An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

Ray, J.; Jagoda, E.; Sheth, M. U.; Galante, J.; Amgalan, D.; Gschwind, A. R.; Munger, C. J.; Huang, J.; Munson, G.; Murphy, M.; Mattei, E.; Barry, T.; Singh, V.; Baskaran, A.; Kang, H.; Katsevich, E.; Steinmetz, L. M.; Engreitz, J.

doi:10.1101/2025.09.16.676677

bioRxiv · 10.1101/2025.09.16.676677

An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

Ray, J.·Jagoda, E.·Sheth, M. U.·Galante, J.·Amgalan, D.·Gschwind, A. R.·Munger, C. J.·Huang, J.·Munson, G.·Murphy, M.·Mattei, E.·Barry, T.·Singh, V.·Baskaran, A.·Kang, H.·Katsevich, E.·Steinmetz, L. M.·Engreitz, J.

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Abstract

Identifying the impact of distal regulatory elements on gene expression is a core challenge in human genetics. Large-scale CRISPR screens have not captured lower effect size element-gene interactions due to selection bias and limited statistical power. We developed a framework for highly powered CRISPR screens, consisting of Direct-Capture Targeted Perturb-seq (DC-TAP-seq), unbiased target selection, and a pipeline accounting for statistical power. Surveying 10,000 random distal element-gene pairs revealed most element-gene interactions have effect sizes <10%, which were virtually undetectable in prior studies. Most interactions occur within 100kb, many elements bind CTCF without classical enhancer chromatin, and housekeeping genes have similar frequencies of distal regulatory elements but with weaker effects. We also highlight limitations of predictive models and suggest that new models consider elements with smaller effect sizes. Our study provides an expanded view of distal regulatory elements and a framework for building more comprehensive maps of distal regulation.

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Ray, J., Jagoda, E., Sheth, M. U., Galante, J., Amgalan, D., Gschwind, A. R., Munger, C. J., Huang, J., Munson, G., Murphy, M., Mattei, E., Barry, T., Singh, V., Baskaran, A., Kang, H., Katsevich, E., Steinmetz, L. M., Engreitz, J.. 2025-09-17. An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq. https://doi.org/10.1101/2025.09.16.676677

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