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Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize
Tong Li1,2, Liangwei Yin1, Claire E Stoll1
1Department of Biology, Miami University, Oxford, Ohio 45056, USA.
Plant Physiology
|September 29, 2022
Summary
Genomic imprinting in maize involves parent-of-origin gene expression, influenced by transposable elements (TEs) and conserved noncoding sequences (CNSs). This study identified numerous imprinted genes and CNSs, revealing insights into epigenetic regulation and relaxed selection.
Area of Science:
- Epigenetics and Genomics
- Plant Molecular Biology
Background:
- Genomic imprinting is an epigenetic phenomenon causing parent-of-origin-specific gene expression.
- In plants, imprinting is linked to transposable elements (TEs), with demethylation of TEs hypothesized to drive imprinting.
Purpose of the Study:
- To investigate the role of transposable elements (TEs) and conserved noncoding sequences (CNSs) in genomic imprinting in maize (Zea mays).
- To identify paternally and maternally expressed imprinted genes (PEGs and MEGs) and imprinted CNSs.
Main Methods:
- High-throughput RNA sequencing of maize endosperms.
- Analysis of endosperms with newly silenced Mutator (Mu) transposons.
- Assessment of DNA methylation and H3K27me3 levels in imprinted regions.
Main Results:
- Identified 110 paternally expressed imprinted genes (PEGs) and 139 maternally expressed imprinted genes (MEGs).
- Found parent-of-origin effects on 407 conserved noncoding sequences (CNSs), largely independent of associated genes.
- Observed relaxed selection on imprinted CNSs and PEGs, with imprinting potentially causing relaxed selection in PEGs.
Conclusions:
- Transposable elements (TEs) and conserved noncoding sequences (CNSs) play crucial roles in maize genomic imprinting.
- Epigenetic modifications, including DNA methylation and H3K27me3, are involved in imprinting regulation.
- Imprinting may contribute to relaxed selection pressures on certain genes.
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