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Yan H, Liu Y, Zhang K, Song J, Xu W, Su Z. Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress. Front Genet 2019; 10:306. [PMID: 31001332 PMCID: PMC6456666 DOI: 10.3389/fgene.2019.00306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/20/2019] [Indexed: 11/22/2022] Open
Abstract
Light is essential to plant growth and development. Extended darkness causes dramatic gene expression changes, leading to leaf senescence, hypocotyl growth, petiole elongation, reduced leaf area, and early flowering, etc. However, the underlying mechanism of response to darkness at epigenetic levels remains largely unknown. In this study, we conducted ChIP-seq to generate global epigenomic profiles of H3K4me3 under 3-day extended darkness and normal light conditions in Arabidopsis. We applied chromatin state analysis together with self-organization mapping (SOM) to study the combination of epigenetic regulation under dark stress. The SOM map clusters the segments on the genome according to multiple diverse epigenomic datasets, which breaks the limit of dispersed distribution of epigenetic marks on the genome. Through SOM analysis, we also found that the signals of H3K4me3 were mainly increased after darkness. Analysis of H3K4me3-changed genes together with differentially expressed genes indicated that the genes showing dark-increased H3K4me3 were most involved in senescence and autophagy, and cross-talk existed between dark-induced and natural senescence. In summary, we studied the regulation of the epigenetic H3K4me3 marks of Arabidopsis in response to dark stress using chromatin state and SOM analyses. Our study revealed the regulatory mechanisms of the epigenome in response to dark stress, and SOM analysis based on chromatin states used in our study will also be helpful for other studies on dynamic changes of multiple epigenetic marks.
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Affiliation(s)
- Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.,College of Life Sciences, Qingdao University, Qingdao, China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.,Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - James Song
- Henan Experimental High School, Zhengzhou, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 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: 11] [Impact Index Per Article: 2.2] [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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Xue C, Liu S, Chen C, Zhu J, Yang X, Zhou Y, Guo R, Liu X, Gong Z. Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa. Proteomics 2019; 18. [PMID: 29106068 DOI: 10.1002/pmic.201700036] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/11/2017] [Indexed: 01/26/2023]
Abstract
Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.
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Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Xibin Yang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Rui Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Xiaoyu Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
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Meller B, Kuźnicki D, Arasimowicz-Jelonek M, Deckert J, Floryszak-Wieczorek J. BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2018; 9:1228. [PMID: 30233606 PMCID: PMC6135045 DOI: 10.3389/fpls.2018.01228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 05/23/2023]
Abstract
In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. "Sarpo Mira" to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.
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Affiliation(s)
- Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Deckert
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice. Nat Commun 2018; 9:3516. [PMID: 30158538 PMCID: PMC6115402 DOI: 10.1038/s41467-018-05829-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are essential regulators of gene expression in eukaryotes. Despite increasing knowledge on the function of lncRNAs, little is known about their effects on crop yield. Here, we identify a lncRNA transcribed from the antisense strand of neighbouring gene LRK (leucine-rich repeat receptor kinase) cluster named LAIR (LRK Antisense Intergenic RNA). LAIR overexpression increases rice grain yield and upregulates the expression of several LRK genes. Additionally, chromatin immunoprecipitation assay results indicate H3K4me3 and H4K16ac are significantly enriched at the activated LRK1 genomic region. LAIR binds histone modification proteins OsMOF and OsWDR5 in rice cells, which are enriched in LRK1 gene region. Moreover, LAIR is demonstrated to bind 5' and 3' untranslated regions of LRK1 gene. Overall, this study reveals the role of lncRNA LAIR in regulating rice grain yield and lncRNAs may be useful targets for crop breeding.
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Liu S, Xue C, Fang Y, Chen G, Peng X, Zhou Y, Chen C, Liu G, Gu M, Wang K, Zhang W, Wu Y, Gong Z. Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice. Mol Cell Proteomics 2018; 17:1922-1936. [PMID: 30021883 DOI: 10.1074/mcp.ra118.000640] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/07/2018] [Indexed: 11/06/2022] Open
Abstract
Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. In addition, a genomic localization analysis of histone Kcr by ChIP-seq was performed to assess the relevance between histone Kcr and the genome. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in gene body, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr-facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome and might mark other cis-regulatory DNA elements that are different from IPA1, a transcription activator in rice seedlings. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
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Affiliation(s)
- Shuai Liu
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Chao Xue
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Yuan Fang
- §The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Chen
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Xiaojun Peng
- ¶Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Yong Zhou
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Guanqing Liu
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Kai Wang
- ‖Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenli Zhang
- §The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufeng Wu
- §The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiyun Gong
- From the ‡Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China;
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Traewachiwiphak S, Yokthongwattana C, Ves-Urai P, Charoensawan V, Yokthongwattana K. Gene expression and promoter characterization of heat-shock protein 90B gene (HSP90B) in the model unicellular green alga Chlamydomonas reinhardtii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:107-116. [PMID: 29807581 DOI: 10.1016/j.plantsci.2018.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/11/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
Molecular chaperones or heat shock proteins are a large protein family with important functions in every cellular organism. Among all types of the heat shock proteins, information on the ER-localized HSP90 protein (HSP90B) and its encoding gene is relatively scarce in the literature, especially in photosynthetic organisms. In this study, expression profiles as well as promoter sequence of the HSP90B gene were investigated in the model green alga Chlamydomonas reinhardtii. We have found that HSP90B is strongly induced by heat and ER stresses, while other short-term exposure to abiotic stresses, such as salinity, dark-to-light transition or light stress does not appear to affect the expression. Promoter truncation analysis as well as chromatin immunoprecipitation using the antibodies recognizing histone H3 and acetylated histone H3, revealed a putative core constitutive promoter sequence between -1 to -253 bp from the transcription start site. Our results also suggested that the nucleotides upstream of the core promoter may contain repressive elements such as putative repressor binding site(s).
