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A computational workflow to identify allele-specific expression and epigenetic modification in maize.

Xiaoxing Wei1, Xiangfeng Wang

  • 1Department of Basic Medicine, Medical College of Qinghai University, Xining 810016, China.

Genomics, Proteomics & Bioinformatics
|July 30, 2013
PubMed
Summary

This study introduces a computational framework to identify allele-specific gene expression in hybrid maize. The method links gene expression patterns with epigenetic modifications, aiding in understanding hybrid vigor.

Keywords:
Allele-specific expressionEpigenetic modificationHybrid maizeIllumina sequencingPoisson model

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Area of Science:

  • Genomics
  • Plant Biology
  • Computational Biology

Background:

  • Allele-specific expression (ASE) is influenced by cis-elements and epigenetic modifications.
  • ASE is a potential contributor to heterosis (hybrid vigor) in plants.
  • Understanding ASE in hybrids is crucial for crop improvement.

Purpose of the Study:

  • To develop a computational framework for identifying allele-specifically expressed genes in hybrid maize.
  • To simultaneously analyze allele-specific gene expression and epigenetic modifications.
  • To investigate the relationship between ASE and epigenetic landscape in maize hybrids.

Main Methods:

  • Utilized Illumina high-throughput sequencing for transcriptomics, H3K27me3 histone modification, and DNA methylation data in hybrid maize seedlings.
  • Developed a computational pipeline to detect nucleotide polymorphisms and structural variations for distinguishing parental alleles.
  • Employed a modified Chi-square test based on the Poisson distribution to identify allele-specific expression and epigenetic modifications.

Main Results:

  • Successfully identified allele-specifically expressed genes by integrating gene expression and epigenetic data.
  • Characterized the epigenetic modification landscape associated with allele-specific gene expression in maize hybrids.
  • The framework effectively distinguishes paternally and maternally derived sequencing reads.

Conclusions:

  • The developed computational framework provides a robust method for studying allele-specific gene expression and its epigenetic regulation in hybrid maize.
  • This approach can help elucidate the genetic and epigenetic basis of heterosis.
  • Further research can leverage this framework to explore ASE in other plant species and hybrid systems.