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Shao Z, Chen J, Wang S, Wang W, Zhu L. Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.). ENVIRONMENT INTERNATIONAL 2024; 187:108737. [PMID: 38735075 DOI: 10.1016/j.envint.2024.108737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1-71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87-95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = -4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.
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Affiliation(s)
- Zexi Shao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Jie Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Shuyuan Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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Heath H, Peng S, Szmatola T, Ryan S, Bellone R, Kalbfleisch T, Petersen J, Finno C. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. RESEARCH SQUARE 2024:rs.3.rs-4182812. [PMID: 38645140 PMCID: PMC11030527 DOI: 10.21203/rs.3.rs-4182812/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.
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Heath HD, Peng S, Szmatola T, Bellone RR, Kalbfleisch T, Petersen JL, Finno CJ. A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573798. [PMID: 38260378 PMCID: PMC10802363 DOI: 10.1101/2023.12.31.573798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results In this work, we introduce and highlight the significance of an equine ASE analysis, containing integrated long- and short-read RNA sequencing data, along with insight from histone modification data, from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues. Conclusions This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues and foster a deeper understanding of the impact of allelic imbalance in equine health and disease at the molecular level.
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Deris Zayeri Z, Parsi A, Shahrabi S, Kargar M, Davari N, Saki N. Epigenetic and metabolic reprogramming in inflammatory bowel diseases: diagnostic and prognostic biomarkers in colorectal cancer. Cancer Cell Int 2023; 23:264. [PMID: 37936149 PMCID: PMC10631091 DOI: 10.1186/s12935-023-03117-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND AND AIM "Inflammatory bowel disease" (IBD) is a chronic, relapsing inflammatory disease of the intestinal tract that typically begins at a young age and might transit to colorectal cancer (CRC). In this manuscript, we discussed the epigenetic and metabolic change to present a extensive view of IBDs transition to CRC. This study discusses the possible biomarkers for evaluating the condition of IBDs patients, especially before the transition to CRC. RESEARCH APPROACH We searched "PubMed" and "Google Scholar" using the keywords from 2000 to 2022. DISCUSSION In this manuscript, interesting titles associated with IBD and CRC are discussed to present a broad view regarding the epigenetic and metabolic reprogramming and the biomarkers. CONCLUSION Epigenetics can be the main reason in IBD transition to CRC, and Hypermethylation of several genes, such as VIM, OSM4, SEPT9, GATA4 and GATA5, NDRG4, BMP3, ITGA4 and plus hypomethylation of LINE1 can be used in IBD and CRC management. Epigenetic, metabolisms and microbiome-derived biomarkers, such as Linoleic acid and 12 hydroxy 8,10-octadecadienoic acid, Serum M2-pyruvate kinase and Six metabolic genes (NAT2, XDH, GPX3, AKR1C4, SPHK and ADCY5) expression are valuable biomarkers for early detection and transition to CRC condition. Some miRs, such as miR-31, miR-139-5p, miR -155, miR-17, miR-223, miR-370-3p, miR-31, miR -106a, miR -135b and miR-320 can be used as biomarkers to estimate IBD transition to CRC condition.
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Affiliation(s)
- Zeinab Deris Zayeri
- Golestan Hospital Clinical Research Development Unit, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abazar Parsi
- Alimentary Tract Research Center, Clinical Sciences Research Inistitute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeid Shahrabi
- Department of Biochemistry and Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Masoud Kargar
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nader Davari
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Wang J, Wu Q, Ou C, Lu G, Yu H. Research on Xiaoyao Powder in the treatment of depression based on epigenetics and quality markers. Front Neurosci 2023; 17:1223451. [PMID: 37694120 PMCID: PMC10483571 DOI: 10.3389/fnins.2023.1223451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/26/2023] [Indexed: 09/12/2023] Open
Abstract
Depression has become one of the most common public health issues around the world, and the incidence has been increasing in recent years. A large amount of clinical investigations have proven that the treatment of depression is difficult. The prognosis is poor, and the fatality rate is high. At present, western medicine is the preferred treatment for depression, but it often causes adverse clinical reactions such as dry mouth, blurred vision, and memory loss, etc. The herbal compound Xiaoyao Powder is a traditional medicine for soothing the liver and relieving depression, strengthening the spleen, and nourishing the blood. It can reduce adverse reactions. It is effective in treating depression. In this study, we elucidate the function of Xiaoyao Powder in anti-depression from the perspective of clinical application and pharmacological mechanisms such as regulating epigenetic and chemical quality markers to provide empirical and experimental theoretical results that contribute to developing future depression therapy with Xiaoyao Powder.
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Affiliation(s)
| | | | | | - Guangying Lu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Huayun Yu
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Padilla A, Manganaro JF, Huesgen L, Roess DA, Brown MA, Crans DC. Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases. Molecules 2023; 28:molecules28042000. [PMID: 36838987 PMCID: PMC9967872 DOI: 10.3390/molecules28042000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
A comprehensive understanding of the mechanisms involved in epigenetic changes in gene expression is essential to the clinical management of diseases linked to the SMYD family of lysine methyltransferases. The five known SMYD enzymes catalyze the transfer of donor methyl groups from S-adenosylmethionine (SAM) to specific lysines on histones and non-histone substrates. SMYDs family members have distinct tissue distributions and tissue-specific functions, including regulation of development, cell differentiation, and embryogenesis. Diseases associated with SMYDs include the repressed transcription of SMYD1 genes needed for the formation of ion channels in the heart leading to heart failure, SMYD2 overexpression in esophageal squamous cell carcinoma (ESCC) or p53-related cancers, and poor prognosis associated with SMYD3 overexpression in more than 14 types of cancer including breast cancer, colon cancer, prostate cancer, lung cancer, and pancreatic cancer. Given the importance of epigenetics in various pathologies, the development of epigenetic inhibitors has attracted considerable attention from the pharmaceutical industry. The pharmacologic development of the inhibitors involves the identification of molecules regulating both functional SMYD SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) and MYND (Myeloid-Nervy-DEAF1) domains, a process facilitated by available X-ray structures for SMYD1, SMYD2, and SMYD3. Important leads for potential pharmaceutical agents have been reported for SMYD2 and SMYD3 enzymes, and six epigenetic inhibitors have been developed for drugs used to treat myelodysplastic syndrome (Vidaza, Dacogen), cutaneous T-cell lymphoma (Zoinza, Isrodax), and peripheral T-cell lymphoma (Beleodag, Epidaza). The recently demonstrated reversal of SMYD histone methylation suggests that reversing the epigenetic effects of SMYDs in cancerous tissues may be a desirable target for pharmacological development.