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Affiliation(s)
- Somchoke Traewachiwiphak
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok 10900, Thailand
| | - Parthompong Ves-Urai
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand; Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kittisak Yokthongwattana
- Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama 6 Rd., Bangkok 10400, Thailand.
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Nguyen NH, Cheong JJ. H2A.Z-containing nucleosomes are evicted to activate AtMYB44 transcription in response to salt stress. Biochem Biophys Res Commun 2018; 499:1039-1043. [DOI: 10.1016/j.bbrc.2018.04.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 11/17/2022]
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Li Y, Xiao J, Chen L, Huang X, Cheng Z, Han B, Zhang Q, Wu C. Rice Functional Genomics Research: Past Decade and Future. MOLECULAR PLANT 2018; 11:359-380. [PMID: 29409893 DOI: 10.1016/j.molp.2018.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/15/2018] [Accepted: 01/23/2018] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.
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Affiliation(s)
- Yan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehui Huang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhukuan Cheng
- National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
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Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
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Xin B, Rohs R. Relationship between histone modifications and transcription factor binding is protein family specific. Genome Res 2018; 28:321-333. [PMID: 29326300 PMCID: PMC5848611 DOI: 10.1101/gr.220079.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/10/2018] [Indexed: 12/20/2022]
Abstract
The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies focusing on BSs within DNA regulatory regions found correlations between HM patterns and TF binding specificities. However, a mechanistic understanding of TF-DNA binding specificity determinants is still not available. The ability to predict in vivo TF binding on a genome-wide scale requires the identification of features that determine TF binding based on evolutionary relationships of DNA binding proteins. To reveal protein family-dependent mechanisms of TF binding, we conducted comprehensive comparisons of HM patterns surrounding BSs and non-BSs with exactly matched core motifs for TFs in three cell lines: 33 TFs in GM12878, 37 TFs in K562, and 18 TFs in H1-hESC. These TFs displayed protein family-specific preferences for HM patterns surrounding BSs, with high agreement among cell lines. Moreover, compared to models based on DNA sequence and shape at flanking regions of BSs, HM-augmented quantitative machine-learning methods resulted in increased performance in a TF family-specific manner. Analysis of the relative importance of features in these models indicated that TFs, displaying larger HM pattern differences between BSs and non-BSs, bound DNA in an HM-specific manner on a protein family-specific basis. We propose that TF family-specific HM preferences reveal distinct mechanisms that assist in guiding TFs to their cognate BSs by altering chromatin structure and accessibility.
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Affiliation(s)
- Beibei Xin
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Remo Rohs
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
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Paul A, Dasgupta P, Roy D, Chaudhuri S. Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties. PLANT MOLECULAR BIOLOGY 2017; 95:63-88. [PMID: 28741224 DOI: 10.1007/s11103-017-0636-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 07/17/2017] [Indexed: 06/07/2023]
Abstract
Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties. Expression analysis indicates that the OsBZ8 gene is highly induced in Nonabokra plants even in the absence of salt stress, whereas in IR64, the expression significantly increases only during salt stress. Sequence analysis and nucleosomal arrangement within the region -2000 to +1000 of OsBZ8 gene show no difference between the two rice varieties. However, there was a considerable difference in histone modifications and DNA methylation at the locus between these varieties. In Nonabokra, the upstream region was hyperacetylated at H3K9 and H3K27, and this acetylation did not change during salt stress. However, in IR64, histone acetylation was observed only during salt stress. Moreover, the upstream region of OsBZ8 gene has highly dynamic nucleosome arrangement in Nonabokra, compared to IR64. Furthermore, loss of DNA methylation was observed at OsBZ8 locus in Nonabokra control plants along with low H3K27me3 and high H3K4me3. Control IR64 plants show high DNA methylation and enriched H3K27me3. Collectively these results indicate a significant difference in chromatin modifications between the rice varieties that regulates differential expression of OsBZ8 gene during salt stress.
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Affiliation(s)
- Amit Paul
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Pratiti Dasgupta
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India.
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63
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You Q, Yi X, Zhang K, Wang C, Ma X, Zhang X, Xu W, Li F, Su Z. Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. Sci Rep 2017; 7:9098. [PMID: 28831143 PMCID: PMC5567255 DOI: 10.1038/s41598-017-09680-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022] Open
Abstract
Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.
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Affiliation(s)
- Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chunchao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences (ICR, CAAS), Anyang, Henan, 455000, 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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64
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Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol 2017; 18:137. [PMID: 28732548 PMCID: PMC5522596 DOI: 10.1186/s13059-017-1273-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant. Result To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes. Conclusions Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1273-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Johan Zicola
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Sarah N Anderson
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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65
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Chen LQ, Luo JH, Cui ZH, Xue M, Wang L, Zhang XY, Pawlowski WP, He Y. ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development. PLANT PHYSIOLOGY 2017; 174:1795-1806. [PMID: 28550207 PMCID: PMC5490889 DOI: 10.1104/pp.16.01944] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/23/2017] [Indexed: 05/19/2023]
Abstract
Methylation of Lys residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis (Arabidopsis thaliana) encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related proteins. Here, we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1 Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.
