scholarly journals Heterochromatin is a quantitative trait associated with spontaneous epiallele formation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yinwen Zhang ◽  
Hosung Jang ◽  
Rui Xiao ◽  
Ioanna Kakoulidou ◽  
Robert S. Piecyk ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Recombinant Inbred Lines ◽  
Three Dimensional ◽  
Feedback Regulation ◽  
Inbred Lines ◽  
Single Base ◽  
Plant Genomes ◽  
Single Base Resolution ◽  
Heterochromatin Silencing

AbstractEpialleles are meiotically heritable variations in expression states that are independent from changes in DNA sequence. Although they are common in plant genomes, their molecular origins are unknown. Here we show, using mutant and experimental populations, that epialleles in Arabidopsis thaliana that result from ectopic hypermethylation are due to feedback regulation of pathways that primarily function to maintain DNA methylation at heterochromatin. Perturbations to maintenance of heterochromatin methylation leads to feedback regulation of DNA methylation in genes. Using single base resolution methylomes from epigenetic recombinant inbred lines (epiRIL), we show that epiallelic variation is abundant in euchromatin, yet, associates with QTL primarily in heterochromatin regions. Mapping three-dimensional chromatin contacts shows that genes that are hotspots for ectopic hypermethylation have increases in contact frequencies with regions possessing H3K9me2. Altogether, these data show that feedback regulation of pathways that have evolved to maintain heterochromatin silencing leads to the origins of spontaneous hypermethylated epialleles.

scholarly journals On the origin and evolutionary consequences of gene body DNA methylation

2016 ◽  
Vol 113 (32) ◽  
pp. 9111-9116 ◽  
Author(s):  
Adam J. Bewick ◽  
Lexiang Ji ◽  
Chad E. Niederhuth ◽  
Eva-Maria Willing ◽  
Brigitte T. Hofmeister ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Recombinant Inbred Lines ◽  
Dna Methyltransferases ◽  
Inbred Lines ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Eutrema Salsugineum ◽  
And Function ◽  
Evolutionary Consequences

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

scholarly journals Bacterial Epigenomics: Coming of Age

mSystems ◽  
2021 ◽  
Author(s):  
Pedro H. Oliveira
Keyword(s):  
Dna Methylation ◽  
Coming Of Age ◽  
Innate Immune ◽  
Physiological Significance ◽  
Single Base ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Single Base Resolution

Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological significance of methylation.

scholarly journals MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data

2014 ◽  
Vol 43 (D1) ◽  
pp. D54-D58 ◽  
Author(s):  
Dong Zou ◽  
Shixiang Sun ◽  
Rujiao Li ◽  
Jiang Liu ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Single Base ◽  
Single Base Resolution ◽  
Generation Sequencing

scholarly journals EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

2019 ◽  
Author(s):  
Romualdas Vaisvila ◽  
V. K. Chaithanya Ponnaluri ◽  
Zhiyi Sun ◽  
Bradley W. Langhorst ◽  
Lana Saleh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Nucleotide Composition ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genomic Features ◽  
Single Base ◽  
Bisulfite Treatment ◽  
Genome Bisulfite Sequencing ◽  
Single Base Resolution

AbstractBisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).

scholarly journals Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress

BMC Genetics ◽  
2014 ◽  
Vol 15 (Suppl 1) ◽  
pp. S9 ◽  
Author(s):  
Dan Liang ◽  
Zhoujia Zhang ◽  
Honglong Wu ◽  
Chunyu Huang ◽  
Peng Shuai ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Drought Stress ◽  
Populus Trichocarpa ◽  
Single Base ◽  
Single Base Resolution

Single-base-resolution methylomes of Populus euphratica reveal the association between DNA methylation and salt stress

2018 ◽  
Vol 14 (6) ◽  
Author(s):  
Yutao Su ◽  
Xiaotao Bai ◽  
Wenlu Yang ◽  
Weiwei Wang ◽  
Zeyuan Chen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Salt Stress ◽  
Populus Euphratica ◽  
Single Base ◽  
Single Base Resolution

scholarly journals QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

PLoS ONE ◽  
2009 ◽  
Vol 4 (2) ◽  
pp. e4318 ◽  
Author(s):  
Sureshkumar Balasubramanian ◽  
Christopher Schwartz ◽  
Anandita Singh ◽  
Norman Warthmann ◽  
Min Chul Kim ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Qtl Mapping ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines

scholarly journals methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser

2014 ◽  
Vol 30 (15) ◽  
pp. 2206-2207 ◽  
Author(s):  
Xin Zhou ◽  
Daofeng Li ◽  
Rebecca F. Lowdon ◽  
Joseph F. Costello ◽  
Ting Wang
Keyword(s):  
Dna Methylation ◽  
Methylation Data ◽  
Visual Integration ◽  
Single Base ◽  
Single Base Resolution
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