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Research ArticleLARGE-SCALE BIOLOGY ARTICLE
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Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

Jinlei Han, Pengxi Wang, Qiongli Wang, Qingfang Lin, Zhiyong Chen, Guangrun Yu, Chenyong Miao, Yihang Dao, Ruoxi Wu, James C. Schnable, Haibao Tang, Kai Wang
Jinlei Han
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Pengxi Wang
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Qiongli Wang
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Qingfang Lin
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Zhiyong Chen
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Guangrun Yu
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Chenyong Miao
bCenter for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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Yihang Dao
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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Ruoxi Wu
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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James C. Schnable
bCenter for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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Haibao Tang
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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  • For correspondence: tanghaibao@gmail.com kwang@fafu.edu.cn
Kai Wang
aKey Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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  • For correspondence: tanghaibao@gmail.com kwang@fafu.edu.cn

Published August 2020. DOI: https://doi.org/10.1105/tpc.19.00716

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  • © 2020 American Society of Plant Biologists. All rights reserved.

Abstract

Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.

  • Received September 16, 2019.
  • Revised May 11, 2020.
  • Accepted May 23, 2020.
  • Published May 29, 2020.
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Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses
Jinlei Han, Pengxi Wang, Qiongli Wang, Qingfang Lin, Zhiyong Chen, Guangrun Yu, Chenyong Miao, Yihang Dao, Ruoxi Wu, James C. Schnable, Haibao Tang, Kai Wang
The Plant Cell Aug 2020, 32 (8) 2457-2473; DOI: 10.1105/tpc.19.00716

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Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses
Jinlei Han, Pengxi Wang, Qiongli Wang, Qingfang Lin, Zhiyong Chen, Guangrun Yu, Chenyong Miao, Yihang Dao, Ruoxi Wu, James C. Schnable, Haibao Tang, Kai Wang
The Plant Cell Aug 2020, 32 (8) 2457-2473; DOI: 10.1105/tpc.19.00716
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The Plant Cell: 32 (8)
The Plant Cell
Vol. 32, Issue 8
Aug 2020
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