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Affiliation(s)
- Li-Qun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Jin-Hong Luo
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
| | - Zhen-Hai Cui
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ming Xue
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
| | - Li Wang
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142
| | - Xiao-Yu Zhang
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | | | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100083, China
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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66
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Latrasse D, Rodriguez-Granados NY, Veluchamy A, Mariappan KG, Bevilacqua C, Crapart N, Camps C, Sommard V, Raynaud C, Dogimont C, Boualem A, Benhamed M, Bendahmane A. The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo. Epigenetics Chromatin 2017; 10:22. [PMID: 28592995 PMCID: PMC5460419 DOI: 10.1186/s13072-017-0132-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/27/2017] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Melon (Cucumis melo) is an important vegetable crop from the Cucurbitaceae family and a reference model specie for sex determination, fruit ripening and vascular fluxes studies. Nevertheless, the nature and role of its epigenome in gene expression regulation and more specifically in sex determination remains largely unknown. RESULTS We have investigated genome wide H3K27me3 and H3K9ac histone modifications and gene expression dynamics, in five melon organs. H3K9ac and H3K27me3 were mainly distributed along gene-rich regions and constrained to gene bodies. H3K9ac was preferentially located at the TSS, whereas H3K27me3 distributed uniformly from TSS to TES. As observed in other species, H3K9ac and H3K27me3 correlated with high and low gene expression levels, respectively. Comparative analyses of unisexual flowers pointed out sex-specific epigenetic states of TFs involved in ethylene response and flower development. Chip-qPCR analysis of laser dissected carpel and stamina primordia, revealed sex-specific histone modification of MADS-box genes. Using sex transition mutants, we demonstrated that the female promoting gene, CmACS11, represses the expression of the male promoting gene CmWIP1 via deposition of H3K27me3. CONCLUSIONS Our findings reveal the organ-specific landscapes of H3K9ac and H3K27me3 in melon. Our results also provide evidence that the sex determination genes recruit histone modifiers to orchestrate unisexual flower development in monoecious species.
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Affiliation(s)
- David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Natalia Y. Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Kiruthiga Gayathri Mariappan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Claudia Bevilacqua
- UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
| | - Nicolas Crapart
- UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
| | - Celine Camps
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Vivien Sommard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Catherine Dogimont
- UR 1052, Unité de Génétique et d’Amélioration des Fruits et Légumes, INRA, BP94, 84143 Montfavet, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
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67
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Berr A, Zhang X, Shen WH. [Reciprocity between active transcription and histone methylation]. Biol Aujourdhui 2017; 210:269-282. [PMID: 28327284 DOI: 10.1051/jbio/2017004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Indexed: 01/08/2023]
Abstract
In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an increasing number of factors have been identified as regulators involved in the establishment, reading or erasure of histone methylations. Their characterization in model organisms such as Arabidopsis has thus unraveled their fundamental roles in the control and regulation of essential developmental processes such as the floral transition, cell differentiation, gametogenesis, and/or the response/adaptation of plants to environmental stresses. In this review, we will focus on the methylation of histones functioning as a mark of activate transcription and we will try to highlight, based on recent findings, the more or less direct links between this mark and gene expression. Thus, we will discuss the different mechanisms allowing the dynamics and the integration of the chromatin states resulting from the different histone methylations in connection with the transcriptional machinery of the RNA polymerase II.
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68
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Wu BH, Chen H, Cai CM, Fang JZ, Wu CC, Huang LY, Wang L, Han ZG. Epigenetic silencing of JMJD5 promotes the proliferation of hepatocellular carcinoma cells by down-regulating the transcription of CDKN1A 686. Oncotarget 2017; 7:6847-63. [PMID: 26760772 PMCID: PMC4872753 DOI: 10.18632/oncotarget.6867] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 12/31/2015] [Indexed: 11/25/2022] Open
Abstract
Proteins that contain jumonji C (JmjC) domains have recently been identified as major contributors to various malignant human cancers through epigenetic remodeling. However, the roles of these family members in the pathogenesis of hepatocellular carcinoma (HCC) are obscure. By mining public databases, we found that the HCC patients with lower JmjC domain-containing protein 5 (JMJD5) expression exhibited shorter survival time. We then confirmed that JMJD5 expression was indeed decreased in HCC specimens, which was caused by the altered epigenetic histone modifications, the decreased H3K9ac, H3K27ac and H3K4me2/3 together with the increased trimethylation of H3K27 and H3K9 on the JMJD5 promoter. Functional experiments revealed that JMJD5 knockdown promoted HCC cell proliferation and in vivo tumorigenicity by accelerating the G1/S transition of the cell cycle; in contrast, ectopic JMJD5 expression had the opposite effects. At molecular mechanism, we found that, in HCC cell lines including TP53-null Hep3B, JMJD5 knockdown led to the down-regulation of CDKN1A and ectopic expression of JMJD5 not only increased but also rescued CDKN1A transcription. Moreover, CDKN1A knockdown could abrogate the effect of JMJD5 knockdown or overexpression on cell proliferation, suggesting that JMJD5 inhibits HCC cell proliferation mainly by activating CDKN1A expression. We further revealed that JMJD5 directly enhances CDKN1A transcription by binding to CDKN1A's promoter independent of H3K36me2 demethylase activity. In short, we first prove that JMJD5 is a tumor suppressor gene in HCC pathogenesis, and the epigenetic silencing of JMJD5 promotes HCC cell proliferation by directly down-regulating CDKN1A transcription.
