Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China.
Xi-liang
XL
Wang
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China songshh@big.ac.cn husn@big.ac.cn.
Shu-hui
SH
Song
Mudanjiang Youbo Pharmaceutical Co., Ltd, Heilongjiang 157011, China.
Yong-Sheng
YS
Wu
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China.
Yu-Li
YL
Li
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
Ting-ting
TT
Chen
State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China.
Zhi-yuan
ZY
Huang
Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA.
Shuo
S
Liu
Department of Zoology, University of Oxford, UK.
Thomas L
TL
Dunwell
Beckman Research Institute, City of Hope Medical Centre, Duarte, CA 91010, USA.
Gerd P
GP
Pfeifer
School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK.
Jim M
JM
Dunwell
School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK.
Raheema
R
Wamaedeesa
School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK Agricultural Biotechnology Research Institute, Faisalabad 38000, Pakistan.
Ihsan
I
Ullah
Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA Department of Chemistry, University of California, Riverside, CA 92521, USA.
Yinsheng
Y
Wang
Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China songshh@big.ac.cn husn@big.ac.cn.
Song-nian
SN
Hu
D044503:5-Methylcytosine / Q000031:analogs & derivatives; D002853:Chromatography, Liquid; D002874:Chromosome Mapping; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D053719:Tandem Mass Spectrometry
D004251:DNA Transposable Elements; D018744:DNA, Plant; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
5-hydroxymethylcytosine; 5hmC profiles; heterochromatin; rice; transposable element.