Kostic, S. | Search bioRxiv

bioRxiv2025

Extending cis-regulatory networks using chromatin-RNA interactions

Cis-regulatory networks are essential for determining gene transcriptional states, yet the mechanisms that mediate cellular signaling and enhancer-promoter communications are not yet well understood. Here, we integrate high-resolution enhancer-promoter interactions obtained using targeted chromosome conformation capture and RNA-DNA contacts from RADICL-seq to uncover the role of RNA in modulating enhancer-promoter interactions. Both datasets were generated from human induced pluripotent cells at different stages across neural differentiation. As expected, most enhancer-promoter interactions were dynamic with only 38% shared across all cell states and 68% of promoter interacting regions overlapped at least one annotated neural enhancer. Integration with RADICL-seq data revealed a 9.3-fold enrichment for cis-interacting DNA regions to associate with at least one RNA. Among 18,346 cis-interacting promoters, only 1,170 (6.3%) lacked any RNA association, whereas 3,702 (28%) showed stable RNA association and 13,579 (74%) displayed dynamic RNA association across differentiation. Promoters associated with RNA engaged with higher number of enhancers and exhibited higher expression levels, while enhancers with RNA associations showed higher levels of chromatin activation marks. Promoters with dynamic RNA association were also more likely to be differentially expressed and enriched for relevant biological processes, phenotypes and diseases. Importantly, RNA-DNA association dynamics correlated strongly with DNA-DNA interaction dynamics; gain of RNA association on enhancers was typically accompanied by enhancer-promoter interaction gain, whereas concurrent RNA association gain on both promoter and enhancers frequently led to interaction loss. The correlation of RNA association on cis-interaction dynamics across differentiation were also captured in the community structure of the DNA-RNA network. Together, our results reveal extensive coupling between RNA-DNA and DNA-DNA networks supporting a coordinating role of RNA in gene regulation.

genomics↗

bioRxiv2023

Movement-related increases in subthalamic activity optimize locomotion

The subthalamic nucleus (STN) is traditionally thought to restrict movement. Lesion or prolonged STN inhibition increases movement vigor and propensity, while optogenetic excitation typically has opposing effects. Subthalamic and motor activity are also inversely correlated in movement disorders. However, most STN neurons exhibit movement-related increases in firing. To address this paradox, STN activity was recorded and manipulated in head-fixed mice at rest and during self-initiated and -paced treadmill locomotion. The majority of STN neurons (type 1) exhibited locomotion-dependent increases in activity, with half encoding the locomotor cycle. A minority of neurons exhibited dips in activity or were uncorrelated with movement. Brief optogenetic inhibition of the dorsolateral STN (where type 1 neurons are concentrated) slowed and prematurely terminated locomotion. In Q175 Huntingtons disease mice abnormally brief, low-velocity locomotion was specifically associated with type 1 hypoactivity. Together these data argue that movement-related increases in STN activity contribute to optimal locomotor performance.

neuroscience↗