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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
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Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize
Fei-Man Hsu1,2, Ming-Ren Yen2, Chi-Ting Wang2
1Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
Epigenetics & Chromatin
|September 1, 2017
Summary
We developed a cost-effective method to map DNA methylation in maize, revealing how methylation patterns and small RNAs regulate gene expression and the transition to flowering.
Area of Science:
- Plant epigenetics
- Genomics
- Molecular biology
Background:
- DNA methylation is crucial for plant gene regulation.
- Genome-wide DNA methylation profiling in large plant genomes like maize is challenging due to cost.
- Region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) offers an alternative approach.
Purpose of the Study:
- To adapt and apply ROI-directed RRBS for maize DNA methylation profiling.
- To investigate the relationship between DNA methylation, gene expression, and developmental transitions in maize.
Main Methods:
- Developed a computational pipeline for selecting restriction enzymes for ROI-directed RRBS.
- Experimentally validated enzyme selection for enrichment in maize promoters and gene bodies.
- Integrated epigenomic (RRBS, MNase-seq) and transcriptomic data with small RNA sequencing (siRNA-seq).
Main Results:
- Identified tissue-specific methylation patterns (mCHH islands) correlated with differential gene expression.
- Found transcription factor binding sites near mCHH islands involved in flowering regulation.
- Demonstrated tissue-specific accumulation of 21nt-siRNAs in mCHH islands, linked to chromatin accessibility and TF regulation.
Conclusions:
- ROI-directed RRBS is effective for DNA methylation analysis in large plant genomes.
- DNA methylation, siRNAs, and chromatin accessibility are interdependent factors controlling maize vegetative-to-reproductive phase transition.
- Provided new insights into maize epigenomic landscapes and gene regulation.