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Affiliation(s)
- Bing-Hao Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Hui Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Chun-Miao Cai
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Jia-Zhu Fang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Chong-Chao Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li-Yu Huang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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69
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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70
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Lu L, Chen X, Sanders D, Qian S, Zhong X. High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in Arabidopsis and rice. Epigenetics 2016; 10:1044-53. [PMID: 26646900 DOI: 10.1080/15592294.2015.1104446] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Histone acetylation and deacetylation are key epigenetic gene regulatory mechanisms that play critical roles in eukaryotes. Acetylation of histone 4 lysine 16 (H4K16ac) is implicated in many cellular processes. However, its biological function and relationship with transcription are largely unexplored in plants. We generated first genome-wide high-resolution maps of H4K16ac in Arabidopsis thaliana and Oryza sativa. We showed that H4K16ac is preferentially enriched around the transcription start sites and positively correlates with gene expression levels. Co-existence of H4K16ac and H3K23ac is correlated with high gene expression levels, suggesting a potentially combinatorial effect of H4K16ac and H3K23ac histone 3 lysine 23 acetylation on gene expression. Our data further revealed that while genes enriched with both H4K16ac and H3K23ac are ubiquitously expressed, genes enriched with only H4K16ac or H3K23ac showed significantly distinct expression patterns in association with particular developmental stages. Unexpectedly, and unlike in Arabidopsis, there are significant levels of both H4K16ac and H3K23ac in the lowly expressed genes in rice. Furthermore, we found that H4K16ac-enriched genes are associated with different biological processes in Arabidopsis and rice, suggesting a potentially species-specific role of H4K16ac in plants. Together, our genome-wide profiling reveals the conserved and unique distribution patterns of H4K16ac and H3K23ac in Arabidopsis and rice and provides a foundation for further understanding their function in plants.
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Affiliation(s)
- Li Lu
- a Wisconsin Institute for Discovery
| | | | - Dean Sanders
- b Laboratory of Genetics; University of Wisconsin-Madison ; Madison , WI , USA
| | | | - Xuehua Zhong
- a Wisconsin Institute for Discovery.,b Laboratory of Genetics; University of Wisconsin-Madison ; Madison , WI , USA
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71
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Knockdown of WHIRLY1 Affects Drought Stress-Induced Leaf Senescence and Histone Modifications of the Senescence-Associated Gene HvS40. PLANTS 2016; 5:plants5030037. [PMID: 27608048 PMCID: PMC5039745 DOI: 10.3390/plants5030037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 01/02/2023]
Abstract
The plastid-nucleus located protein WHIRLY1 has been described as an upstream regulator of leaf senescence, binding to the promoter of senescence-associated genes like HvS40. To investigate the impact of WHIRLY1 on drought stress-induced, premature senescence, transgenic barley plants with an RNAi-mediated knockdown of the HvWHIRLY1 gene were grown under normal and drought stress conditions. The course of leaf senescence in these lines was monitored by physiological parameters and studies on the expression of senescence- and drought stress-related genes. Drought treatment accelerated leaf senescence in WT plants, whereas WHIRLY 1 knockdown lines (RNAi-W1) showed a stay-green phenotype. Expression of both senescence-associated and drought stress-responsive genes, was delayed in the transgenic plants. Notably, expression of transcription factors of the WRKY and NAC families, which are known to function in senescence- and stress-related signaling pathways, was affected in plants with impaired accumulation of WHIRLY1, indicating that WHIRLY1 acts as an upstream regulator of drought stress-induced senescence. To reveal the epigenetic indexing of HvS40 at the onset of drought-induced senescence in WT and RNAi-W1 lines, stress-responsive loading with histone modifications of promoter and coding sequences of HvS40 was analyzed by chromatin immunoprecipitation and quantified by qRT-PCR. In the wildtype, the euchromatic mark H3K9ac of the HvS40 gene was low under control conditions and was established in response to drought treatment, indicating the action of epigenetic mechanisms in response to drought stress. However, drought stress caused no significant increase in H3K9ac in plants impaired in accumulation of WHIRLY1. The results show that WHIRLY1 knockdown sets in motion a delay in senescence that involves all aspects of gene expression, including changes in chromatin structure.
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Qiu Z, Li R, Zhang S, Wang K, Xu M, Li J, Du Y, Yu H, Cui X. Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development. MOLECULAR PLANT 2016; 9:1168-1182. [PMID: 27250572 DOI: 10.1016/j.molp.2016.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/10/2016] [Accepted: 05/23/2016] [Indexed: 05/29/2023]
Abstract
Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which depends on the orchestrated accessibility of regulatory proteins to promoters and other cis-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the developmental process. To understand the regulatory mechanism and functional elements modulating morphological and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites (DHSs) from the fruit tissues of the tomato cultivar "Moneymaker" at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening.
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Affiliation(s)
- Zhengkun Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongchen Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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73
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Marand AP, Zhang T, Zhu B, Jiang J. Towards genome-wide prediction and characterization of enhancers in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:131-139. [PMID: 27321818 DOI: 10.1016/j.bbagrm.2016.06.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 11/19/2022]
Abstract
Enhancers are important cis-regulatory DNA elements that regulate transcription programs by recruiting transcription factors and directing them to the promoters of target genes in a cell-type/tissue-specific manner. The expression of a gene can be regulated by one or multiple enhancers at different developmental stages and/or in different tissues. Enhancers are difficult to identify because of their unpredictable positions relative to their cognate promoters. Remarkably, only a handful of enhancers have been identified in plant species largely due to the lack of general approaches for enhancer identification. Extensive genomic and epigenomic research in mammalian species has revealed that the genomic locations of enhancers can be predicted based on the binding sites of transcriptional co-factors and several distinct features associated with open chromatin. Here we review the methodologies used in enhancer prediction in mammalian species. We also review the recent applications of these methodologies in Arabidopsis thaliana and discuss the future directions of enhancer identification in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Vialette-Guiraud ACM, Andres-Robin A, Chambrier P, Tavares R, Scutt CP. The analysis of Gene Regulatory Networks in plant evo-devo. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2549-63. [PMID: 27006484 DOI: 10.1093/jxb/erw119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. Many of the species that occupy key positions in plant phylogeny are poorly adapted as laboratory models and so we focus here on techniques that can be efficiently applied to both model and non-model species of interest to plant evo-devo. We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. Finally, we argue for the better integration of molecular data with information from paleobotanical, paleoecological, and paleogeographical studies to provide the fullest possible picture of the processes that have shaped the evolution of plant development.
