Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
Huaishun Shen,Huaishun Shen,Hang He,Jigang Li,Jigang Li,Wei Chen,Xuncheng Wang,Lan Guo,Zhiyu Peng,Guangming He,Guangming He,Shangwei Zhong,Shangwei Zhong,Yijun Qi,William Terzaghi,William Terzaghi,Xing Wang Deng,Xing Wang Deng +17 more
TLDR
It is found that increased DNA methylation in both hybrid genomes, possibly directed by the RdDM pathway, may play a role in heterosis and 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids.Abstract:
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in heterosis.read more
Citations
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RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
Marjori Matzke,Rebecca A. Mosher +1 more
TL;DR: RNA-directed DNA methylation, the major small RNA-mediated epigenetic pathway in plants, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
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The expanding world of small RNAs in plants
TL;DR: The biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNas, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation are discussed.
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In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning
TL;DR: The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase, linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin.
Journal ArticleDOI
Correction: Corrigendum: Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids
Li Yang,Bosheng Li,Xiao-yu Zheng,Jigang Li,Mei Yang,Xinnian Dong,Guangming He,Chengcai An,Xing Wang Deng +8 more
TL;DR: The F1 hybrids from two combinations (Col-0 and C24 and Ler & C24) show no heterosis for biotrophic bacteria defence in the authors' study.
Journal ArticleDOI
Genomic and epigenetic insights into the molecular bases of heterosis
Z. Jeffrey Chen,Z. Jeffrey Chen +1 more
TL;DR: Genetic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids.
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