scholarly journals Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

2018 ◽  
Vol 115 (5) ◽  
pp. E1069-E1074 ◽  
Author(s):  
Yu Zhang ◽  
C. Jake Harris ◽  
Qikun Liu ◽  
Wanlu Liu ◽  
Israel Ausin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Large Scale ◽  
Bisulfite Conversion ◽  
Quantitative Measurements ◽  
Comparative Epigenomics ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing ◽  
Tremendous Amount ◽  
Dna Methylation Analysis ◽  
Generation Sequencing

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 regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 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 50 high-quality wild-type controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their effect on DNA methylation. In addition to confirming existing relationships, we revealed unanticipated connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at nonoverlapping 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 genomics datasets.

scholarly journals Genome-wide DNA methylation analysis of the porcine hypothalamus-pituitary-ovary axis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Xiao-Long Yuan ◽  
Zhe Zhang ◽  
Bin Li ◽  
Ning Gao ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Genome Wide ◽  
Dna Methylation Analysis

scholarly journals Genome-Wide DNA Methylation Analysis in Male Methamphetamine Users With Different Addiction Qualities

2020 ◽  
Vol 11 ◽  
Author(s):  
Liang Liu ◽  
Tao Luo ◽  
Huixi Dong ◽  
Chenxi Zhang ◽  
Tieqiao Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Genome Wide ◽  
Dna Methylation Analysis

scholarly journals Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles

2020 ◽  
Author(s):  
Benjamin I Laufer ◽  
Hyeyeon Hwang ◽  
Julia M Jianu ◽  
Charles E Mordaunt ◽  
Ian F Korf ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Down Syndrome ◽  
Early Life ◽  
Trisomy 21 ◽  
Bisulfite Sequencing ◽  
Dried Blood Spots ◽  
Whole Genome ◽  
Genome Wide ◽  
Low Pass ◽  
Genome Bisulfite Sequencing

Abstract Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q < 0.05) differentially methylated regions (DMRs) that distinguished DS from typical development and idiopathic developmental delay were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons with previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q < 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q < 0.05) enriched for blood-specific chromatin states. A ~28 kb block of hypermethylation was observed on chromosome 21 in the RUNX1 locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q < 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early life mechanisms of epigenomic dysregulation resulting from trisomy 21.

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