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Affiliation(s)
- Aurélie C M Vialette-Guiraud
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Amélie Andres-Robin
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Évolutive (UMR 5558 - CNRS/université Lyon 1/université de Lyon), Bâtiment Gregor Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Charles P Scutt
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
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75
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Salvini M, Fambrini M, Giorgetti L, Pugliesi C. Molecular aspects of zygotic embryogenesis in sunflower (Helianthus annuus L.): correlation of positive histone marks with HaWUS expression and putative link HaWUS/HaL1L. PLANTA 2016; 243:199-215. [PMID: 26377219 DOI: 10.1007/s00425-015-2405-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/06/2015] [Indexed: 06/05/2023]
Abstract
The link HaWUS/ HaL1L , the opposite transcriptional behavior, and the decrease/increase in positive histone marks bond to both genes suggest an inhibitory effect of WUS on HaL1L in sunflower zygotic embryos. In Arabidopsis, a group of transcription factors implicated in the earliest events of embryogenesis is the WUSCHEL-RELATED HOMEOBOX (WOX) protein family including WUSCHEL (WUS) and other 14 WOX protein, some of which contain a conserved WUS-box domain in addition to the homeodomain. WUS transcripts appear very early in embryogenesis, at the 16-cell embryo stage, but gradually become restricted to the center of the developing shoot apical meristem (SAM) primordium and continues to be expressed in cells of the niche/organizing center of SAM and floral meristems to maintain stem cell population. Moreover, WUS has decisive roles in the embryonic program presumably promoting the vegetative-to-embryonic transition and/or maintaining the identity of the embryonic stem cells. However, data on the direct interaction between WUS and key genes for seed development (as LEC1 and L1L) are not collected. The novelty of this report consists in the characterization of Helianthus annuus WUS (HaWUS) gene and in its analysis regarding the pattern of the methylated lysine 4 (K4) of the Histone H3 and of the acetylated histone H3 during the zygotic embryo development. Also, a parallel investigation was performed for HaL1L gene since two copies of the WUS-binding site (WUSATA), previously identified on HaL1L nucleotide sequence, were able to be bound by the HaWUS recombinant protein suggesting a not described effect of HaWUS on HaL1L transcription.
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Affiliation(s)
- Mariangela Salvini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Marco Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Giorgetti
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Moruzzi 1, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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76
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Zhang Z, He L, Hu S, Wang Y, Lai Q, Yang P, Yu Q, Zhang S, Xiong F, Simsekyilmaz S, Ning Q, Li J, Zhang D, Zhang H, Xiang X, Zhou Z, Sun H, Wang CY. AAL exacerbates pro-inflammatory response in macrophages by regulating Mincle/Syk/Card9 signaling along with the Nlrp3 inflammasome assembly. Am J Transl Res 2015; 7:1812-1825. [PMID: 26692926 PMCID: PMC4656759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 07/07/2015] [Indexed: 06/05/2023]
Abstract
Previously, we demonstrated that Agrocybe aegerita lectin (AAL), a galectin isolated from edible mushroom Agrocybe aegerita, exerts potent anti-tumor activity, while the mechanisms by which AAL suppresses tumor growth are yet to be elucidated. Here, we conducted studies with focus for its impact on the cecal ligation and puncture (CLP)-induced innate immune response. Administration of AAL significantly exacerbated the severity of CLP-induced septic shock as manifested the increased lethality. AAL promoted inflammatory cytokine production by preferentially regulating macrophage activation and recruitment. Mechanistic studies revealed that AAL likely targets macrophages through receptor Mincle to activate Syk/Card9 signaling, which then couples to the Nlrp3 inflammasome assembly. It was further noted that AAL markedly promotes H3K4 di- and trimethylation, by which it enhances Hmgb1 expression. Specifically, AAL induced macrophages secretion of copious amount of Hmgb1 as manifested the Hmgb1 cytoplasmic translocation along with the detection of extracellular Hmgb1. AAL also stimulated a significant increase for nuclear Hmgb1, which then formed a complex with RelA, and thereby enhancing NF-κB transcriptional activity. Together, our data suggest that AAL may possess important pharmaceutical properties in the regulation of innate immune response.
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Affiliation(s)
- Zhijun Zhang
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Long He
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Shuang Hu
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Yi Wang
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Qiaohong Lai
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Ping Yang
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Qilin Yu
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Shu Zhang
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Fei Xiong
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Sakine Simsekyilmaz
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Qin Ning
- Department of Infectious Disease, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
| | - Jinxiu Li
- Department of Emergency Medicine, Institute of Emergency Medicine and Rare Diseases, The Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Dongshan Zhang
- Department of Emergency Medicine, Institute of Emergency Medicine and Rare Diseases, The Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Hongliang Zhang
- Department of Emergency Medicine, Institute of Emergency Medicine and Rare Diseases, The Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Xudong Xiang
- Department of Emergency Medicine, Institute of Emergency Medicine and Rare Diseases, The Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Zhiguang Zhou
- Diabetes Center, Key Laboratory of Diabetes Immunology, The Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Hui Sun
- College of Life Sciences, Wuhan UniversityWuhan, China
| | - Cong-Yi Wang
- The Center for Biomedical Research, Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology1095 Jiefang Ave., Wuhan 430030, China
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77
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Ay N, Janack B, Fischer A, Reuter G, Humbeck K. Alterations of histone modifications at the senescence-associated gene HvS40 in barley during senescence. PLANT MOLECULAR BIOLOGY 2015; 89:127-41. [PMID: 26249045 DOI: 10.1007/s11103-015-0358-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 08/02/2015] [Indexed: 05/09/2023]
Abstract
The barley gene HvS40, encoding a putative regulator of leaf senescence, is strongly induced during leaf senescence. As shown by chromatin immunoprecipitation, euchromatic histone modification H3K9ac is added at promoter close to ATG and coding sequence of HvS40 after onset of senescence. In parallel, level of heterochromatic H3K9me2 decreases at this gene. Bisulfite sequencing revealed no DNA-methylation in this region, but a heavily methylated DNA-island, starting 664 bp upstream from translational start site in both, mature and senescent leaves. A decrease in DNA methylation in senescing leaves could be shown at one specific CpG motif at the end of this methylation island. In addition, global changes in chromatin structure during senescence were analyzed via immunocytology, revealing senescence-associated changes in spatial distribution of heterochromatic H3K9me2 patterns in the nuclei. Our results prove a senescence-specific mechanism, altering histone modification marks at distinct sequences of the senescence-associated gene HvS40 and altering distribution of heterochromatic areas in the nuclei.
