Overview
Our DNA represents the full library of genetic information inherited from each of our parents. Typically, the two parental copies of a gene are treated equally in the cell. However, we study a unique class of genes subject to genomic imprinting, an epigenetic phenomenon resulting in genes exclusively or predominantly expressed from a single parental allele. We seek to delineate the basic regulatory mechanisms underlying imprinted gene expression, and in doing so, we expect to uncover principles regarding epigenetic control of gene regulation and chromatin organization that broadly apply across diverse cell types, tissues, and organisms.
The functions of imprinted genes are enriched in biological pathways related to growth, metabolism, and neurological development. This is reflected in the notably high expression of imprinted genes in the placenta and brain, as well as the prominent metabolic and neurodevelopmental phenotypes in imprinted disorders. We seek to characterize the cellular and physiological functions of imprinted genes in the brain, with an emphasis on non-coding RNAs. We expect to find new non-coding RNA functions with direct implications for understanding biological processes dysregulated in imprinted disorders. As evidence of this, our previous studies on an imprinted long non-coding RNA led to the first targeted therapy for Angelman syndrome, now in clinical trials.
Our research program aims to address major open questions in three project areas:
1) Molecular mechanisms controlling imprinted gene expression. [epigenetics, chromatin structure, enhancers]
2) Neuronal functions of imprinted non-coding RNAs. [long non-coding RNAs, microRNAs, small nucleolar RNAs]
3) New therapeutic opportunities for imprinted disorders. [neurodevelopmental disorders, Angelman syndrome, Prader-Willi syndrome]
Our research directions balance hypothesis-driven research using established methods with exploratory research using new high-throughput methods. This enables us to test data driven models while remaining open to unexpected, paradigm-shifting discoveries.
Recent Progress
Therapeutic modulation of an imprinted long non-coding RNA in Angelman syndrome. Imprinted long non-coding RNAs are cis-acting silencers of nearby protein-coding genes and are critically involved in genomic imprinting. In collaboration with Arthur Beaudet’s lab, we showed that neuronal knockdown of a paternally expressed long non-coding RNA unsilenced paternal Ube3a and corrected the molecular deficits in a mouse model of Angelman syndrome (Meng et al. Nature 2015). The successful completion of this proof-of-concept study stimulated the genesis of active Angelman syndrome drug discovery programs at Ionis Pharmaceuticals, Roche, and GeneTx Biotherapeutics. It continues to serve as a paradigm for how fundamental discoveries of non-coding RNAs can be rapidly translated to novel therapeutic strategies. In ongoing efforts, we seek to determine the molecular mechanisms of cis-acting repression by long non-coding RNAs.
Restoration of ube3a protein levels in angelman syndrome mouse brain by delivery of antisense oligonucleotide (ASO) targeting a long non-coding RNA.
Evolutionary insights into imprinted expression of microRNAs. Many imprinted genes with parental bias in expression have antagonistic functions in nutrient control and growth, in agreement with the parental conflict hypothesis. However, the evolutionary pressures driving imprinted expression of non-coding RNAs are not known. We characterized the activity of a large cluster of microRNAs that are maternally expressed in neurons. Using small RNA-seq and AGO2 enhanced crosslinking and immunoprecipitation (eCLIP)-seq, we showed that maternally expressed microRNAs promote silencing of paternally expressed transcripts and inhibit synaptic activity (Whipple et al. Mol Cell 2020). Based on our findings, we propose that imprinted microRNAs increase matrilineal inclusive fitness by antagonizing paternally driven gene programs.
MULTI-ELECTRODE ARRAY AND PATCH CLAMP ELECTROPHYSIOLOGY ON NEURONS WITH CRISPR-MEDIATED DELETION OF MATERNALLY EXPRESSED MICRO RNAS.
A model system for investigating cell type-specific control of imprinted expression. We have developed an accessible model system for examining the mechanisms controlling imprinted expression and the function of imprinted genes during cellular differentiation. We isolated embryonic stem cells (ESCs) from an F1 hybrid cross of divergent mouse strains (M.m.musculus x M.m.castaneus), enabling quantification and manipulation of allelic effects by strain- specific single nucleotide polymorphisms. In order to examine changes in imprinted expression during differentiation, we then integrated a doxycycline-inducible transgene for Neurogenin2, a transcription factor that drives differentiation to functional excitatory ‘induced neurons’ within two weeks. During differentiation, we observed dynamic changes in imprinted expression, similar to previous in vivo findings. We are now using this simple system to identify regulators of cell type-specific imprinted expression.
In vitro differentiation of mouse embryonic stem cells to excitatory glutamatergic neurons by Ngn2 induction (Video by Amanda Whipple)
Seminars
Watch a recording of Amanda Whipple’s seminar presentation on imprinted genes. After reviewing the basics of genomic imprinting, she shares her lab's current work investigating imprinted genes in the brain and applications toward neurodevelopmental disorders like Angelman syndrome.
Watch a recording of Amanda Whipple’s seminar presentation from the Harvard Institute for RNA Medicine (May 2020).
Watch a recording of Amanda Whipple's seminar presentation from the RNA Collaborative (November 2023). After a basic introduction to genomic imprinting, Amanda highlights recent work from the lab exploring the role of chromatin structure in regulating imprinted gene expression.