disorder (MDD). 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.

Contribution to Science

Mechanisms of Gene Regulation. Pre-mRNA splicing is a fundamental step in eukaryotic gene expression. It is conducted by the spliceosome, a large biological machine that was poorly characterized when I started my thesis research. I successfully developed an affinity purification approach and isolated the first functional spliceosome assembled in vitro. In collaboration with other colleagues, we obtained an electron microscopic view of the spliceosome and identified 145 distinct spliceosomal proteins, many of which have known roles in gene transcription, mRNA export and translation. We also discovered that Aly, an mRNA export factor, is specifically recruited to spliced mRNA by the splicing reaction and promotes efficient mRNA export. We further demonstrated the recruitment of Aly is mediated by direct protein-protein interactions with the splicing factor, UAP56. These studies provided mechanistic insight into the well-known phenomenon that intron-containing genes are often expressed more highly in mammalian cells than their cDNA counterparts, and offered the first biochemical evidence that multiple steps of gene expression, such as gene transcription, splicing and export, are functionally coupled.

  • Zhou Z and Reed R* (1998). Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing. EMBO J, 17(7): 2095-106. PMID9524131.
  • Zhou Z#, Luo MJ#, Straesser K, Katahira J, Hurt E and Reed R* (2000). The protein Aly links pre-messenger RNA splicing to nuclear export in metazoans. Nature, 407: 401-405. PMID11014198.
  • Zhou Z, Licklider LJ, Gygi SP and Reed R* (2002). Comprehensive proteomic analysis of the human spliceosome. Nature, 419: 182-185. PMID12226669.
  • Zhou Z, Sim J, Griffith J and Reed R* (2002). Purification and electron microscopic visualization of functional human spliceosomes. Proc Natl Acad Sci USA, 99: 12203-12207. PMID12215496.

Molecular basis of Rett syndrome (RTT). RTT is a debilitating neurodevelopmental disorder caused by mutations in the gene encoding methyl-CpG binding protein 2 (MeCP2). One characteristic feature of RTT is the regression of learned motor and language skills after 6-18 months of normal development. The onset of the disease coincides with synaptic maturation driven by sensory experience in humans. As a postdoctoral fellow, I started to pursue the role of MeCP2 in neuronal activity-dependent gene regulation and investigate the possibility that defective experience-dependent synaptic maturation may underlie the pathogenesis of RTT. I found that MeCP2 is selectively phosphorylated in the brain in a neuronal activity-dependent manner and this event mediates dendritic morphogenesis and spine maturation. Together with other colleagues, we found that activity-dependent phosphorylation of MeCP2 is indispensable for synapse development and function in animal models of Rett syndrome. I went on and led a research team demonstrating that MeCP2 regulates gene expression and neuronal development in a brain region, neuronal cell type and age-specific manner, paving the way to investigate the pathogenesis of Rett syndrome in cell types of interest.

  • Zhou Z#, Hong E#, Cohen S, Zhao W, Ho SY, Chen W, Savner E, Hu L, Steen J, Weitz C and Greenberg ME* (2006). Brain-specific phosphorylation of MeCP2 regulates activity-dependent Bdnf transcription, dendritic growth, and spine maturation. Neuron, 52: 255–269. PMID17046689.
  • Cohen S, Gabel HW, Hutchinson AN, Sadacca LA, Ebert DA, Harmin DA, Greenberg RS, Verdine VK, Zhou Z, Wetsel WC, West AE and Greenberg ME* (2011). Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function. Neuron, 72: 72-85. PMID21982370.
  • Wang IT#, Reyes AR#, and Zhou Z* (2013). Neuronal morphology in MeCP2 mouse models is intrinsically variable and depends on age, cell type, and Mecp2 mutation. Neurobiology of Disease, 58C: 3-12. PMID23659895.
  • Zhao YT#, Goffin D#, Johnson BS# and Zhou Z* (2013). Loss of MeCP2 function is associated with distinct gene expression changes in the striatum. Neurobiology of Disease, 59C: 257-266. PMID23948639.