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Affiliation(s)
- Alyssa Padilla
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - John F. Manganaro
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Lydia Huesgen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Deborah A. Roess
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Mark A. Brown
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA
- Graduate Degree Program in Ecology, Department of Ethnic Studies, Global Health and Health Disparities, Colorado School of Public Health, Colorado State University, Fort Collins, CO 80523-1612, USA
- Correspondence: (M.A.B.); (D.C.C.)
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Correspondence: (M.A.B.); (D.C.C.)
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Shang JY, Cai XW, Su YN, Zhang ZC, Wang X, Zhao N, He XJ. Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2438-2454. [PMID: 36354145 DOI: 10.1111/jipb.13406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.
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Affiliation(s)
- Ji-Yun Shang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Chen Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin Wang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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A review on CRISPR/Cas-based epigenetic regulation in plants. Int J Biol Macromol 2022; 219:1261-1271. [DOI: 10.1016/j.ijbiomac.2022.08.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 08/29/2022] [Indexed: 01/09/2023]
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9
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Berger TC, Taubøll E, Heuser K. The potential role of DNA methylation as preventive treatment target of epileptogenesis. Front Cell Neurosci 2022; 16:931356. [PMID: 35936496 PMCID: PMC9353008 DOI: 10.3389/fncel.2022.931356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacological therapy of epilepsy has so far been limited to symptomatic treatment aimed at neuronal targets, with the result of an unchanged high proportion of patients lacking seizure control. The dissection of the intricate pathological mechanisms that transform normal brain matter to a focus for epileptic seizures—the process of epileptogenesis—could yield targets for novel treatment strategies preventing the development or progression of epilepsy. While many pathological features of epileptogenesis have been identified, obvious shortcomings in drug development are now believed to be based on the lack of knowledge of molecular upstream mechanisms, such as DNA methylation (DNAm), and as well as a failure to recognize glial cell involvement in epileptogenesis. This article highlights the potential role of DNAm and related gene expression (GE) as a treatment target in epileptogenesis.
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Affiliation(s)
- Toni Christoph Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Toni Christoph Berger
| | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Kjell Heuser
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10
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Dasgupta P, Prasad P, Bag SK, Chaudhuri S. Dynamicity of histone H3K27ac and H3K27me3 modifications regulate the cold-responsive gene expression in Oryza sativa L. ssp. indica. Genomics 2022; 114:110433. [PMID: 35863676 DOI: 10.1016/j.ygeno.2022.110433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/15/2022] [Accepted: 07/10/2022] [Indexed: 11/29/2022]
Abstract
Cultivated in tropical and subtropical regions, Oryza sativa L. ssp. indica is largely affected by cold-stress, especially at the seedling stage. The present model of the stress-responsive regulatory network in plants entails the role of genetic and epigenetic factors in stress-responsive gene expression. Despite extensive transcriptomic studies, the regulation of various epigenetic factors in plants cold-stress response is less explored. The present study addresses the effect of genome-wide changes of H3K27 modifications on gene expression in IR64 rice, during cold-stress. Our results suggest a positive correlation between the changes in H3K27 modifications and stress-responsive gene activation in indica rice. Cold-induced enrichment of H3K27 acetylation promotes nucleosomal rearrangement, thereby facilitating the accessibility of the transcriptional machinery at the stress-responsive loci for transcription activation. Although H3K27ac exhibits uniform distribution throughout the loci of enriched genes; occupancy of H3K27me3 is biased to intergenic regions. Integration of the ChIP-seq data with transcriptome indicated that upregulation of stress-responsive TFs, photosynthesis-TCA-related, water-deficit genes, redox and JA signalling components, was associated with differential changes of H3K27ac and H3K27me3 levels. Furthermore, cold-induced upregulation of histone acetyltransferases and downregulation of DNA methyltransferases was noted through the antagonistic switch of H3K27ac and H3K27me3. Moreover, motif analysis of H3K27ac and H3K27me3 enriched regions are associated with putative stress responsive transcription factors binding sites, GAGA element and histone H3K27demethylase. Collectively our analysis suggests that differential expression of various chromatin and DNA modifiers coupled with increased H3K27ac and depleted H3K27me3 increases DNA accessibility, thereby promoting transcription of the cold-responsive genes in indica rice.
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Affiliation(s)
- Pratiti Dasgupta
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India
| | - Priti Prasad
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
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11
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The Arabidopsis DREAM complex antagonizes WDR5A to modulate histone H3K4me2/3 deposition for a subset of genome repression. Proc Natl Acad Sci U S A 2022; 119:e2206075119. [PMID: 35759663 PMCID: PMC9271193 DOI: 10.1073/pnas.2206075119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The master transcriptional repressor DREAM (dimerization partner, RB-like, E2F and multivulval class B) complex regulates the cell cycle in eukaryotes, but much remains unknown about how it transmits repressive signals on chromatin to the primary transcriptional machinery (e.g., RNA polymerase II [Pol II]). Through a forward genetic screen, we identified BTE1 (barrier of transcription elongation 1), a plant-specific component of the DREAM complex. The subsequent characterization demonstrated that DREAM complex containing BTE1 antagonizes the activity of Complex Proteins Associated with Set1 (COMPASS)-like complex to repress H3K4me3 occupancy and inhibits Pol II elongation at DREAM target genes. We showed that BTE1 is recruited to chromatin at the promoter-proximal regions of target genes by E2F transcription factors. DREAM target genes exhibit characteristic enrichment of H2A.Z and H3K4me2 modification on chromatin. We further showed that BTE1 directly interacts with WDR5A, a core component of COMPASS-like complex, repressing WDR5A chromatin binding and the elongation of transcription on DREAM target genes. H3K4me3 is known to correlate with the Pol II transcription activation and promotes efficient elongation. Thus, our study illustrates a transcriptional repression mechanism by which the DREAM complex dampens H3K4me3 deposition at a set of genes through its interaction with WDR5A.
