The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements
Abstract Background Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial...
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2019-07-01
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Series: | Genome Biology |
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Online Access: | http://link.springer.com/article/10.1186/s13059-019-1746-8 |
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Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zijuan Li Meiyue Wang Kande Lin Yilin Xie Jingyu Guo Luhuan Ye Yili Zhuang Wan Teng Xiaojuan Ran Yiping Tong Yongbiao Xue Wenli Zhang Yijing Zhang |
spellingShingle |
Zijuan Li Meiyue Wang Kande Lin Yilin Xie Jingyu Guo Luhuan Ye Yili Zhuang Wan Teng Xiaojuan Ran Yiping Tong Yongbiao Xue Wenli Zhang Yijing Zhang The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements Genome Biology Bread wheat Allohexaploid Epigenomic map Chromatin signature Regulatory element Promoter |
author_facet |
Zijuan Li Meiyue Wang Kande Lin Yilin Xie Jingyu Guo Luhuan Ye Yili Zhuang Wan Teng Xiaojuan Ran Yiping Tong Yongbiao Xue Wenli Zhang Yijing Zhang |
author_sort |
Zijuan Li |
title |
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
title_short |
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
title_full |
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
title_fullStr |
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
title_full_unstemmed |
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
title_sort |
bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2019-07-01 |
description |
Abstract Background Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies. Results In the present study, through comprehensive analyses of the open chromatin, DNA methylome, seven major chromatin marks, and transcriptomic data generated for seedlings of allohexaploid wheat, we detected distinct chromatin architectural features surrounding various functional elements, including genes, promoters, enhancer-like elements, and transposons. Thousands of new genic regions and cis-regulatory elements are identified based on the combinatorial pattern of chromatin features. Roughly 1.5% of the genome encodes a subset of active regulatory elements, including promoters and enhancer-like elements, which are characterized by a high degree of chromatin openness and histone acetylation, an abundance of CpG islands, and low DNA methylation levels. A comparison across sub-genomes reveals that evolutionary selection on gene regulation is targeted at the sequence and chromatin feature levels. The divergent enrichment of cis-elements between enhancer-like sequences and promoters implies these functional elements are targeted by different transcription factors. Conclusions We herein present a systematic epigenomic map for the annotation of cis-regulatory elements in the bread wheat genome, which provides new insights into the connections between chromatin modifications and cis-regulatory activities in allohexaploid wheat. |
topic |
Bread wheat Allohexaploid Epigenomic map Chromatin signature Regulatory element Promoter |
url |
http://link.springer.com/article/10.1186/s13059-019-1746-8 |
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doaj-ca0ef10794454298a51d011b8abf91ed2020-11-25T03:02:55ZengBMCGenome Biology1474-760X2019-07-0120111610.1186/s13059-019-1746-8The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elementsZijuan Li0Meiyue Wang1Kande Lin2Yilin Xie3Jingyu Guo4Luhuan Ye5Yili Zhuang6Wan Teng7Xiaojuan Ran8Yiping Tong9Yongbiao Xue10Wenli Zhang11Yijing Zhang12National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesState Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesState Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNational Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesAbstract Background Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies. Results In the present study, through comprehensive analyses of the open chromatin, DNA methylome, seven major chromatin marks, and transcriptomic data generated for seedlings of allohexaploid wheat, we detected distinct chromatin architectural features surrounding various functional elements, including genes, promoters, enhancer-like elements, and transposons. Thousands of new genic regions and cis-regulatory elements are identified based on the combinatorial pattern of chromatin features. Roughly 1.5% of the genome encodes a subset of active regulatory elements, including promoters and enhancer-like elements, which are characterized by a high degree of chromatin openness and histone acetylation, an abundance of CpG islands, and low DNA methylation levels. A comparison across sub-genomes reveals that evolutionary selection on gene regulation is targeted at the sequence and chromatin feature levels. The divergent enrichment of cis-elements between enhancer-like sequences and promoters implies these functional elements are targeted by different transcription factors. Conclusions We herein present a systematic epigenomic map for the annotation of cis-regulatory elements in the bread wheat genome, which provides new insights into the connections between chromatin modifications and cis-regulatory activities in allohexaploid wheat.http://link.springer.com/article/10.1186/s13059-019-1746-8Bread wheatAllohexaploidEpigenomic mapChromatin signatureRegulatory elementPromoter |