Parallel functional testing identifies enhancers active in early postnatal mouse brain

Lambert, JT and Su-Feher, L and Cichewicz, K and Warren, TL and Zdilar, I and Wang, Y and Lim, KJ and Haigh, JL and Morse, SJ and Canales, CP and Stradleigh, TW and Castillo Palacios, E and Haghani, V and Moss, SD and Parolini, H and Quintero, D and Shrestha, D and Vogt, D and Byrne, LC and Nord, AS (2021) Parallel functional testing identifies enhancers active in early postnatal mouse brain. eLife, 10. pp. 1-27. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.69479

Abstract

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.

More Information

Identification Number:	https://doi.org/10.7554/eLife.69479
Status:	Published
Refereed:	Yes
Publisher:	eLife Sciences Publications
Additional Information:	(C) Copyright Lambert et al.
Uncontrolled Keywords:	MPRA, enhancer, genetics, genomics, mouse, neurodevelopment, neuroscience, Animals, Brain, Enhancer Elements, Genetic, High-Throughput Nucleotide Sequencing, Mice, 0601 Biochemistry and Cell Biology,
Depositing User (symplectic)	Deposited by Haigh, Jessica
Date Deposited:	09 Aug 2023 12:51
Last Modified:	29 Aug 2023 10:39
Item Type:	Article