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12
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Wong CH, Li CH, Man Tong JH, Zheng D, He Q, Luo Z, Lou UK, Wang J, To KF, Chen Y. The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer. Mol Ther 2022; 30:1597-1609. [PMID: 35121112 PMCID: PMC9077372 DOI: 10.1016/j.ymthe.2022.01.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Long non-coding RNA HOX Transcript Antisense RNA (HOTAIR) is overexpressed in multiple cancers with diverse genetic profiles. Importantly, since HOTAIR heavily contributes to cancer progression by promoting tumor growth and metastasis, HOTAIR becomes a potential target for cancer therapy. However, the underlying mechanism leading to HOTAIR deregulation is largely unexplored. Here, we performed a pan-cancer analysis using more than 4,200 samples and found that intragenic exon CpG island (Ex-CGI) was hypermethylated and was positively correlated to HOTAIR expression. Also, we revealed that Ex-CGI methylation promotes HOTAIR expression through enhancing the transcription elongation process. Furthermore, we linked up the aberrant intragenic tri-methylation on H3 at lysine 4 (H3K4me3) and Ex-CGI DNA methylation in promoting transcription elongation of HOTAIR. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis downregulated HOTAIR expression and inhibited cell growth in many cancers. To our knowledge, this is the first time that a positive feedback loop that involved CDK9-mediated phosphorylation of RNA Polymerase II Serine 2 (RNA PolII Ser2), H3K4me3, and intragenic DNA methylation, which induced robust transcriptional elongation and heavily contributed to the upregulation of oncogenic lncRNA in cancer has been demonstrated. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis could be a novel therapy in many cancers through inhibiting the HOTAIR expression.
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Affiliation(s)
- Chi Hin Wong
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Chi Han Li
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Joanna Hung Man Tong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Duo Zheng
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen 518055, China
| | - Qifang He
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Zhiyuan Luo
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ut Kei Lou
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Jiatong Wang
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518087, China.
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13
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Sun C, Li D, Gao Z, Gao L, Shang L, Wang M, Qiao J, Ding S, Li C, Geisler M, Jiang D, Qi Y, Qian Q. OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:118-134. [PMID: 34726825 DOI: 10.1111/jipb.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.
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Affiliation(s)
- Chendong Sun
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Lin'an Hangzhou, 311300, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Lei Gao
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiyue Qiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Dean Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
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14
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Drosou V, Kapazoglou A, Letsiou S, Tsaftaris AS, Argiriou A. Drought induces variation in the DNA methylation status of the barley HvDME promoter. JOURNAL OF PLANT RESEARCH 2021; 134:1351-1362. [PMID: 34510287 DOI: 10.1007/s10265-021-01342-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Cytosine methylation is an epigenetic modification with essential roles in diverse plant biological processes including vegetative and reproductive development and responsiveness to environmental stimuli. A dynamic process involving DNA methyltransferases and DNA demethylases establishes cytosine DNA methylation levels and distribution along the genome. A DNA demethylase gene from barley (Hordeum vulgare), DEMETER (HvDME), the homologue of the Arabidopsis thaliana DME (AtDME), has been characterized previously and found to respond to drought conditions. Here, the promoter of the HvDME gene was analysed further by in silico and DNA methylation analysis. The effect of drought conditions on the DNA methylation status of HvDME was investigated at single-cytosine resolution using bisulfite sequencing. It was demonstrated that the HvDME promoter can be divided into two discrete regions, in terms of DNA methylation level and density; a relatively unmethylated region proximal to the translational start site that is depleted of non-CG (CHG, CHH) methylation and another distal region, approximately 1500 bp upstream of the translational start site, enriched in CG, as well as non-CG methylation. Drought stress provoked alterations in the methylation status of the HvDME promoter distal region, whereas the DNA methylation of the proximal region remained unaffected. Computational analysis of the HvDME promoter revealed the presence of several putative regulatory elements related to drought responsiveness, as well as transposable elements (TEs) that may affect DNA methylation. Overall, our results expand our investigations of the epigenetic regulation of the HvDME gene in response to drought stress in barley and may contribute to further understanding of the epigenetic mechanisms underlying abiotic stress responses in barley and other cereals.
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Affiliation(s)
- Victoria Drosou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece
| | - Aliki Kapazoglou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece.
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Lykovrysi, 14123, Athens, Greece.
| | - Sophia Letsiou
- Laboratory of Biochemistry, Department of Research and Development, APIVITA S.A., Industrial Park of Markopoulo Mesogaias, Markopoulo Attiki, 19003, Athens, Greece
| | | | - Anagnostis Argiriou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thermi, 57001, Thessaloniki, Greece
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15
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Mendieta JP, Marand AP, Ricci WA, Zhang X, Schmitz RJ. Leveraging histone modifications to improve genome annotations. G3 (BETHESDA, MD.) 2021; 11:jkab263. [PMID: 34568920 PMCID: PMC8473982 DOI: 10.1093/g3journal/jkab263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Z. mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2128 base pairs, and we identified 2529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2724 in Setaria viridis, 2446 in Sorghum bicolor, 8631 in Glycine max, and 2585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.
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Affiliation(s)
| | | | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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16
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Wang H, Dang J, Wu D, Xie Z, Yan S, Luo J, Guo Q, Liang G. Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica). PLANT METHODS 2021; 17:93. [PMID: 34479588 PMCID: PMC8418031 DOI: 10.1186/s13007-021-00792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/24/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. RESULTS We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. CONCLUSIONS qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Shuang Yan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jingnan Luo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China.
