SFARI has been a leader in using whole-genome sequencing (WGS) to interrogate the genetic causes of autism spectrum disorder (ASD). Yet, initial analyses of these data have demonstrated the difficulty in interpreting noncoding variants¹ and highlighted the need for functional interrogation of putative risk variants in noncoding regulatory sequences. It is widely assumed that noncoding variants contribute to ASD by altering gene expression in the brain. However, the historically poor annotation of noncoding sequences in the human genome, and their poorly understood grammar, have rendered the interpretation of noncoding variants challenging.

Over the past decade, Len Pennacchio’s laboratory has made substantial progress toward identifying transcriptional enhancers in the genome at scale and validating their functions in vivo. For example, Pennacchio’s group used chromatin immunoprecipitation-sequencing (ChIP-seq) from mouse and human brain tissues to identify initial collections of developmentally active brain enhancers, and they generated the first high-resolution time-series mapping the brain’s chromatin landscape throughout mouse development². Additionally, Pennacchio’s team has pioneered the use of high-throughput transgenic mouse assays for the in vivo validation of enhancers (e.g., Nord et al.³ ) and used such assays to test >3,000 candidate enhancers to date.

Pennacchio proposes to harness these unprecedented resources to interrogate the consequences of noncoding ASD variants on gene expression. Specifically, his laboratory plans to: 1) perform an integrative analysis of epigenomically predicted brain enhancers and sequence variants from the Simons Simplex Collection to identify regulatory sequences that harbor ASD-associated variants and prioritize them for functional validation; 2) use high-throughput mouse transgenic assays to validate the reference alleles of predicted enhancers in vivo and determine the exact brain regions in which they are normally active; and 3) use these in vivo methods to uncover whether and how ASD-associated sequence variants impact the activity of each validated brain enhancer. Collectively, this work will uncover how noncoding ASD-associated variants alter enhancer function in vivo, improving our mechanistic understanding of how noncoding sequence changes contribute to ASD and providing entry points for downstream therapies.