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Updated: Jul 6, 2025

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Genetic effects of sequence-conserved enhancer-like elements on human complex traits.

Xiang Zhu1,2,3, Shining Ma4,5, Wing Hung Wong6,7

  • 1Department of Statistics, The Pennsylvania State University, 326 Thomas Building, University Park, 16802, PA, USA. xiangzhu@psu.edu.

Genome Biology
|January 3, 2024
PubMed
Summary

Identifying functional DNA elements combining sequence conservation and biochemical activity helps understand complex traits and diseases. This approach improves gene prioritization for conditions like obesity and schizophrenia.

Keywords:
Data integrationEnhancerFine mappingGene prioritizationGenome-wide association studyHeritabilitySequence conservationTissue specificity

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Area of Science:

  • Genomics and Bioinformatics
  • Evolutionary Biology
  • Human Complex Traits

Background:

  • Most human genome-wide association studies (GWAS) findings are in non-coding DNA, hindering mechanistic understanding and clinical application.
  • Evolutionarily conserved and biochemically active non-coding sequences are potential key to interpreting GWAS results.
  • Systematic examination of these functional elements across human tissues and traits is lacking.

Purpose of the Study:

  • To develop a scalable strategy for identifying functional elements with high human-mouse sequence conservation and enhancer-like activity.
  • To assess the role of these elements in the heritability and genetic architecture of complex human traits.
  • To prioritize candidate genes for complex traits using integrated evolutionary and biochemical data.

Main Methods:

  • Developed a strategy to identify functional elements based on sequence conservation and enhancer-like biochemical activity.
  • Applied the strategy to 313 epigenomic datasets across 106 human tissues/cell types.
  • Integrated findings with 468 GWAS datasets from European (EUR) and East Asian (EAS) ancestries.

Main Results:

  • Identified functional elements show significant tissue-specific enrichment of heritability and causal variants for numerous traits.
  • Enrichment was stronger compared to enhancers lacking sequence conservation.
  • Prioritized candidate genes relevant to body mass index (BMI) and schizophrenia, including novel associations.

Conclusions:

  • Sequence-conserved, enhancer-like elements significantly impact complex traits across diverse human tissues.
  • The integrated strategy provides a generalizable approach to elucidate the genetic basis of human diseases.
  • This method enhances understanding of regulatory mechanisms underlying complex traits.