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17
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Li SF, Lv CC, Lan LN, Jiang KL, Zhang YL, Li N, Deng CL, Gao WJ. DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus. HORTICULTURE RESEARCH 2021; 8:198. [PMID: 34465747 PMCID: PMC8408194 DOI: 10.1038/s41438-021-00633-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 05/04/2023]
Abstract
DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Can-Can Lv
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Kai-Lu Jiang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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18
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Wang T, Lu Q, Song H, Hu N, Wei Y, Li P, Liu Y, Zhao Z, Liu J, Zhang B, Peng R. DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet ( Setaria italica L.). FRONTIERS IN PLANT SCIENCE 2021; 12:741415. [PMID: 34512708 PMCID: PMC8429616 DOI: 10.3389/fpls.2021.741415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.
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Affiliation(s)
- Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
- Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Quanwei Lu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Zilin Zhao
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Renhai Peng
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
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19
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The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles. Int J Mol Sci 2021; 22:ijms22168618. [PMID: 34445323 PMCID: PMC8395315 DOI: 10.3390/ijms22168618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
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20
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Catoni M, Zabet NR. Analysis of Plant DNA Methylation Profiles Using R. Methods Mol Biol 2021; 2250:219-238. [PMID: 33900608 DOI: 10.1007/978-1-0716-1134-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
DNA methylation is a transgenerational stable epigenetic modification able to regulate gene expression and genome stability. The analysis of DNA methylation by genome-wide bisulfite sequencing become the main genomic approach to study epigenetics in many organisms; leading to standardization of the alignment and methylation call procedures. However, subsequent steps of the computational analysis should be tailored to the biological questions and the organisms used. Since most bioinformatics tools designed for epigenetic studies are built using mammalian models, they are potentially unsuitable for organisms with substantially different epigenetic regulation, such as plants. Therefore, in this chapter we propose a computational workflow for the analysis, visualization, and interpretation of data obtained from alignment of whole genome bisulfite sequencing of plant samples. Using almost exclusively the R working environment we will examine in depth how to tackle some plant-related issues during epigenetic analysis.
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Affiliation(s)
- Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Nicolae Radu Zabet
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
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21
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Oldroyd BP, Yagound B. The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200115. [PMID: 33866805 PMCID: PMC8059649 DOI: 10.1098/rstb.2020.0115] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eusocial insects can be defined as those that live in colonies and have distinct queens and workers. For most species, queens and workers arise from a common genome, and so caste-specific developmental trajectories must arise from epigenetic processes. In this review, we examine the epigenetic mechanisms that may be involved in the regulation of caste dimorphism. Early work on honeybees suggested that DNA methylation plays a causal role in the divergent development of queen and worker castes. This view has now been challenged by studies that did not find consistent associations between methylation and caste in honeybees and other species. Evidence for the involvement of methylation in modulating behaviour of adult workers is also inconsistent. Thus, the functional significance of DNA methylation in social insects remains equivocal. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Benjamin P. Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
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22
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Li S, Chen K, Grierson D. Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening. Cells 2021; 10:1136. [PMID: 34066675 PMCID: PMC8151651 DOI: 10.3390/cells10051136] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.
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Affiliation(s)
- Shan Li
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
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23
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Ma X, Zhao H, Yan H, Sheng M, Cao Y, Yang K, Xu H, Xu W, Gao Z, Su Z. Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data. Comput Struct Biotechnol J 2021; 19:2708-2718. [PMID: 34093986 PMCID: PMC8131310 DOI: 10.1016/j.csbj.2021.04.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/07/2023] Open
Abstract
Bamboo, one of the most crucial nontimber forest resources worldwide, has the capacity for rapid growth. In recent years, the genome of moso bamboo (Phyllostachys edulis) has been decoded, and a large amount of transcriptome data has been published. In this study, we generated the genome-wide profiles of the histone modification H3K4me3 in leaf, stem, and root tissues of bamboo. The trends in the distribution patterns were similar to those in rice. We developed a processing pipeline for predicting novel transcripts to refine the structural annotation of the genome using H3K4me3 ChIP-seq data and 29 RNA-seq datasets. As a result, 12,460 novel transcripts were predicted in the bamboo genome. Compared with the transcripts in the newly released version 2.0 of the bamboo genome, these novel transcripts are tissue-specific and shorter, and most have a single exon. Some representative novel transcripts were validated by semiquantitative RT-PCR and qRT-PCR analyses. Furthermore, we put these novel transcripts back into the ChIP-seq analysis pipeline and discovered that the percentages of H3K4me3 in genic elements were increased. Overall, this work integrated transcriptomic data and epigenomic data to refine the annotation of the genome in order to discover more functional genes and study bamboo growth and development, and the application of this predicted pipeline may help refine the structural annotation of the genome in other species.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hansheng Zhao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.,College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hao Xu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds. PLANTS 2021; 10:plants10040706. [PMID: 33917507 PMCID: PMC8067477 DOI: 10.3390/plants10040706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 01/23/2023]
Abstract
Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.
