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Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm
Published on: January 28, 2011
Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis
Huy Q Dinh1, Manu Dubin, Fritz J Sedlazeck
1Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna, Vienna, Austria.
Plos One
|August 23, 2012
Summary
A new method called BiSS (Bisulfite Sequencing Scorer) improves whole genome DNA methylation mapping. It analyzes more cytosine sites and provides a more accurate methylation rate for plants like Arabidopsis.
Area of Science:
- Epigenetics
- Genomics
- Bioinformatics
Background:
- Bisulfite sequencing (BS-Seq) is crucial for mapping DNA methylation at single base resolution.
- Previous BS-Seq analysis of Arabidopsis flower buds yielded the first complete methylome with a 6.7% methylation rate.
- Existing read mapping methods for BS-Seq data have limitations.
Purpose of the Study:
- To introduce BiSS (Bisulfite Sequencing Scorer), a novel method for mapping bisulfite-converted sequencing reads.
- To develop an adaptive error estimation model for BS-Seq data analysis.
- To re-analyze the Arabidopsis methylome using BiSS for improved accuracy and information extraction.
Main Methods:
- BiSS utilizes Smith-Waterman alignment for mapping bisulfite-converted reads to a reference genome.
- An adaptive error estimation accounts for sequencing, bisulfite conversion, and mapping errors.
- The method was applied to existing Arabidopsis flower bud methylome data.
Main Results:
- BiSS mapped significantly more reads to the reference genome compared to previous methods.
- It identified the methylation status of an additional 10% of cytosines.
- The estimated whole genome methylation rate for Arabidopsis flower buds was revised to 7.7%.
Conclusions:
- BiSS offers a more comprehensive analysis of BS-Seq data, exploring it more extensively.
- The method provides a more accurate methylome map and methylation rate.
- BiSS enhances downstream analysis by providing methylation status and degree estimates for each genomic site.