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Affiliation(s)
- Nicole Ay
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Bianka Janack
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Andreas Fischer
- Department of Genetics, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Gunter Reuter
- Department of Genetics, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Klaus Humbeck
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany.
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78
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Perduns R, Horst-Niessen I, Peterhansel C. Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters. PLANT PHYSIOLOGY 2015; 168:1378-88. [PMID: 26111542 PMCID: PMC4528772 DOI: 10.1104/pp.15.00934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
Histone modifications contribute to gene regulation in eukaryotes. We analyzed genome-wide histone H3 Lysine (Lys) 4 trimethylation and histone H3 Lys 9 acetylation (two modifications typically associated with active genes) in meristematic cells at the base and expanded cells in the blade of the maize (Zea mays) leaf. These data were compared with transcript levels of associated genes. For individual genes, regulations (fold changes) of histone modifications and transcript levels were much better correlated than absolute intensities. When focusing on regulated histone modification sites, we identified highly regulated secondary H3 Lys 9 acetylation peaks on upstream promoters (regulated secondary upstream peaks [R-SUPs]) on 10% of all genes. R-SUPs were more often found on genes that were up-regulated toward the blade than on down-regulated genes and specifically, photosynthetic genes. Among those genes, we identified six genes encoding enzymes of the C4 cycle and a significant enrichment of genes associated with the C4 trait derived from transcriptomic studies. On the DNA level, R-SUPs are frequently associated with ethylene-responsive elements. Based on these data, we suggest coevolution of epigenetic promoter elements during the establishment of C4 photosynthesis.
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Affiliation(s)
- Renke Perduns
- Institute of Botany, Leibniz University Hannover, 30419 Hannover, Germany
| | - Ina Horst-Niessen
- Institute of Botany, Leibniz University Hannover, 30419 Hannover, Germany
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79
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Zhang W, Garcia N, Feng Y, Zhao H, Messing J. Genome-wide histone acetylation correlates with active transcription in maize. Genomics 2015; 106:214-20. [PMID: 26021446 DOI: 10.1016/j.ygeno.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/14/2015] [Accepted: 05/21/2015] [Indexed: 11/29/2022]
Abstract
Gene expression is regulated at many different levels during the life cycle of all plant species. Recent investigations have taken advantage of next-generation sequencing to study the relevance of DNA methylation and sRNAs in controlling tissue-specific gene expression in maize at the genome-wide level. Here, we profiled H3K27ac in maize, which has one of the largest sequenced plant genomes due to the amplification of retrotransposons. Because transcribed genes represent only a small proportion of its genome, gene-specific epigenetic modifications are concentrated in a relatively small percentage of the genome. Indeed, H3K27ac marks are mostly in gene-rich, in contrast to gene-poor regions. A large proportion of those marks are located in transcribed regions of genes, including 111 out of 458 known genetic loci. Moreover, increased transcription correlates with the presence of H3K27ac modification in gene bodies. Using maize as an example, we suggest that H3K27ac marks actively transcribed genes in plants.
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Affiliation(s)
- Wei Zhang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Nelson Garcia
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Han Zhao
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA.
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80
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Ouma WZ, Mejia-Guerra MK, Yilmaz A, Pareja-Tobes P, Li W, Doseff AI, Grotewold E. Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq). Sci Rep 2015; 5:8635. [PMID: 25727450 PMCID: PMC4345404 DOI: 10.1038/srep08635] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/12/2015] [Indexed: 12/04/2022] Open
Abstract
Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen was the finding that 30%–40% of unaligned reads were actually alignable. To validate these observations, we investigated the characteristics of the previously unaligned reads corresponding to TAL1, a human TF involved in lineage specification of hemopoietic cells. We show that, while unmapped ChIP-Seq read datasets contain foreign DNA sequences, additional TFBSs can be identified from the previously unaligned ChIP-Seq reads. Our results indicate that the re-evaluation of previously unaligned reads from ChIP-Seq experiments will significantly contribute to TF target identification and determination of emerging properties of GRNs.
