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Guan Y, Zhou M, Zhang C, Han Z, Zhang Y, Wu Z, Zhu Y. Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton. PLANTS (BASEL, SWITZERLAND) 2024; 13:2079. [PMID: 39124197 PMCID: PMC11314067 DOI: 10.3390/plants13152079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed ITGs in G. hirsutum cotton, through transcriptome profiling based on deep sequencing data, as well as chromatin immunoprecipitation, followed by sequencing (ChIP-seq) of histone modifications and how the ITGs evolved. Totals of 17,567 and 8249 ITGs were identified in G. hirsutum and Gossypium arboreum, respectively. The expression of ITGs in G. hirsutum was significantly higher than that in G. arboreum. Moreover, longer exons were observed in G. hirsutum ITGs. Notably, 42.3% of the ITGs from G. hirsutum were generated by the long terminal repeat (LTR) insertions, while their proportion in genic genes was 19.9%. The H3K27ac and H3K4me3 modification proportions and intensities of ITGs were equivalent to genic genes. The H3K4me1 modifications were lower in ITGs. Additionally, evolution analyses revealed that the ITGs from G. hirsutum were mainly produced around 6.6 and 1.6 million years ago (Mya), later than the pegged time for genic genes, which is 7.0 Mya. The characterization of ITGs helps to elucidate the evolution of cotton genomes and shed more light on their biological functions in the transcriptional regulation of eukaryotic genes, along with the roles of histone modifications in speciation and diversification.
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Affiliation(s)
- Yongzhuo Guan
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingao Zhou
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Congyu Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zixuan Han
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yinbao Zhang
- Xinjiang Jinfengyuan Seed Co., Ltd., Aksu City 843100, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430072, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
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Zhang A, Wei Y, Shi Y, Deng X, Gao J, Feng Y, Zheng D, Cheng X, Li Z, Wang T, Wang K, Liu F, Peng R, Zhang W. Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2021; 12:761059. [PMID: 34975944 PMCID: PMC8714964 DOI: 10.3389/fpls.2021.761059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Cotton is an excellent model for studying crop polyploidization and domestication. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenomes in allotetraploid cotton. However, the detailed profiling and functional characterization of broad H3K4me3 and H3K27me3 are still understudied in cotton. In this study, we conducted H3K4me3- and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating the expression of genes between A and D subgenomes, respectively. More importantly, H3K4me3 exhibited enrichment level-, position-, and distance-related impacts on expression levels of related genes. Distinct GO term enrichment occurred between A/D-specific and homeologous genes with broad H3K4me3 enrichment in promoters and gene bodies, suggesting that broad H3K4me3-marked genes might have some unique biological functions between A and D subgenome. An anticorrelation between H3K27me3 enrichment and expression levels of homeologous genes was more pronounced in the A subgenome relative to the D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3 and H3K27me3 marks can indirectly influence gene expression through regulatory networks with TF mediation. Thus, our study provides detailed insights into functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfunctionalization of homeologous genes, therefore serving as a driving force for polyploidization and domestication in cotton.
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Affiliation(s)
- Aicen Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Yangyang Wei
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Xiaojuan Deng
- College of Agronomy, Xinjiang Agricultural University, Ürümqi, China
| | - Jingjing Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
| | - Zhaoguo Li
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tao Wang
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Kunbo Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Renhai Peng
- Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China
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Islam MT, Wang LC, Chen IJ, Lo KL, Lo WS. Arabidopsis JMJ17 promotes cotyledon greening during de-etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings. THE NEW PHYTOLOGIST 2021; 231:1023-1039. [PMID: 33666236 DOI: 10.1111/nph.17327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored. Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype. Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitation-quantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay. JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during de-etiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.
