Parallel functional testing identifies enhancers active in early postnatal mouse brain

Jason T. Lambert, Linda Su-Feher, Karol Cichewicz, Tracy L. Warren, Iva Zdilar, Yurong Wang, Kenneth J. Lim, Jessica Haigh, Sarah J. Morse, Cesar P. Canales, Tyler W. Stradleigh, Erika Castillo Palacios, Viktoria Haghani, Spencer Moss, Hannah Parolini, Diana Quintero, Diwash Shrestha, Daniel Vogt, Leah C. Byrne, Alex S. Nord

Research output: Contribution to journalArticlepeer-review


Enhancers are cis-regulatory elements that play critical regulatory roles in modulating developmental transcription programs and driving cell-type specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays (MPRAs) has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted a self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identified and validated putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in the brain.

Original languageEnglish (US)
Article numbere69479
StatePublished - Oct 2021

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


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