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Affiliation(s)
- Wilberforce Zachary Ouma
- 1] Molecular, Cellular and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH, USA [2] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA
| | - Maria Katherine Mejia-Guerra
- 1] Molecular, Cellular and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH, USA [2] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA
| | - Alper Yilmaz
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Pablo Pareja-Tobes
- Oh no sequences! Research group, Era7 Information Technologies SLU, Granada, Spain
| | - Wei Li
- 1] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA [2] Department Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Andrea I Doseff
- 1] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA [2] Department Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Erich Grotewold
- 1] Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH, USA [2] Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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81
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Abstract
tRNAs are widely believed to segregate into two classes, I and II. Computational analysis of eukaryotic tRNA entries in Genomic tRNA Database, however, leads to new, albeit paradoxical, presence of more than a thousand class-I tRNAs with uncharacteristic long variable arms (V-arms), like in class-II. Out of 62,202 tRNAs from 69 eukaryotes, as many as 1431 class-I tRNAs have these novel extended V-arms, and we refer to them as paradoxical tRNAs (pxtRNAs). A great majority of these 1431 pxtRNA genes are located in intergenic regions, about 18% embedded in introns of genes or ESTs, and just one in 3'UTR. A check on the conservations of 2D and 3D base pairs for each position of these pxtRNAs reveals a few variations, but they seem to have almost all the known features (already known identity and conserved elements of tRNA). Analyses of the A-Box and B-Box of these pxtRNA genes in eukaryotes display salient deviations from the previously annotated conserved features of the standard promoters, whereas the transcription termination signals are just canonical and non-canonical runs of thymidine, similar to the ones in standard tRNA genes. There is just one such pxtRNA(ProAGG) gene in the entire human genome, and the availability of data allows epigenetic analysis of this human pxtRNA(ProAGG) in three different cell lines, H1 hESC, K562, and NHEK, to assess the level of its expression. Histone acetylation and methylation of this lone pxtRNA(ProAGG) gene in human differ from that of the nine standard human tRNA(ProAGG) genes. The V-arm nucleotide sequences and their secondary structures in pxtRNA differ from that of class-II tRNA. Considering these differences, hypotheses of alternative splicing, non-canonical intron and gene transfer are examined to partially improve the Cove scores of these pxtRNAs and to critically question their antecedence and novelty.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Arpa Samadder
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Pijush Das
- b Cancer Biology & Inflammatory Disorder Division , Indian Institute of Chemical Biology , Kolkata , India
| | - Smarajit Das
- c Department of Medical Biochemistry and Cell Biology , Institute of Biomedicine, University of Gothenburg , Gothenburg , Sweden
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India.,d Gyanxet, BF 286 Salt Lake, Kolkata , India
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82
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Mursalimov S, Permyakova N, Deineko E, Houben A, Demidov D. Cytomixis doesn't induce obvious changes in chromatin modifications and programmed cell death in tobacco male meiocytes. FRONTIERS IN PLANT SCIENCE 2015; 6:846. [PMID: 26528310 PMCID: PMC4600909 DOI: 10.3389/fpls.2015.00846] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/25/2015] [Indexed: 05/16/2023]
Abstract
Cytomixis is a poorly studied process of nuclear migration between plant cells. It is so far unknown what drives cytomixis and what is the functional state of the chromatin migrating between cells. Using immunostaining, we have analyzed the distribution of posttranslational histone modifications (methylation, acetylation, and phosphorylation) that reflect the functional state of chromatin in the tobacco microsporocytes involved in cytomixis. We demonstrate that the chromatin in the cytomictic cells does not differ from the chromatin in intact microsporocytes according to all 14 analyzed histone modification types. We have also for the first time demonstrated that the migrating chromatin contains normal structures of the synaptonemal complex (SC) and lacks any signs of apoptosis. As has been shown, the chromatin migrating between cells in cytomixis is neither selectively heterochromatized nor degraded both before its migration to another cell and after it enters a recipient cell as micronuclei. We also showed that cytomictic chromatin contains marks typical for transcriptionally active chromatin as well as heterochromatin. Moreover, marks typical for chromosome condensation, SC formation and key proteins required for the formation of bivalents were also detected at migrated chromatin.
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Affiliation(s)
- Sergey Mursalimov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of SciencesNovosibirsk, Russia
| | - Natalya Permyakova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of SciencesNovosibirsk, Russia
| | - Elena Deineko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of SciencesNovosibirsk, Russia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant ResearchStadt Seeland, Germany
| | - Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant ResearchStadt Seeland, Germany
- *Correspondence: Dmitri Demidov,
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83
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Hu Y, Lai Y. Identification and expression analysis of rice histone genes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 86:55-65. [PMID: 25461700 DOI: 10.1016/j.plaphy.2014.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/17/2014] [Indexed: 05/10/2023]
Abstract
Histones, acting as the core of nucleosome, are the chief protein component of chromatin. They play an important role in gene regulation by covalent modification at several sites and histone variants replacement. Five major families of histones exist: H1, H2A, H2B, H3 and H4. The protein sequences within each family appear to be highly conserved. In this paper, we identified 60 histone proteins in rice (Oryza sativa) including 14 H2A, 15 H2B, 16 H3, 11 H4 and 4 H1. Sequence analysis indicates that histone protein sequences in plant are more variable than in animal. Interestingly, we found a rice-specific H4 variant which showed several amino acid substitutions with canonical protein and was expressed in different tissues in a low level. Expression analysis indicates that a subset of histone genes were expressed in a similar pattern and many of them responded to stress conditions. Specifically, we found that two H2A.Z genes were down-regulated by stress in leaves but not in roots suggesting that they might be involved in stress response.
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Affiliation(s)
- Yongfeng Hu
- Jingchu University of Technology, 448000 Jingmen, China.
| | - Yan Lai
- Jingchu University of Technology, 448000 Jingmen, China
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84
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Abstract
The first ncRNA found was an alanine tRNA in baker's yeast, and the first detected microRNAs (miRNAs) promoted ncRNA research to a whole new level. Research on ncRNAs in animals has focused on the medical field, while in plant scientists are more concerned with improving agronomic traits. In 2010, we constructed a plant miRNA database named PMRD to meet the demand for miRNA research in plants. To provide a way to do fundamental research on plant ncRNAs and take full advantage of tremendous public resources, we designed an updated platform called plant ncRNA database (PNRD) based on its predecessor PMRD, which is accessible at http://structuralbiology.cau.edu.cn/PNRD. We collected a total of 25739 entries of 11 different types of ncRNAs from 150 plant species. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.
