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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Evidence for compensatory evolution within pleiotropic regulatory elements.

Zane Kliesmete1, Peter Orchard1,2, Victor Yan Kin Lee1,3

  • 1Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians Universität München, 82152 Munich, Germany.

Genome Research
|September 10, 2024
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Summary
This summary is machine-generated.

Pleiotropy, or gene expression across many tissues, predicts cis-regulatory element (CRE) functional conservation. Highly pleiotropic CREs show conserved accessibility and gene expression, despite lower DNA sequence conservation.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Regulatory Biology

Background:

  • Pleiotropy, defined as gene expression across multiple tissues, is a known predictor of protein sequence and expression conservation.
  • The impact of pleiotropy on the evolution of cis-regulatory elements (CREs) remains less understood.

Purpose of the Study:

  • To investigate the effect of pleiotropy on the evolutionary dynamics of cis-regulatory elements (CREs).
  • To determine if pleiotropy influences the functional conservation of CREs.

Main Methods:

  • Reanalyzed Epigenomics Roadmap data for nine fetal tissues to quantify the pleiotropic degree of nearly 500,000 CREs.
  • Generated ATAC-seq and RNA-seq data from human and macaque samples to assess CRE functional conservation.
  • Analyzed transcription factor binding repertoires and DNA sequence conservation of orthologous sites.

Main Results:

  • CREs with higher pleiotropy exhibited greater conservation in chromatin accessibility and associated gene expression.
  • This trend of increased functional conservation with higher pleiotropy extended to transcription factor binding patterns.
  • Conversely, pleiotropic CREs showed lower DNA sequence conservation compared to species-specific CREs.

Conclusions:

  • Pleiotropy is a significant predictor of functional conservation in cis-regulatory elements (CREs).
  • The apparent lack of sequence conservation in functionally conserved pleiotropic CREs may be due to within-element compensatory evolution.
  • Functional conservation of CREs, influenced by pleiotropy, is not always reflected in direct DNA sequence conservation.