Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations
Justine Lee,
Siwei Chen,
Roudabeh Vakil Monfared,
Pieter Derdeyn,
Kenneth Leong,
Tiffany Chang,
Kevin Beier,
Pierre Baldi,
Amal Alachkar
Affiliations
Justine Lee
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
Siwei Chen
Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA
Roudabeh Vakil Monfared
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
Pieter Derdeyn
Mathematical, Computational, and Systems Biology Program, University of California, Irvine, Irvine, CA, USA
Kenneth Leong
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
Tiffany Chang
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
Kevin Beier
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, School of medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697-4560, USA; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697-4560, USA; Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
Pierre Baldi
Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA; Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA; Corresponding author
Amal Alachkar
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA; Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA; Corresponding author
Summary: Research shows that brain circuits controlling vital physiological processes are closely linked with endogenous time-keeping systems. In this study, we aimed to examine oscillatory gene expression patterns of well-characterized neuronal circuits by reanalyzing publicly available transcriptomic data from a spatiotemporal gene expression atlas of a non-human primate. Unexpectedly, brain structures known for regulating circadian processes (e.g., hypothalamic nuclei) did not exhibit robust cycling expression. In contrast, basal ganglia nuclei, not typically associated with circadian physiology, displayed the most dynamic cycling behavior of its genes marked by sharp temporally defined expression peaks. Intriguingly, the mammillary bodies, considered hypothalamic nuclei, exhibited gene expression patterns resembling the basal ganglia, prompting reevaluation of their classification. Our results emphasize the potential for high throughput circadian gene expression analysis to deepen our understanding of the functional synchronization across brain structures that influence physiological processes and resulting complex behaviors.