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Zhou C, Zhou H, Ma X, Yang H, Wang P, Wang G, Zheng L, Zhang Y, Liu X. Genome-Wide Identification and Characterization of Main Histone Modifications in Sorghum Decipher Regulatory Mechanisms Involved by mRNA and Long Noncoding RNA Genes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2337-2347. [PMID: 33555853 DOI: 10.1021/acs.jafc.0c07035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Post-translational modifications of histones play an important chromatic role of a transcript activity in eukaryotes. Even though mRNA and long noncoding RNA (lncRNA) genes share similar biogenetic processes, these transcript classes may differ in many ways. However, knowledge about the crosstalk between histone methylations and the two types of sorghum genes is still ambiguous. In the present study, we reveal the genome-wide distribution of six histone modifications, namely, di- and trimethylation of H3K4 (H3K4me2 and H3K4me3), H3K27 (H3K27me2 and H3K27me3), and H3K36 (H3K36me2 and H3K36me3) in sorghum and analyze their functional relationships. Unlike other histone methylation, the codecoration of H3K4me3 and H3K36me3 is negatively associated with the production of lincRNAs in the context of active expression of mRNA genes. Our data demonstrated that H3K4me3 may act as a complementary component to H3K36me3 in the transcriptional regulatory process. Moreover, we observe that both H3K4me3 and H3K36me3 are involved in the negative-going regulation of plant lincRNA and mRNA genes. Our data provide a genome-wide landscape of histone methylation in sorghum, decrypt its reciprocity, and shed light on its transcriptional regulation roles in mRNA and lncRNA genes.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Xueping Ma
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Huilan Yang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Ping Wang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Guodong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Lanlan Zheng
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
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Foroozani M, Vandal MP, Smith AP. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. PLANTA 2021; 253:4. [PMID: 33387051 DOI: 10.1007/s00425-020-03520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.
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Affiliation(s)
- Maryam Foroozani
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matthew P Vandal
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. THE NEW PHYTOLOGIST 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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Ouyang W, Cao Z, Xiong D, Li G, Li X. Decoding the plant genome: From epigenome to 3D organization. J Genet Genomics 2020; 47:425-435. [PMID: 33023833 DOI: 10.1016/j.jgg.2020.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022]
Abstract
The linear genome of eukaryotes is partitioned into diverse chromatin states and packaged into a three-dimensional (3D) structure, which has functional implications in DNA replication, DNA repair, and transcriptional regulation. Over the past decades, research on plant functional genomics and epigenomics has made great progress, with thousands of genes cloned and molecular mechanisms of diverse biological processes elucidated. Recently, 3D genome research has gradually attracted great attention of many plant researchers. Herein, we briefly review the progress in genomic and epigenomic research in plants, with a focus on Arabidopsis and rice, and summarize the currently used technologies and advances in plant 3D genome organization studies. We also discuss the relationships between one-dimensional linear genome sequences, epigenomic states, and the 3D chromatin architecture. This review provides basis for future research on plant 3D genomics.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Department of Resources and Environment, Henan University of Engineering, Zhengzhou, 451191, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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29
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Wang L, Qiao H. Chromatin regulation in plant hormone and plant stress responses. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:164-170. [PMID: 33142261 PMCID: PMC8237520 DOI: 10.1016/j.pbi.2020.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 05/05/2023]
Abstract
The gene expression is tightly regulated temporally and spatially to ensure the plant and animal proper development, function, growth, and survival under different environmental conditions. Chromatin regulation plays a central role in the gene expression by providing transcription factors and the transcription machinery with dynamic access to an otherwise tightly packaged genome. In this review, we will summarize recent progress in understanding the roles of chromatin regulation in the gene expression, and their contribution to the plant hormone and stress responses. We highlight the most recent publications within this topic and underline the roles of chromatin regulation in gene expression.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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30
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Grzybkowska D, Nowak K, Gaj MD. Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis. Int J Mol Sci 2020; 21:E6849. [PMID: 32961931 PMCID: PMC7555384 DOI: 10.3390/ijms21186849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.
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Affiliation(s)
| | | | - Małgorzata D. Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; (D.G.); (K.N.)
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31
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Seidl MF, Kramer HM, Cook DE, Fiorin GL, van den Berg GCM, Faino L, Thomma BPHJ. Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium. mBio 2020; 11:e01714-20. [PMID: 32900804 PMCID: PMC7482064 DOI: 10.1128/mbio.01714-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
Centromeres are chromosomal regions that are crucial for chromosome segregation during mitosis and meiosis, and failed centromere formation can contribute to chromosomal anomalies. Despite this conserved function, centromeres differ significantly between and even within species. Thus far, systematic studies into the organization and evolution of fungal centromeres remain scarce. In this study, we identified the centromeres in each of the 10 species of the fungal genus Verticillium and characterized their organization and evolution. Chromatin immunoprecipitation of the centromere-specific histone CenH3 (ChIP-seq) and chromatin conformation capture (Hi-C) followed by high-throughput sequencing identified eight conserved, large (∼150-kb), AT-, and repeat-rich regional centromeres that are embedded in heterochromatin in the plant pathogen Verticillium dahliae Using Hi-C, we similarly identified repeat-rich centromeres in the other Verticillium species. Strikingly, a single degenerated long terminal repeat (LTR) retrotransposon is strongly associated with centromeric regions in some but not all Verticillium species. Extensive chromosomal rearrangements occurred during Verticillium evolution, of which some could be linked to centromeres, suggesting that centromeres contributed to chromosomal evolution. The size and organization of centromeres differ considerably between species, and centromere size was found to correlate with the genome-wide repeat content. Overall, our study highlights the contribution of repetitive elements to the diversity and rapid evolution of centromeres within the fungal genus VerticilliumIMPORTANCE The genus Verticillium contains 10 species of plant-associated fungi, some of which are notorious pathogens. Verticillium species evolved by frequent chromosomal rearrangements that contribute to genome plasticity. Centromeres are instrumental for separation of chromosomes during mitosis and meiosis, and failed centromere functionality can lead to chromosomal anomalies. Here, we used a combination of experimental techniques to identify and characterize centromeres in each of the Verticillium species. Intriguingly, we could strongly associate a single repetitive element to the centromeres of some of the Verticillium species. The presence of this element in the centromeres coincides with increased centromere sizes and genome-wide repeat expansions. Collectively, our findings signify a role of repetitive elements in the function, organization, and rapid evolution of centromeres in a set of closely related fungal species.
