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Related Experiment Videos

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network.

Xiangyu Pan1, Zhaoxia Ma2, Xinqi Sun2

  • 1Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Department of Medical Research, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.

Genomics, Proteomics & Bioinformatics
|December 9, 2022
PubMed

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Summary
This summary is machine-generated.

Researchers developed a new method to study gene regulatory networks (GRNs) in developing ruminant stomachs. This approach identified key genetic elements and transcription factors crucial for rumen development and innovation.

Area of Science:

  • Developmental Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Trait innovation arises from genetic information processed through gene regulatory networks (GRNs) during development.
  • Understanding the evolution of complex traits like the ruminant stomach requires integrating genetic and developmental data.

Purpose of the Study:

  • To develop a method (CNEReg) for interpreting conserved non-coding elements (CNEs) and integrating multi-omics data into GRNs.
  • To investigate the genetic basis of ruminant multi-chambered stomach innovation during development.

Main Methods:

  • Generated paired expression and chromatin accessibility data during sheep rumen and esophagus development.
  • Developed a conserved non-coding element interpretation method (CNEReg) to build a developmental GRN.
Keywords:
Conserved non-coding elementGene regulatory networkRuminantToolkit transcription factorTrait innovation

Related Experiment Videos

  • Identified ruminant-specific CNEs (active-RSCNEs) and toolkit transcription factors (TTFs) regulating rumen development.

    • Main Results:

    • Identified 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs).
    • Constructed a developmental GRN comprising 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.
    • Discovered 6 TTFs and 16 active-RSCNEs that functionally distinguish the rumen from the esophagus.

    Conclusions:

    • The CNEReg method provides a systematic approach to understanding gene regulation evolution in complex traits.
    • Specific TTFs and active-RSCNEs play critical roles in the evolutionary innovation of the ruminant stomach.
    • This study integrates evo-devo concepts with developmental multi-omics data to explain trait evolution.