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Affiliation(s)
- Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenhai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yi Ling
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, 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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85
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Riffo-Campos ÁL, Castillo J, Tur G, González-Figueroa P, Georgieva EI, Rodríguez JL, López-Rodas G, Rodrigo MI, Franco L. Nucleosome-specific, time-dependent changes in histone modifications during activation of the early growth response 1 (Egr1) gene. J Biol Chem 2014; 290:197-208. [PMID: 25378406 DOI: 10.1074/jbc.m114.579292] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Histone post-translational modifications and nucleosome remodeling are coordinate events involved in eukaryotic transcriptional regulation. There are relatively few data on the time course with which these events occur in individual nucleosomes. As a contribution to fill this gap, we first describe the nature and time course of structural changes in the nucleosomes -2, -1, and +1 of the murine Egr1 gene upon induction. To initiate the transient activation of the gene, we used the stimulation of MLP29 cells with phorbol esters and the in vivo activation after partial hepatectomy. In both models, nucleosomes -1 and +1 are partially evicted, whereas nucleosomes +1 and -2 slide downstream during transcription. The sliding of the latter nucleosome allows the EGR1 protein to bind its site, resulting in the repression of the gene. To decide whether EGR1 is involved in the sliding of nucleosome -2, Egr1 was knocked down. In the absence of detectable EGR1, the nucleosome still slides and remains downstream longer than in control cells, suggesting that the product of the gene may be rather involved in the returning of the nucleosome to the basal position. Moreover, the presence of eight epigenetic histone marks has been determined at a mononucleosomal level in that chromatin region. H3S10phK14ac, H3K4me3, H3K9me3, and H3K27me3 are characteristic of nucleosome +1, and H3K9ac and H4K16ac are mainly found in nucleosome -1, and H3K27ac predominates in nucleosomes -2 and -1. The temporal changes in these marks suggest distinct functions for some of them, although changes in H3K4me3 may result from histone turnover.
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Affiliation(s)
- Ángela L Riffo-Campos
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Josefa Castillo
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Gema Tur
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Paula González-Figueroa
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Elena I Georgieva
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - José L Rodríguez
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and
| | - Gerardo López-Rodas
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - M Isabel Rodrigo
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
| | - Luis Franco
- From the Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, 46100 Valencia and Institute of Health Research INCLIVA, 46010 Valencia, Spain
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86
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Perfus-Barbeoch L, Castagnone-Sereno P, Reichelt M, Fneich S, Roquis D, Pratx L, Cosseau C, Grunau C, Abad P. Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: the case of the root-knot nematode Meloidogyne incognita. Front Physiol 2014; 5:211. [PMID: 24936189 PMCID: PMC4047830 DOI: 10.3389/fphys.2014.00211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/15/2014] [Indexed: 01/01/2023] Open
Abstract
Root-knot nematodes of the genus Meloidogyne are biotrophic plant parasites that exhibit different life cycles and reproduction modes, ranging from classical amphimixis to obligatory mitotic parthenogenesis (apomixis), depending on the species. Meloidogyne incognita, an apomictic species, exhibits a worldwide distribution and a wide host range affecting more than 3000 plant species. Furthermore, evidences suggest that apomixis does not prevent M. incognita from adapting to its environment in contrast to what is expected from mitotic parthenogenesis that should theoretically produce clonal progenies. This raises questions about mechanisms of genome plasticity leading to genetic variation and adaptive evolution in apomictic animals. We reasoned that epigenetic mechanisms might in part be responsible for the generation of phenotypic variants that provide potential for rapid adaptation. We established therefore a pipeline to investigate the principal carriers of epigenetic information, DNA methylation and post-translational histone modifications. Even if M. incognita possesses the epigenetic machinery i.e., chromatin modifying enzymes, 5-methyl-cytosine and 5-hydroxy-methyl-cytosine content is absent or very weak. In contrast, we demonstrated that the canonical histone modifications are present and chromatin shows typical nucleosome structure. This work is the first characterization of carriers of epigenetic information in M. incognita and constitutes a preamble to further investigate if M. incognita development and its adaptation to plant hosts are under epigenetic control. Our pipeline should allow performing similar types of studies in any non-model organism.
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Affiliation(s)
- Laetitia Perfus-Barbeoch
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | - Philippe Castagnone-Sereno
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | | | - Sara Fneich
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - David Roquis
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Loris Pratx
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | - Céline Cosseau
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Christoph Grunau
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Pierre Abad
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
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87
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Li J, Gao Y, Petkov S, Purup S, Hyttel P, Callesen H. Passage number of porcine embryonic germ cells affects epigenetic status and blastocyst rate following somatic cell nuclear transfer. Anim Reprod Sci 2014; 147:39-46. [DOI: 10.1016/j.anireprosci.2014.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/18/2014] [Accepted: 03/16/2014] [Indexed: 12/01/2022]
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88
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Shi J, Dong A, Shen WH. Epigenetic regulation of rice flowering and reproduction. FRONTIERS IN PLANT SCIENCE 2014; 5:803. [PMID: 25674094 PMCID: PMC4309181 DOI: 10.3389/fpls.2014.00803] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/22/2014] [Indexed: 05/19/2023]
Abstract
Current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant Arabidopsis thaliana. Rice (Oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. During the past few years, an increasing number of studies have reported the impact of DNA methylation, non-coding RNAs and histone modifications on transcription regulation, flowering time control, and reproduction in rice. Here, we review these studies to provide an updated complete view about chromatin modifiers characterized in rice and in particular on their roles in epigenetic regulation of flowering time, reproduction, and seed development.
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Affiliation(s)
- Jinlei Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan UniversityShanghai, China
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de StrasbourgStrasbourg, France
- *Correspondence: Wen-Hui Shen, CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cédex, France e-mail:
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89
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Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. J Biosci 2013; 38:971-87. [DOI: 10.1007/s12038-013-9388-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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