Genetics/Genomics

Abstract

CS-7-4 - Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

Sunday, July 15
4:18 PM - 4:38 PM

Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the “landscape” of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify novel regulatory mechanisms has yet to be fully explored. Here, we re-processed the raw data of over five hundred publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments, and also filtered them based on sequencing depth and efficiency of bisulfite conversion. This enabled us to identify high-confidence differentially methylated regions (hcDMRs) by comparing each “test” library to over fifty high-quality “wild-type” controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their impact on DNA methylation. In addition to confirming existing relationships, we revealed novel connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at non-overlapping regions of CMT2 targeted heterochromatin. Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes, and can also be adopted for other omics datasets.


 

Co-Authors

Yu Zhang – Souther University of Science and Technology; Jake Harris – University of California, Los Angeles; QIkun Liu – University of California, Los Angeles; Haifeng Wang – Fujian Agriculture and Forestry University; Steven Jacobsen – University of California, Los Angeles

Jixian Zhai

Associate Professor
Southern University of Science and Technology

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CS-7-4 - Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis



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