Pathophysiology of Rett syndrome (RTT). Major advances in RTT research have greatly benefited from studies of knockout, conditional knockout, and conditional rescue mouse models of MeCP2. However, nearly one-third of RTT mutations are missense mutations in the methyl-CpG binding domain (MBD) of MeCP2. To specifically address the contribution of these missense mutations to RTT etiology and provide the research community with clinically relevant mouse models, I led a research team that developed the first knockin mouse model faithfully recapitulating an RTT-associated MeCP2 T158A mutation, and subsequently expanded this to other common mutations such as T158M and R106W. We were the first to demonstrate that missense mutations in the MBD impair MeCP2 binding to methylated DNA in vivo and concomitantly reduce MeCP2 protein stability. Through transgenic studies, we demonstrated that elevating MeCP2 T158M mutant expression improves MeCP2 binding to DNA and significantly ameliorates RTT-like phenotypes, encouraging therapeutic avenues that target MeCP2 protein stability or MeCP2 expression as treatment for RTT. Through studies of these unique mouse models, my lab also found that MeCP2 modulates gene expression in a cellular compartment-dependent and cell type-specific manner. By overcoming X-linked cellular heterogeneity in mosaic female models of RTT, we were the first to uncover cell and non-cell autonomous gene expression changes related to RTT etiology. Our findings have enhanced the understanding of RTT pathogenesis and pointed the field to a direction of examining MeCP2 function in cellular context of clinical interest.

  • Goffin D, Allen M, Amorim M, Zhang L, Wang I-TJ, Reyes A-RS, Mercado-Berton A, Ong C, Cohen S, Hu L, Blendy JA, Carlson G,Siegel S, Greenberg ME and Zhou Z* (2012). Rett Syndrome mutation MeCP2 T158A mutation disrupts DNA binding, protein stability and ERP responses. Nature Neuroscience, 15: 274-283. PMID22119903.
  • GoffinD, Brodkin ES, BlendyJA, SiegelSJ and ZhouZ* (2014). Cellular origins of auditory event-related potential deficits in Rett syndrome. Nature Neuroscience, 17(6): 804-806. PMID24777420.
  • Lamonica JM, Kwon DY, Goffin D, Fenik P, Johnson BS, Cui Y, Guo H, Veasey S and Zhou Z* (2017). Elevating expression of MeCP2 T158M rescues DNA binding and Rett syndrome-like phenotypes. Journal of Clinical Investigation, 127 (5): 1889-1904. PMID28394263.
  • 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 ZhouZ* (2017). Biotin tagging of MeCP2 reveals contextual insights into the Rett syndrome transcriptome. Nature Medicine, 23(10): 1203-1214. PMID28920956.

Pathophysiology of CDKL5 deficiency disorder (CDD). While I was studying MeCP2 phosphorylation and trying to identify its up-stream kinase, several human genetic studies linked mutations in the X-linked gene encoding cyclin-dependent kinase-like 5 (CDKL5) to atypical RTT, a variant with early-onset epileptic features. In vitro biochemistry and cell culture studies supported an interaction between CDKL5 and MeCP2. However, experimental evidence remained contentious. I decided to take a genetic approach and investigate CDKL5 function in vivo, and therefore led a research team in the development and characterization of the first knockout mouse model of CDKL5. My lab found that CDKL5 dysfunction disrupts many key signal transduction pathways and long-range neural circuit communication, leading to CDD-like phenotypes in mice. We then carried out conditional knockout studies to dissect the cellular origin of these phenotypes and uncovered crucial roles for CDKL5 in glutamatergic neurons for learning and memory and in GABAergic neurons for social interaction and repetitive behaviors. We have now developed conditional rescue mouse lines to assess the reversibility of CDD-related phenotypes and knockin mouse models bearing CDD patient mutations to support preclinical studies.

  • Wang IT, Allen M, GoffinD, ZhuX, Fairless AH, Brodkin ES, SiegelSJ, MarshED, BlendyJA, and ZhouZ* (2012). Loss of CDKL5 disrupts kinome profile and ERP response leading to autistic-like phenotypes in mice. Proc Natl Acad Sci USA.109: 21516-21521. PMID23236174.
  • Tang S, Wang I-T, Yue C, Takano H, Terzic B, Pance K, Lee JY, Cui Y, Coulter DA* and Zhou Z* (*co-corresponding) (2017). Loss of CDKL5 in glutamatergic neurons disrupts hippocampal microcircuitry and leads to memory impairment in mice. Journal of Neuroscience, 37(31): 7420-7437. PMID28674172.
  • Tang S#, Terzic B#, Wang I-T, Sarmieto N, Sizov K, Cui Y, Takano H, Marsh ED, Zhou Z* and Coulter DA* (*co-corresponding) (2019): 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. PMID:31201320.
  • Mulcahey PJ#, Tang S#, Takano H#, White A, Davila Portillo DR, Kane OM, Marsh ED, Zhou Z, Coulter DA (2020): Aged heterozygous Cdkl5 mutant mice exhibit spontaneous epileptic spasms. Experimental Neurology 332: 113388. PMID:32585155.

