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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
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Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism.

Evin M Padhi1, Tristan J Hayeck2,3, Zhang Cheng4

  • 1Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.

Human Genomics
|July 14, 2021
PubMed
Summary

De novo variants (DNVs) in the brain-specific enhancer hs737 are linked to autism. This enhancer targets the EBF3 gene, which is significantly associated with neurodevelopmental disorders (NDDs), offering new insights into NDDs.

Keywords:
AutismDe novoEBF3EnhancerGene regulatory networkGenomeNeurodevelopmental disorderVarianths737

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Area of Science:

  • Genetics
  • Neurodevelopmental Disorders
  • Genomic Regulation

Background:

  • Previous research linked protein-coding de novo variants (DNVs) to neurodevelopmental disorders (NDDs).
  • The role of noncoding DNVs in NDDs was unclear, with only a general increase in genetic burden observed.
  • This study investigated DNVs in functional noncoding elements, specifically brain enhancers.

Purpose of the Study:

  • To identify specific noncoding elements targeted by de novo variants (DNVs) in autism.
  • To investigate the functional consequences of DNVs in enhancers.
  • To understand the role of these enhancers in the genetic architecture of neurodevelopmental disorders (NDDs).

Main Methods:

  • Whole-genome sequencing data from 2671 families with autism were analyzed.
  • A statistical model was adapted to detect DNVs in noncoding regions, focusing on brain enhancers.
  • In vitro assays and epigenomic analyses were used to characterize enhancer function and target genes.

Main Results:

  • An excess of DNVs was identified in the brain-specific enhancer hs737 across discovery, replication, and combined cohorts.
  • DNVs in hs737 were associated with shared phenotypes including male sex, intact cognition, and hypotonia or motor delay.
  • hs737 was found to target the EBF3 gene, which is genome-wide significant for NDDs, and its DNVs reduced enhancer activity in vitro.

Conclusions:

  • De novo variants (DNVs) in the hs737 enhancer are associated with autism.
  • The enhancer hs737 targets the EBF3 gene, a key player in neurodevelopmental disorders (NDDs).
  • This research advances the understanding of noncoding variation's impact on gene regulatory networks in NDDs.