Epigenetics and Noncoding RNAs in Development and Human Diseases

Our research philosophy combines various disciplines (biochemistry, genetics, chemistry, human genetics/genomics, and bioinformatics) to understand the functions and mechanisms of epigenetics and noncoding RNAs in neurodevelopmental and neurodegenerative disorders.

New DNA Modifications in Development and Diseases

5-Methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), has been discovered in mammalian cells, particularly in embryonic stem (ES) cells and neuronal cells.  Because current sequencing methods cannot differentiate 5-mC from 5-hmC, the immediate challenge is to develop robust methods to ascertain the positions of 5-hmC within the mammalian genome, a problem best addressed by adapting a new chemical labeling technology that we have developed. We have shown that 5-hmC in duplex DNA can be specifically labeled with chemically modified glucose, allowing various labeling groups such as biotin to be installed onto 5-hmC.  In this way, we can affinity capture DNA fragments containing the modified 5-hmC and develop sequencing methods to determine the precise locations of 5-hmC. Using this approach, we have mapped the genome-wide distribution of 5-hmC in human ES cells and during neurodevelopment and aging. Currently we focus on the development of new technology to map 5-hmC at single-base resolution as well as  the role of 5-hmC and Tet proteins in normal development and human diseases.

Modulation of the Small RNA Pathway

Small noncoding RNA guides, including microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and endogenous small interfering RNAs (esiRNAs), are 18 to 30 nucleotides in length and can shape diverse cellular pathways. Understanding the mechanism of the small RNA pathway is of great importance. Despite the identification of the major siRNA/miRNA pathway components over the last decade, much more remains to be uncovered about the regulation of the RNAi pathway itself. We are interested in how the small RNA pathway is regulated in general.

Dissection of the RNAi/miRNA pathway using a chemical biology approach

Chemical biology is defined as the use of small molecules to probe gene function, pathways, and cellular phenotypes relevant to health and disease. This approach has proved a powerful tool for dissecting various biological pathways, understanding gene functions, and developing novel therapeutic interventions for human diseases. To dissect cellular components that modulate RNAi using a chemical biology approach, we have developed a novel cell-based assay to monitor the activity of the RNAi pathway. Using this system and an initial collection of 2,000 diversified compounds, we performed a pilot screen and identified several potent RNAi enhancers. We have found that one small molecule, RNAi-E, could enhance siRNA-mediated mRNA degradation and promote the biogenesis of endogenous miRNAs. RNAi-E could facilitate the interaction between TAR RNA-binding protein (TRBP) and RNAs. Furthermore, this RNAi-enhancing activity of RNAi-E is TRBP-dependent. RNAi-E represents the first ever small-molecule enhancer of RNA interference. We are continuing to use our reporter system to identify additional small molecules modulating the RNAi pathway and determine their molecular targets. Our goal is to identify different classes of compounds that could modulate the activity of the RNAi pathway by targeting to distinct components within the pathway.

Crosstalk between small regulatory RNAs and epigenetic regulation in neurogenesis

Neurogenesis in adult mammalian brains occurs throughout life. The cellular basis for adult neurogenesis is adult neural stem cells (aNSCs), which exhibit the two essential properties of stem cells: self-renewal and multipotency. It has been suggested that new neurons in the DG are important for hippocampus-dependent learning. Blocking of adult neurogenesis can lead to deficits in learning and memory. Adult neurogenesis is regulated at many levels by both extrinsic and intrinsic factors, such as genetic and epigenetic programs. The importance of epigenetic regulation in brain development and neurological disorders has been well documented. De novo mutations in MeCP2 give rise to the neurodevelopmental disorder Rett syndrome. Our recent studies have revealed that specific miRNAs could be epigenetically regulated by MeCP2 in aNSCs. We demonstrated that one of the miRNAs regulated by MeCP2, miR-137, modulates the proliferation and differentiation of aNSCs in vitro and in vivo. Overexpression of miR-137 promoted the proliferation of aNSCs, whereas a reduction of miR-137 enhanced aNSC differentiation. We further showed that miR-137 posttranscriptionally repressed the expression of Ezh2, a histone methyltransferase and a member of the Polycomb group (PcG) protein family, which provides the first evidence that crosstalk between miRNA and epigenetic regulation contributes to the modulation of adult neurogenesis.

Fragile X Mental Retardation Protein in MicroRNA pathway and Stem cells

Fragile X syndrome, a common form of inherited mental retardation, is mainly caused by massive expansion of CGG triplet repeats located in the 5’-untranslated region of the fragile X mental retardation -1 (FMR1) gene. In patients with fragile X syndrome, the expanded CGG triplet repeats are hypermethylated and the expression of the FMR1 gene is repressed, which leads to the absence of FMR1 protein (FMRP) and subsequent mental retardation. FMRP is an RNA-binding protein that shuttles between the nucleus and cytoplasm. FMRP has been implicated in protein translation and proposed to be involved in the local regulation of protein synthesis at synapses. However the mechanism regulating synaptic translation is poorly understood. Our finding of biochemical and genetic interactions between FMRP and the microRNA pathway not only opens up an interesting and exciting line of investigation in fragile X syndrome but also provides the first link between the miRNA pathway and human genetic disorders. We are continuing to use fragile X syndrome as a disease model to study microRNA-mediated translational regulation in learning and memory.

We have also explored the role of Fmrp in stem cell biology in both Drosophila and mouse. In Drosophila, we showed that dFmr1 is required for both GSC maintenance and repressing differentiation. Furthermore, we demonstrate that in Drosophila ovary, dFmr1 protein interacts with Argonaute protein 1 (AGO1), a key component of the miRNA pathway. Thus dFmr1 could modulate the fate of GSCs, likely via the miRNA pathway. We also found that the loss of fragile X mental retardation protein (Fmrp) increases the proliferation of and alters the fate specification of adult neural stem cells in mouse. We demonstrated that Fmrp regulates the protein expression of several components critical for aNSC function, including CDK4, cyclin D1, and GSK3β. Dysregulation of GSK3β led to reduced Wnt signaling pathway activity, which altered the expression of neurogenin1 and the fate specification of aNSCs. We will continue to explore the contribution of the altered adult neurogenesis to the pathogenesis of fragile X syndrome in the next several years.

Noncoding RNAs in Neurodegeneration

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a newly identified neurodegenerative disorder that results from the intermediate expansion (55-200 repeats) of trinucleotide CGG repeats in the 5’ UTR of the FMR1 gene. FXTAS is now considered one of the most common inheritable neurodegenerative disorders in males. Our previous work has demonstrated that overproduced riboCGG (rCGG) repeats in the 5’ UTR of FMR1 mRNA are toxic, which provided the first example of RNA itself being sufficient to cause neurodegeneration. Over the last several years, there is growing evidence to suggest that noncoding RNAs could play important roles in several neurodegenerative disorders. Our working model is that, via specific interactions with rCGG repeat-binding protein(s), fragile X premutation rCGG repeats interfere with specific pathway(s) and cause neuronal cell death/neurodegeneration. To test this model, we have recently identified proteins that bind specifically to rCGG repeats, including Pur α and hnRNP A2/B1. We are exploring the molecular basis of rCGG-mediated neurodegeneration and hope that our work might provide a framework for how RNAs are able to cause neurodegeneration in general.