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Affiliation(s)
- Michael F Seidl
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | | | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Environmental Biology Department, Sapienza Università di Roma, Rome, Italy
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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Jin J, Gui S, Li Q, Wang Y, Zhang H, Zhu Z, Chen H, Sun Y, Zou Y, Huang X, Ding Y. The transcription factor GATA10 regulates fertility conversion of a two-line hybrid tms5 mutant rice via the modulation of Ub L40 expression. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1034-1056. [PMID: 31486580 PMCID: PMC7383616 DOI: 10.1111/jipb.12871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/30/2019] [Indexed: 05/03/2023]
Abstract
The thermosensitive genic male sterile 5 (tms5) mutation causes thermosensitive genic male sterility in rice (Oryza sativa) through loss of RNase ZS1 function, which influences ubiquitin fusion ribosomal protein L40 (UbL40 ) messenger RNA levels during male development. Here, we used ATAC-seq, combined with analysis of H3K9ac and H3K4me2, to identify changes in accessible chromatin during fertility conversion of the two-line hybrid rice Wuxiang S (WXS) derived from a mutant tms5 allele. Furthermore, RNA-seq and bioinformatic analyses identified specific transcription factors (TFs) in differentially accessible chromatin regions. Among these TFs, only GATA10 targeted UbL40 . Osgata10 knockout mutations, which resulted in low expression of UbL40 and a tendency toward male fertility, confirmed that GATA10 regulated fertility conversion via the modulation of UbL40 . Meanwhile, GATA10 acted as a mediator for interactions with ERF65, which revealed that transcriptional regulation is a complex process involving multiple complexes of TFs, namely TF modules. It appears that the ERF141/MADS7/MADS50/MYB modules affect metabolic processes that control anther and pollen development, especially cell wall formation. Our analysis revealed that these modules directly or indirectly affect metabolic pathway-related genes to coordinate plant growth with proper anther development, and furthermore, that GATA10 regulates fertility conversion via the modulation of UbL40 expression.
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Affiliation(s)
- Jing Jin
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Qian Li
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Ying Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Hongyuan Zhang
- Institute of VegetableWuhan Academy of Agricultural SciencesWuhan430072China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Hao Chen
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Yueyang Sun
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Yu Zou
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
| | - Xingguo Huang
- Wuhan Wuda Tianyuau Bio‐Tech Co., Ltd.Wuhan430070China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life SciencesWuhan UniversityWuhan430072China
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N'Diaye A, Byrns B, Cory AT, Nilsen KT, Walkowiak S, Sharpe A, Robinson SJ, Pozniak CJ. Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat. THE PLANT GENOME 2020; 13:e20027. [PMID: 33016606 DOI: 10.1002/tpg2.20027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.
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Affiliation(s)
- Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Brook Byrns
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Aron T Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Kirby T Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Andrew Sharpe
- Global Institute for Food Security, Saskatoon, SK, Canada, S7N 0W9
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Lu Y, Zhou DX, Zhao Y. Understanding epigenomics based on the rice model. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1345-1363. [PMID: 31897514 DOI: 10.1007/s00122-019-03518-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.
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Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Xing L, Qi S, Zhou H, Zhang W, Zhang C, Ma W, Zhang Q, Shah K, Han M, Zhao J. Epigenomic Regulatory Mechanism in Vegetative Phase Transition of Malus hupehensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4812-4829. [PMID: 32227940 DOI: 10.1021/acs.jafc.0c00478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In woody plants, phase transitions substantially affect growth and development. Although there has been considerable interest in the regulatory mechanisms underlying phase changes, the associated epigenetic modifications remain relatively uncharacterized. We examined the DNA methylation changes and the transcriptional responses in adult and juvenile Malus hupehensis leaves. The DNA methylations were 66.61% and 68.3% in the CG context, 49.12% and 52.44% in the CHG context, and 7.02% and 8.22% in the CHH context for the adult and juvenile leaves, respectively. The number of differentially methylated regions in all contexts distributed in the genic regions varied. Additionally, inhibited DNA methylation in adult leaves activated the transcription of indole-3-acetic acid related genes in the signaling, response, and transport pathways. Moreover, the opposite methylation and expression patterns were observed for the SPL and AP2 family genes between the adult and juvenile leaves. Both gene families contribute to the M. hupehensis vegetative phase transition. Furthermore, the hyper-/hypomethylation of the gene body or promoter of transcription factor genes may lead to up-/downregulated gene expression. The methylation levels of the WRKY (22), NAC (21), ERF (8), WOX (2), KNAT (6), EIN3 (2), SCL (7), ZAT (7), and HSF (4) genes were higher in the adult leaves than in the juvenile leaves, whereas the opposite pattern was observed for the TCP (2), MADS-box (11), and DOF (3) genes. An analysis of the correlation between methylation and transcription indicated the methylation of the gene body in all contexts and the methylation of the promoter in the CG and CHG contexts are negatively correlated with gene expression. However, the methylation of the promoter in the CHH context is positively correlated with gene expression. These findings reflect the diversity in the epigenetic regulation of gene expression and may be useful for elucidating the epigenetic regulatory mechanism underlying the M. hupehensis vegetative phase transition.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture Rural Affairs, 712100 Yangling, Shaanxi, People's Republic of China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, 712100 Yangling, Shaanxi, People's Republic of China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Hua Zhou
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Wei Zhang
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Qingwei Zhang
- College of Life Science, Southwest University, Chongqing, People's Republic of China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, 712100 Yangling, Shaanxi, People's Republic of China
| | - Juan Zhao
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture Rural Affairs, 712100 Yangling, Shaanxi, People's Republic of China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, 712100 Yangling, Shaanxi, People's Republic of China
- College of Mechanical and Electronic Engineering, Northwest A & F University, 712100 Yangling, Shaanxi, People's Republic of China
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Morgado L, Johannes F. Computational tools for plant small RNA detection and categorization. Brief Bioinform 2020; 20:1181-1192. [PMID: 29059285 PMCID: PMC6781577 DOI: 10.1093/bib/bbx136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/09/2017] [Indexed: 01/06/2023] Open
Abstract
Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.
