Summary
We are interested in how neurons reshape their epigenomic and transcriptomic architecture. Neurons cannot be replaced through cell division and thus must adapt to survive through stress, aging or neurodegenerative disease. Our research focuses on how neurons regulate RNA splicing and DNA methylation to respond to changes in their environment.
TDP-43 and RNA Splicing
TDP-43 is an RNA-binding protein and splicing repressor, dysregulated in several age-related neurodegenerative diseases including Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD) and Alzheimer’s Disease (AD). During disease, TDP-43 translocates from the nucleus to the cytosol. This loss of nuclear TDP-43 causes novel RNA splicing events, called cryptic exons (CE). Inclusion of a cryptic exon can then reduce levels of the target genes. We depleted TDP-43 from human iPSC-derived neurons and performed epigenomic, transcriptomic, splicing, and proteomic experiments. This multi-omics exploration of TDP-43 has led to several new discoveries, including novel pathologic splicing of an ALS/TDP-associated synaptic gene, UNC13A. We are interested in understanding the physiological roles of cryptic splicing and the effects on protein function.
RNA Splicing in C. elegans
Cryptic splicing varies between cell types, even for ubiquitously expressed genes, suggesting specific regulatory mechanisms. The C. elegans TDP-43 ortholog, TDP-1, is ubiquitously expressed and required for splicing regulation. We are interested in using C. elegans to explore mechanisms regulating the tissue-specificity of cryptic splicing. C. elegans, the free-living nematode is an excellent system for these studies due to their optical accessibility and conserved mechanisms of RNA metabolism and neuronal aging.
Neuronal DNA (de)methylation
DNA demethylation is a gene regulatory mechanism generally correlated with increased gene expression. Most demethylation occurs passively during DNA replication. However, as non-dividing cells, neurons must use active DNA demethylation, which requires removal of the methylated nucleotide and DNA repair through DNA synthesis. We discovered that neurons undergo widespread DNA synthesis at neuronal enhancers to repair recurrent single-stranded DNA breaks at sites of DNA demethylation. We are interested in how neurons use DNA demethylation to regulate gene expression to survive acute stress.