Epigenetic basis of autism and major depressive disorder (MDD). 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 confer significantly greater susceptibility to psychiatric conditions later in life, yet the epigenetic mechanisms by which environmental factors interact with genetic programs in the nervous system remain poorly understood. Sponsored by the Biobehavioral Research Awards for Innovative New Scientists (BRAINS) from NIMH, I led a research team that conceived a novel, Cre-dependent biotinylation strategy and developed a series of genetically modified mice that allow for genome-wide profiling of DNA methylation, histone modifications and RNA expression from cell types of interest, thus overcoming the extensive cellular heterogeneity of the brain. My lab found that long genes implicated in autism harbor broad enhancer-like chromatin domains and causally link chromatin genes to autism etiology. My lab has also developed a computational pipeline to identify an integrated epigenetic code in target cell types and in response to environmental stimuli. Furthermore, to investigate the causal role of stress-induced epigenetic changes to behavioral maladaptation, my research team adopted a modified CRISPR/Cas9 strategy to alter DNA methylation and histone acetylation at loci of interest. Having established a chronic unpredictable stress (CUS) paradigm to induce the expression of MDD-like phenotypes in our genetically modified mice, we are currently in the process of employing genomic and genome-editing expertise to interrogate the epigenetic mechanisms underlying the pathogenesis of MDD.

  • Wood KH, Johnson BS, Welsh SA, Lee JY, Cui Y, Krizman E, Brodkin ES, Blendy JA, Robinson MB, Bartolomei MS and Zhou Z* (2016): Tagging of Methyl-CpG-binding Domain Proteins Reveals Different Spatiotemporal Expression and Supports Distinct Functions. Epigenomics 4: 455-473. PMID27066839.
  • Kwon DY, Zhao YT, Lamonica JM and Zhou Z* (2017). Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC. Nature Communications, 8:15315. Doi:10.1038/ncomms15315. PMID28497787.
  • Zhao YT, Kwon DY, Johnson BS, Fasolino M, Lamonica JM, Kim YJ, Zhao BS, He C, Vahedi G, Kim TH and Zhou Z* (2018). Long genes linked to autism harbor broad enhancer-like chromatin domains. Genome Research, 28:933-942. PMID: 29848492.
  • Kwon DY, Hu P, Zhao Y-T, Beagan JA, Nofziger JH, Cui Y, Xu B, Zaitseva D, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z* (2020): Neuronal YY1 in the prefrontal cortex regulates transcriptionaland behavioral responses to chronic stress. BioRxiv, doi: https://doi.org/10.1101/2020.07.06.190280

Lab Members

Zhaolan (Joe)ZhouPIzhaolan@pennmedicine.upenn.edu
AndrewEdmonsonPostdoctoral Fellowedmondson@email.chop.edu
DavidGoldbergPh.D. Studentgolddc72@pennmedicine.upenn.edu
ErinNugentResearch SpecialistErin.Nugent@pennmedicine.upenn.edu
EmilyShiplettResearch Specialistemily.shiplett@pennmedicine.upenn.edu
Xie PhilipSongPostdoctoral Fellowxie.song@pennmedicine.upenn.edu
Zijie (Jack)xiaPostdoctoral Fellowzijie.xia@pennmedicine.upenn.edu
BingXuPostdoctoral Fellowbingling2002@gmail.com
NishaKrishnanUndergrauate Studentknisha@sas.upenn.edu
GregDonahueSenior Data Analystgdonahue@pennmedicine.upenn.edu
AnnO'Brien JenkinsResearch Specialistaoj@pennmedicine.upenn.edu
NaomiTakenakaMA, Research Specialist, Lab Managerntaken@pennmedicine.upenn.edu
MelindaYinResearch Specialistmelinda.yin@pennmedicine.upenn.edu