Stephens, G. S. | Search bioRxiv

bioRxiv2026

A user-friendly single-nucleus RNA sequencing pipeline to identify alterations in gene expression in small brain circuits

Single-cell or single-nucleus RNA sequencing are common methods to investigate gene expression. However, to clarify the genes in specific types of cells in a small circuit there are limitations to current approaches. Here we present modifications to standard protocols to overcome the limitations and do so in a manner that will be accessible to novices. Then the modified methods are applied to a question about a small area of the brain, the dentate gyrus (DG) of the mouse, where information about cell types was of interest. The question arose from data acquired in a mouse model of Alzheimers disease where early hyperactivity of the principal cells, granule cells (GCs), was identified that was difficult to explain by existing data. Therefore, we investigated altered gene expression in GCs, and other DG cell types that influence GCs, to identify putative mechanisms. Validations of the modified methods are addressed, comparisons are made to other methods, and comparisons of mouse and human data are presented.

neuroscience↗

bioRxiv2025

Discovery of Small Molecules and a Druggable Groove That Regulate DNA Binding and Release of the AP1 Transcription Factor DeltaFOSB

{Delta}FOSB, a member of the AP1 family of transcription factors, mediates long-term neuroadaptations underlying drug addiction, seizure-related cognitive decline, dyskinesias, and several other chronic conditions. AP1 transcription factors are notoriously difficult to modulate pharmacologically due to the absence of well-defined binding pockets. Here, we identify a novel site on {Delta}FOSB, located outside the DNA-binding cleft, that accommodates small molecules. We show that sulfonic acid-containing compounds bind to this site via an induced-fit mechanism, reorienting side chains critical for DNA binding, and that they may hinder the {Delta}FOSB bZIP -helix from binding to the major groove of DNA. In vivo, direct administration of one such compound, JPC0661, into the brain reduces {Delta}FOSB occupancy at genomic AP1 consensus sites by approximately 60% as determined by CUT&RUN-sequencing. These findings suggest that DNA binding and release by AP1 transcription factors can be controlled via small molecules that dock into a novel site that falls outside of the DNA-binding cleft. Minimal sequence conservation across 29 bZIP domain-containing transcription factors in this druggable groove suggests that it can be exploited to develop AP1-subunit-selective compounds. Our studies thus reveal a novel strategy to design small-molecule inhibitors of {Delta}FOSB and other members of the bZIP transcription factor family.

neuroscience↗