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Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize

Overview of attention for article published in Epigenetics & Chromatin, August 2017
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Title
Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize
Published in
Epigenetics & Chromatin, August 2017
DOI 10.1186/s13072-017-0148-y
Pubmed ID
Authors

Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang, Pao-Yang Chen

Abstract

DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5 Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI- and CviQI-digested fragments are precisely enriched in promoters and gene bodies, respectively. We proceeded with comparisons of epigenomes and transcriptomes between shoots and tassels and found that the occurrences of highly methylated, tissue-specific, mCHH islands upstream of transcription start sites (TSSs) were positively correlated with differential gene expression. Furthermore, 5' regulatory regions between TSS and mCHH islands often contain putative binding sites of known transcription factors (TFs) that regulate the flowering process and the timing of the transition from the vegetative to the reproductive phase. By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation. Our ROI-directed RRBS pipeline is eminently applicable to DNA methylation profiling of large genomes. Our results provide novel insights into the tissue-specific epigenomic landscapes in maize, demonstrating that DNA methylation and siRNA and chromatin accessibility constitute a critical, interdependent component that orchestrates the transition from the vegetative to the reproductive phase.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 36 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 36 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 33%
Researcher 6 17%
Student > Bachelor 5 14%
Student > Master 3 8%
Other 2 6%
Other 1 3%
Unknown 7 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 19 53%
Biochemistry, Genetics and Molecular Biology 7 19%
Nursing and Health Professions 1 3%
Immunology and Microbiology 1 3%
Unknown 8 22%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 August 2017.
All research outputs
#10,351,758
of 11,676,441 outputs
Outputs from Epigenetics & Chromatin
#298
of 319 outputs
Outputs of similar age
#221,628
of 262,742 outputs
Outputs of similar age from Epigenetics & Chromatin
#6
of 7 outputs
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