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Affiliation(s)
- Lionel Morgado
- Corresponding author: Lionel Morgado, Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 25 7, 9747 AG Groningen, The Netherlands. Tel.: +31 685 585 827; E-mail:
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Rajkumar MS, Shankar R, Garg R, Jain M. Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars. Genomics 2020; 112:3537-3548. [PMID: 32278023 DOI: 10.1016/j.ygeno.2020.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
Abstract
DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rama Shankar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Zheng Y, Ge J, Bao C, Chang W, Liu J, Shao J, Liu X, Su L, Pan L, Zhou DX. Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response. MOLECULAR PLANT 2020; 13:598-611. [PMID: 31891777 DOI: 10.1016/j.molp.2019.12.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Epigenetic regulation of gene expression is important for plant adaptation to environmental changes. Previous results showed that Arabidopsis RPD3-like histone deacetylase HDA9 is known to function in repressing plant response to stress in Arabidopsis. However, how HDA9 targets to specific chromatin loci and controls gene expression networks involved in plant response to stress remains largely unclear. Here, we show that HDA9 represses stress tolerance response by interacting with and regulating the DNA binding and transcriptional activity of WRKY53, which functions as a high-hierarchy positive regulator of stress response. We found that WRKY53 is post-translationally modified by lysine acetylation at multiple sites, some of which are removed by HDA9, resulting in inhibition of WRKY53 transcription activity. Conversely, WRKY53 negatively regulates HDA9 histone deacetylase activity. Collectively, our results indicate that HDA9 and WRK53 are reciprocal negative regulators of each other's activities, illustrating how the functional interplay between a chromatin regulator and a transcription factor regulates stress tolerance in plants.
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Affiliation(s)
- Yu Zheng
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China.
| | - Jingyu Ge
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Chun Bao
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Wenwen Chang
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Jingjing Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Jingjie Shao
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lufang Su
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Lei Pan
- Institute for Interdisciplinary Research and Hubei Province Engineering Research Center of Legume Plants, Jianghan University, Wuhan 430056, China
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, CNRS, INRAE, Université Paris-Saclay, Orsay 91405, France.
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Fang Y, Coelho MA, Shu H, Schotanus K, Thimmappa BC, Yadav V, Chen H, Malc EP, Wang J, Mieczkowski PA, Kronmiller B, Tyler BM, Sanyal K, Dong S, Nowrousian M, Heitman J. Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet 2020; 16:e1008646. [PMID: 32150559 PMCID: PMC7082073 DOI: 10.1371/journal.pgen.1008646] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/19/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often repetitive, making them challenging to assemble and identify. Here, we describe centromeres in an oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and during nuclear division. We report an improved genome assembly of the P. sojae reference strain, which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the histone modification H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup including diatoms and Plasmodium falciparum that have relatively short and simple regional centromeres. Identification of P. sojae centromeres in turn also advances the genome assembly. Oomycetes are fungal-like microorganisms that belong to the stramenopiles within the Stramenopila-Alveolata-Rhizaria (SAR) supergroup. The Phytophthora oomycetes are infamous as plant killers, threatening crop production worldwide. Because of the highly repetitive nature of their genomes, assembly of oomycete genomes presents challenges that impede identification of centromeres, which are chromosomal sites mediating faithful chromosome segregation. We report long-read sequencing-based genome assembly of the Phytophthora sojae reference strain, which facilitated the discovery of centromeres. P. sojae harbors large regional centromeres fully embedded in heterochromatin, and enriched for a Copia-like transposon that is also found in discrete clusters in other oomycetes. This study provides insight into the oomycete genome organization, broadens our knowledge of centromere structure, function and evolution in eukaryotes, and may help elucidate the high frequency of aneuploidy during oomycete reproduction.
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Affiliation(s)
- Yufeng Fang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Haidong Shu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Klaas Schotanus
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bhagya C. Thimmappa
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Han Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ewa P. Malc
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy Wang
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Piotr A. Mieczkowski
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brett M. Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Minou Nowrousian
- Lehrstuhl fuer Molekulare und Zellulaere Botanik, Ruhr-Universitaet Bochum, Bochum, Germany
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Zhang W, Wang N, Yang J, Guo H, Liu Z, Zheng X, Li S, Xiang F. The salt-induced transcription factor GmMYB84 confers salinity tolerance in soybean. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110326. [PMID: 31928665 DOI: 10.1016/j.plantsci.2019.110326] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 05/26/2023]
Abstract
Transcription factor activation and DNA methylation are important plant responses to abiotic stress. Here, we established that the salinity stress-induced expression of the soybean (Glycine max) transcription factor-encoding gene GmMYB84 relies on DNA methylation. The level of DNA methylation at sequences 690 nt to 950 nt upstream of the GmMYB84 transcription initiation codon was markedly reduced in plants exposed to salinity stress, resulting in a higher abundance of transcripts. When challenged with salinity stress, plants constitutively expressing GmMYB84 outperformed untransformed plants with respect to their germination rate, primary root elongation, proline accumulation, antioxidant enzyme activity, membrane integrity, and K+ levels. Arabidopsis thaliana plants heterologously expressing GmMYB84 were more tolerant to salt stress and exhibited higher germination rates than the wild type. Electrophoretic mobility shift assays revealed that GmMYB84 binds to the cis-regulatory sequences of GmAKT1, the homolog of ARABIDOPSIS K+ TRANSPORTER 1 (AKT1). Thus, DNA methylation modulates the salinity stress-induced expression of the soybean transcription factor-encoding gene GmMYB84 and thereby confers salinity stress tolerance.
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Affiliation(s)
- Wenxiao Zhang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Nan Wang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Jingting Yang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Hui Guo
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhenhua Liu
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaojian Zheng
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Shuo Li
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China.
| | - Fengning Xiang
- The Key Laboratory of the Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China.
