How gene expression is controlled at the RNA level to support cellular function is arguably the most important unsolved problem in molecular biology. Our attention is primarily focused on understanding the proteins that bind to RNA and serve as its effectors and regulators. We are investigating the mechanistic principles and phenotypic impact of RNA-binding proteins in two cellular paradigms: 1) neuronal differentiation and neuronal activity-dependent responses, and 2) stem cell maintenance, with an eye toward a related process of cancer development. We employ a broad range of biochemical, genetic, cellular, and computational approaches to obtain a systems-level understanding of the regulatory roles of protein–RNA complexes. We also develop novel methods combining bioengineering, genome editing, and optogenetics to study how disruption of protein-RNA interactions contributes to neurological disorders.
Gene regulation, Post-transcriptional RNA processing, RNA-binding proteins, Gene transcription, messenger RNA (mRNA), non-coding RNA (ncRNA), transfer RNA (tRNA), RNase P, Epigenetics, Chromatin, Neurobiology, Neurological disorders, Stem cells, Cancer, Optogenetics, Bioengineering, Genome editing
1. RNA-binding proteins: linking gene transcription and post-transcriptional processing
RBPs are best known for their regulation of post-transcriptional processing of RNA, but accumulating evidence suggests that a significant portion of their regulatory output derives from their direct impact on gene transcription. How RNA binding is linked to regulation of gene transcription by RBPs and how post-transcriptional processing by the same RBPs might depend on their transcriptional control is largely unknown. We are interested in transcriptionally active RBPs and the mechanisms through which RNA – RBP complexes regulate gene transcription. Using pluripotent stem cells and mouse as a model organism, we study the roles these complexes play in stem cell self-renewal, differentiation, and cancer development.
2. Evolution of alternative transcriptomes during cell lineage commitment
Cells can produce multiple different proteins from a single gene through selective inclusion or exclusion of exons during maturation of a pre-mRNA into a mature mRNA. This process, referred to as alternative splicing, generates a multitude of qualitatively-different proteomes from a single genome to support the functioning of numerous cell types. We are interested in the earliest alternative splicing events that occur at the time of cell lineage commitment. We would like to understand how such events are differentially regulated from those occurring in the progenitor cells, and how alternative splicing contributes to cell lineage commitment compared to the cooperating 'epigenetic' events. Our current focus is on fate-defining alternative splicing events in the neuronal lineage and their misregulation in neurological disorders.
Alternative splicing in neuronal differentiation.
3. Tool development: methods to study cell-to-cell communication
Defective synaptic connectivity is a common causative feature seen in diverse neurological disorders ranging from early developmental disorders to aging and neurodegeneration. Efforts to understand the pathophysiology of these diseases at the molecular level have traditionally been impeded by the lack of suitable technologies. We are developing microfluidics-based, light-operated platforms that take neuronal connectivity as a readout to facilitate studies of the key contributing molecular processes, for instance, through genetic or chemical screens. Our platforms are based on a micro-patterned solid support that allows for directed growth of physically separated populations of neurons engineered to confer sensitivity to optical stimulation. Using different illumination protocols, this strategy enables
dissection of pre- and postsynaptic contributions of different molecules and pathways to synaptic activity. Using these platforms, our current work in the lab aims to decipher the impact of disease-linked mutations in RBPs on neuronal connectivity.
Directed connections between physically separated presynaptic (P1) and postsynaptic (P2) neuronal populations.
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