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Affiliation(s)
- Md Torikul Islam
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Long-Chi Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
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Ma X, Zhao H, Yan H, Sheng M, Cao Y, Yang K, Xu H, Xu W, Gao Z, Su Z. Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data. Comput Struct Biotechnol J 2021; 19:2708-2718. [PMID: 34093986 PMCID: PMC8131310 DOI: 10.1016/j.csbj.2021.04.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/07/2023] Open
Abstract
Bamboo, one of the most crucial nontimber forest resources worldwide, has the capacity for rapid growth. In recent years, the genome of moso bamboo (Phyllostachys edulis) has been decoded, and a large amount of transcriptome data has been published. In this study, we generated the genome-wide profiles of the histone modification H3K4me3 in leaf, stem, and root tissues of bamboo. The trends in the distribution patterns were similar to those in rice. We developed a processing pipeline for predicting novel transcripts to refine the structural annotation of the genome using H3K4me3 ChIP-seq data and 29 RNA-seq datasets. As a result, 12,460 novel transcripts were predicted in the bamboo genome. Compared with the transcripts in the newly released version 2.0 of the bamboo genome, these novel transcripts are tissue-specific and shorter, and most have a single exon. Some representative novel transcripts were validated by semiquantitative RT-PCR and qRT-PCR analyses. Furthermore, we put these novel transcripts back into the ChIP-seq analysis pipeline and discovered that the percentages of H3K4me3 in genic elements were increased. Overall, this work integrated transcriptomic data and epigenomic data to refine the annotation of the genome in order to discover more functional genes and study bamboo growth and development, and the application of this predicted pipeline may help refine the structural annotation of the genome in other species.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hansheng Zhao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.,College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hao Xu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Ranawaka B, Tanurdzic M, Waterhouse P, Naim F. An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant. Mol Biol Rep 2020; 47:9499-9509. [PMID: 33237398 PMCID: PMC7723940 DOI: 10.1007/s11033-020-06013-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/16/2020] [Indexed: 10/26/2022]
Abstract
All flowering plants have evolved through multiple rounds of polyploidy throughout the evolutionary process. Intergenomic interactions between subgenomes in polyploid plants are predicted to induce chromatin modifications such as histone modifications to regulate expression of gene homoeologs. Nicotiana benthamiana is an ancient allotetraploid plant with ecotypes collected from climatically diverse regions of Australia. Studying the chromatin landscape of this unique collection will likely shed light on the importance of chromatin modifications in gene regulation in polyploids as well its implications in adaptation of plants in environmentally diverse conditions. Generally, chromatin immunoprecipitation and high throughput DNA sequencing (ChIP-seq) is used to study chromatin modifications. However, due to the starchy nature of mature N. benthamiana leaves, previously published protocols were unsuitable. The higher amounts of starch in leaves that co-precipitated with nuclei hindered downstream processing of DNA. Here we present an optimised ChIP protocol for N. benthamiana leaves to facilitate comparison of chromatin modifications in two closely related ecotypes. Several steps of ChIP were optimised including tissue harvesting, nuclei isolation, nuclei storage, DNA shearing and DNA recovery. Commonly available antibodies targeting histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 9 dimethylation (H3K9me2) histone modifications were used and success of ChIP was confirmed by PCR and next generation sequencing. Collectively, our optimised method is the first comprehensive ChIP method for mature starchy leaves of N. benthamiana to enable studies of chromatin landscape at the genome-wide scale.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Peter Waterhouse
- Centre for Agriculture and Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Fatima Naim
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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Foroozani M, Zahraeifard S, Oh DH, Wang G, Dassanayake M, Smith AP. Low-Phosphate Chromatin Dynamics Predict a Cell Wall Remodeling Network in Rice Shoots. PLANT PHYSIOLOGY 2020; 182:1494-1509. [PMID: 31857425 PMCID: PMC7054884 DOI: 10.1104/pp.19.01153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exacerbates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin dynamics involved in regulating P homeostasis have not been determined. Here we define distinct chromatin states across the rice (Oryza sativa) genome by integrating multiple chromatin marks, including the H2A.Z histone variant, H3K4me3 modification, and nucleosome positioning. In response to P starvation, 40% of all protein-coding genes exhibit a transition from one chromatin state to another at their transcription start site. Several of these transitions are enriched in subsets of genes differentially expressed under P deficiency. The most prominent subset supports the presence of a coordinated signaling network that targets cell wall structure and is regulated in part via a decrease of H3K4me3 at transcription start sites. The P starvation-induced chromatin dynamics and correlated genes identified here will aid in enhancing P use efficiency in crop plants, benefitting global agriculture.