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Tao X, Feng S, Zhao T, Guan X. Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag. PLANT METHODS 2020; 16:120. [PMID: 32884577 PMCID: PMC7460760 DOI: 10.1186/s13007-020-00664-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/25/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND In 2019, Kaya-Okur et al. reported on the cleavage under targets and tagmentation (CUT&Tag) technology for efficient profiling of epigenetically modified DNA fragments. It was used mainly for cultured cell lines and was especially effective for small samples and single cells. This strategy generated high-resolution and low-background-noise chromatin profiling data for epigenomic analysis. CUT&Tag is well suited to be used in plant cells, especially in tissues from which small samples are taken, such as ovules, anthers, and fibers. RESULTS Here, we present a CUT&Tag protocol step by step using plant nuclei. In this protocol, we quantified the nuclei that can be used in each CUT&Tag reaction, and compared the efficiency of CUT&Tag with chromatin immunoprecipitation with sequencing (ChIP-seq) in the leaves of cotton. A general workflow for the bioinformatic analysis of CUT&Tag is also provided. Results indicated that, compared with ChIP-seq, the CUT&Tag procedure was faster and showed a higher-resolution, lower-background signal than did ChIP. CONCLUSION A CUT&Tag protocol has been refined for plant cells using intact nuclei that have been isolated.
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Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Shouli Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. NATURE PLANTS 2019; 5:1250-1259. [PMID: 31740772 DOI: 10.1038/s41477-019-0548-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Abstract
Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.
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Affiliation(s)
- Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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Zhao T, Zhan Z, Jiang D. Histone modifications and their regulatory roles in plant development and environmental memory. J Genet Genomics 2019; 46:467-476. [PMID: 31813758 DOI: 10.1016/j.jgg.2019.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022]
Abstract
Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China.
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Guo H, Wu T, Li S, He Q, Yang Z, Zhang W, Gan Y, Sun P, Xiang G, Zhang H, Deng H. The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice. Int J Mol Sci 2019; 20:ijms20205089. [PMID: 31615063 PMCID: PMC6829347 DOI: 10.3390/ijms20205089] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/09/2019] [Accepted: 10/12/2019] [Indexed: 01/22/2023] Open
Abstract
Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.
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Affiliation(s)
- Hui Guo
- State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410013, China.
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Tingkai Wu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| | - Shuxing Li
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Qiang He
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Zhanlie Yang
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Wuhan Zhang
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Yu Gan
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Pingyong Sun
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Guanlun Xiang
- Rice Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550006, China.
| | - Hongyu Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| | - Huafeng Deng
- State Key Laboratory of Hybrid Rice, Longping Branch of Graduate School, Central South University, Changsha 410013, China.
- Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Brown K, Takawira LT, O'Neill MM, Mizrachi E, Myburg AA, Hussey SG. Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis. THE NEW PHYTOLOGIST 2019; 223:1937-1951. [PMID: 31063599 DOI: 10.1111/nph.15897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 05/03/2023]
Abstract
Accessible chromatin changes dynamically during development and harbours functional regulatory regions which are poorly understood in the context of wood development. We explored the importance of accessible chromatin in Eucalyptus grandis in immature xylem generally, and MYB transcription factor-mediated transcriptional programmes specifically. We identified biologically reproducible DNase I Hypersensitive Sites (DHSs) and assessed their functional significance in immature xylem through their associations with gene expression, epigenomic data and DNA sequence conservation. We identified in vitro DNA binding sites for six secondary cell wall-associated Eucalyptus MYB (EgrMYB) transcription factors using DAP-seq, reconstructed protein-DNA networks of predicted targets based on binding sites within or outside DHSs and assessed biological enrichment of these networks with published datasets. 25 319 identified immature xylem DHSs were associated with increased transcription and significantly enriched for various epigenetic signatures (H3K4me3, H3K27me3, RNA pol II), conserved noncoding sequences and depleted single nucleotide variants. Predicted networks built from EgrMYB binding sites located in accessible chromatin were significantly enriched for systems biology datasets relevant to wood formation, whereas those occurring in inaccessible chromatin were not. Our study demonstrates that DHSs in E. grandis immature xylem, most of which are intergenic, are of functional significance to gene regulation in this tissue.
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Affiliation(s)
- Katrien Brown
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Marja M O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
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Ayyappan V, Sripathi VR, Kalavacharla V(K, Saha MC, Thimmapuram J, Bhide KP, Fiedler E. Genome-wide identification of histone methylation (H3K9 me2) and acetylation (H4K12 ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics 2019; 20:667. [PMID: 31438854 PMCID: PMC6704705 DOI: 10.1186/s12864-019-6038-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2019] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. RESULTS This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. CONCLUSIONS The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid-monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| | - Venkateswara R. Sripathi
- Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL USA
| | - Venu ( Kal) Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE USA
| | | | | | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
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Liu Y, Tian T, Zhang K, You Q, Yan H, Zhao N, Yi X, Xu W, Su Z. PCSD: a plant chromatin state database. Nucleic Acids Res 2019; 46:D1157-D1167. [PMID: 29040761 PMCID: PMC5753246 DOI: 10.1093/nar/gkx919] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/28/2017] [Indexed: 01/06/2023] Open
Abstract
Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. We collected public and in-house plant epigenomic data sets and applied a Hidden Markov Model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of Arabidopsis thaliana, Oryza sativa and Zea mays, respectively. We constructed a Plant Chromatin State Database (PCSD, http://systemsbiology.cau.edu.cn/chromstates) to integrate detailed information about chromatin states, including the features and distribution of states, segments in states and related genes with segments. The self-organization mapping (SOM) results for these different chromatin signatures and UCSC Genome Browser for visualization were also integrated into the PCSD database. We further provided differential SOM maps between two epigenetic marks for chromatin state comparison and custom tools for new data analysis. The segments and related genes in SOM maps can be searched and used for motif and GO analysis, respectively. In addition, multi-species integration can be used to discover conserved features at the epigenomic level. In summary, our PCSD database integrated the identified chromatin states with epigenetic features and may be beneficial for communities to discover causal functions hidden in plant chromatin.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tian Tian
- 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
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Nannan Zhao
- 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
| | - 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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50
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Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation. PLANT & CELL PHYSIOLOGY 2019; 60:1702-1721. [PMID: 31077318 DOI: 10.1093/pcp/pcz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pen Jia
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Juan Zhao
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
- College of Mechanical and Electronic Engineering, Northwest A & F University, Yangling, Shaanxi, P. R. China
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