Techniques

The Day Lab uses a broad range of technical approaches to answer questions about the molecular and genetic mechanisms that regulate neuronal function and animal behavior.

Molecular genetics

To examine the individual genes, transcripts, and proteins that regulate neuronal function, we employ molecular biology approaches such as CRISPR-Cas9 gene editing and CRISPR-dCas9 epigenetic editing technology, molecular cloning, RT-qPCR, electrophoretic mobility shift assays, gel electrophoresis, western blotting, whole-genome RNA and DNA sequencing, ATAC-seq, chromatin immunoprecipitation, methylated DNA capture/immunoprecipitation, bisulfite sequencing, single-nucleus RNA-seq, single nucleus ATAC-seq, and spatial transcriptomics.

Key publications:
Savell, et al (2016). Extra-coding RNAs regulate neuronal DNA methylation dynamics. Nature Communications. Link
Savell, et al (2019). A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation. eNeuro. Link
Carullo, et al (2020). Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. Nucleic Acids Research. Link
Phillips, et al (2023). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife. Link

Functional genomics and neurobiology

To examine how neurons respond to environmental manipulations and study how genetic and epigenetic mechanisms alter neuronal function, we employ the molecular tools described above in rodent and human-derived neuronal culture systems. We merge this approach with basic pharmacology, viral manipulations, in vitro multi-electrode array neurophysiological recordings, single-molecule RNA FISH, immunohistochemistry, miscroscopy (epifluorescence and confocal), and single-nucleus RNA-seq.

Key publications:
Savell, Tuscher, Zipperly, Duke, Phillips, et al (2020). A dopamine-induced gene expression signature regulates neuronal function and cocaine response. Science Advances. Link
Phillips, Tuscher, et al (2022). An atlas of transcriptionally defined cell populations in the rat ventral tegmental area. Cell Reports. Link
Phillips, et al (2023). Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine. Molecular and Cellular Neuroscience. Link

systems neuroscience

To examine how molecular and genetic mechanisms regulate the function of intact brain circuits, we combine the approaches described above with in vivo tools including freely moving single-unit electrophysiology, ex vivo slice electrophysiology, optogenetics, stereotaxic surgery, pharmacology, behavioral assays, associative learning tasks, and intravenous drug self-administration approaches.

Key publications:
Zipperly, et al (2020). Regulation of dopamine-dependent transcription and cocaine action by Gadd45b. Neuropsychopharmacology. Link
Bach, et al (2024). Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons. Hippocampus, Link
Brida, et al (2025). Reelin marks cocaine-activated striatal neurons, promotes neuronal excitability, and regulates cocaine reward. Science Advances. Link