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Affiliation(s)
- Maryam Foroozani
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Sara Zahraeifard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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Analysis of Epigenetic Modifications During Vegetative and Reproductive Development in Cereals Using Chromatin Immunoprecipitation (ChIP). Methods Mol Biol 2019; 2072:141-156. [PMID: 31541444 DOI: 10.1007/978-1-4939-9865-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The study of heritable genetic changes that do not implicate alterations in the DNA sequence-epigenetics-represents one of the most prolific and expanding fields in plant biology during the last two decades. With a focus on DNA methylation and histone modifications, recent advances also reported the identification of epigenetic regulatory mechanisms that control reproductive development in cereal crop plants. One of the most powerful methods to selectively study interactions between epigenetic factors or specific proteins bound to genomic DNA regions is called chromatin immunoprecipitation (ChIP). ChIP can be widely used to determine the presence of particular histones with posttranslational modifications at specific genomic regions or whether and where specific DNA-binding proteins including transcription factors interact with candidate target genes. ChIP is also an exciting tool to study and compare chromatin states under normal and stress conditions. Here, we present a detailed step-by-step ChIP assay to investigate epigenetic chromatin marks during vegetative and reproductive development in cereals. However, the method described here can be used for all plant tissues and plant species.
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Huang S, Zhang A, Jin JB, Zhao B, Wang TJ, Wu Y, Wang S, Liu Y, Wang J, Guo P, Ahmad R, Liu B, Xu ZY. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. THE NEW PHYTOLOGIST 2019; 223:1372-1387. [PMID: 31038749 DOI: 10.1111/nph.15874] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Under dehydration in plants, antagonistic activities of histone 3 lysine 4 (H3K4) methyltransferase and histone demethylase maintain a dynamic and homeostatic state of gene expression by orientating transcriptional reprogramming toward growth or stress tolerance. However, the histone demethylase that specifically controls histone methylation homeostasis under dehydration stress remains unknown. Here, we document that a histone demethylase, JMJ17, belonging to the KDM5/JARID1 family, plays crucial roles in response to dehydration stress and abscisic acid (ABA) in Arabidopsis thaliana. jmj17 loss-of-function mutants displayed dehydration stress tolerance and ABA hypersensitivity in terms of stomatal closure. JMJ17 specifically demethylated H3K4me1/2/3 via conserved iron-binding amino acids in vitro and in vivo. Moreover, H3K4 demethylase activity of JMJ17 was required for dehydration stress response. Systematic combination of genome-wide chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses revealed that a loss-of-function mutation in JMJ17 caused an ectopic increase in genome-wide H3K4me3 levels and activated a plethora of dehydration stress-responsive genes. Importantly, JMJ17 bound directly to the chromatin of OPEN STOMATA 1 (OST1) and demethylated H3K4me3 for the regulation of OST1 mRNA abundance, thereby modulating the dehydration stress response. Our results demonstrate a new function of a histone demethylase under dehydration stress in plants.
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Affiliation(s)
- Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jing Bo Jin
- Key Laboratory of Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Bo Zhao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yifan Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rafiq Ahmad
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Yan L, Fan G, Li X. Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection. BMC Genomics 2019; 20:234. [PMID: 30898112 PMCID: PMC6429711 DOI: 10.1186/s12864-019-5609-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/14/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Paulownia withes'-broom (PaWB) disease caused by phytoplasma is a serious infectious disease for Paulownia. However, the underlying molecular pathogenesis is not fully understood. Recent studies have demonstrated that histone modifications could play a role in plant defense responses to pathogens. But there is still no available genome-wide histone modification data in non-model ligneous species infected with phytoplasma. RESULTS Here, we provided the first genome-wide profiles of three histone marks (H3K4me3, H3K36me3 and H3K9ac) in Paulownia fortunei under phytoplasma stress by using chromatin immunoprecipitation sequencing (ChIP-Seq). We found that H3K4me3, H3K36me3 and H3K9ac were mainly enriched in the genic regions in P. fortunei with (PFI) and without (PF) phytoplasma infection. ChIP-Seq analysis revealed 1738, 986, and 2577 genes were differentially modified by H3K4me3, H3K36me3 and H3K9ac marks in PFI under phytoplasma infection, respectively. The functional analysis of these genes suggested that most of them were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction. In addition, the combinational analysis of ChIP-Seq and RNA-Seq showed that differential histone methylation and acetylation only affected a small subset of phytoplasma-responsive genes. CONCLUSIONS Taken together, this is the first report of integrated analysis of histone modifications and gene expression involved in Paulownia-phytoplasma interaction. Our results will provide the valuable resources for the mechanism studies of gene regulation in non-model plants upon pathogens attack.
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Affiliation(s)
- Lijun Yan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
| | - Xiaoyu Li
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002 People’s Republic of China
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