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Bobadilla LK, Tranel PJ. Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance. PEST MANAGEMENT SCIENCE 2024; 80:235-244. [PMID: 37595061 DOI: 10.1002/ps.7728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The emergence of herbicide-resistant weeds is a significant threat to modern agriculture. Cross resistance, a phenomenon where resistance to one herbicide confers resistance to another, is a particular concern owing to its unpredictability. Nontarget-site (NTS) cross resistance is especially challenging to predict, as it arises from genes that encode enzymes that do not directly involve the herbicide target site and can affect multiple herbicides. Recent advancements in genomic and structural biology techniques could provide new venues for predicting NTS resistance in weed species. In this review, we present an overview of the latest approaches that could be used. We discuss the use of genomic and epigenomics techniques such as ATAC-seq and DAP-seq to identify transcription factors and cis-regulatory elements associated with resistance traits. Enzyme/protein structure prediction and docking analysis are discussed as an initial step for predicting herbicide binding affinities with key enzymes to identify candidates for subsequent in vitro validation. We also provide example analyses that can be deployed toward elucidating cross resistance and its regulatory patterns. Ultimately, our review provides important insights into the latest scientific advancements and potential directions for predicting and managing herbicide cross resistance in weeds. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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2
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [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: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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3
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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Khan A, Pudhuvai B, Shrestha A, Mishra AK, Shah MP, Koul B, Dey N. CRISPR-mediated iron and folate biofortification in crops: advances and perspectives. Biotechnol Genet Eng Rev 2023:1-31. [PMID: 37092872 DOI: 10.1080/02648725.2023.2205202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Micronutrient deficiency conditions, such as anemia, are the most prevalent global health problem due to inadequate iron and folate in dietary sources. Biofortification advancements can propel the rapid amelioration of nutritionally beneficial components in crops that are required to combat the adverse effects of micronutrient deficiencies on human health. To date, several strategies have been proposed to increase micronutrients in plants to improve food quality, but very few approaches have intrigued `clustered regularly interspaced short palindromic repeats' (CRISPR) modules for the enhancement of iron and folate concentration in the edible parts of plants. In this review, we discuss two important approaches to simultaneously enhance the bioavailability of iron and folate concentrations in rice endosperms by utilizing advanced CRISPR-Cas9-based technology. This includes the 'tuning of cis-elements' and 'enhancer re-shuffling' in the regulatory components of genes that play a vital role in iron and folate biosynthesis/transportation pathways. In particular, base-editing and enhancer re-installation in native promoters of selected genes can lead to enhanced accumulation of iron and folate levels in the rice endosperm. The re-distribution of micronutrients in specific plant organs can be made possible using the above-mentioned contemporary approaches. Overall, the present review discusses the possible approaches for synchronized iron and folate biofortification through modification in regulatory gene circuits employing CRISPR-Cas9 technology.
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Affiliation(s)
- Ahamed Khan
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Baveesh Pudhuvai
- Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Ankita Shrestha
- Division of Microbial and Plant Biotechnology, Department of Biotechnology, Government of India, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Maulin P Shah
- Division of Applied and Environmental Microbiology, Enviro Technology Ltd, Ankleshwar, Gujarat, India
| | - Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Nrisingha Dey
- Division of Microbial and Plant Biotechnology, Department of Biotechnology, Government of India, Institute of Life Sciences, Bhubaneswar, Odisha, India
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5
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Marand AP. Computational Analysis of Maize Enhancer Regulatory Elements Using ATAC-STARR-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524917. [PMID: 36711646 PMCID: PMC9882361 DOI: 10.1101/2023.01.20.524917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The blueprints to development, response to the environment, and cellular function are largely the manifestation of distinct gene expression programs controlled by the spatiotemporal activity of cis-regulatory elements. Although biochemical methods for identifying accessible chromatin - a hallmark of active cis-regulatory elements - have been developed, approaches capable of measuring and quantifying cis-regulatory activity are only beginning to be realized. Massively Parallel Reporter Assays coupled to chromatin accessibility profiling present a high-throughput solution for testing the transcription-activating capacity of millions of putatively regulatory DNA sequences in parallel. However, clear computational pipelines for analyzing these high-throughput sequencing-based reporter assays are lacking. In this protocol, I layout and rationalize a computational framework for the processing and analysis of Assay for Transposase Accessible Chromatin profiling followed by Self-Transcribed Active Regulatory Region sequencing (ATAC-STARR-seq) data from a recent study in Zea mays. The approach described herein can be adapted to other sequencing-based reporter assays and is largely agnostic to the model organism with the appropriate input substitutions.
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Wrightsman T, Marand AP, Crisp PA, Springer NM, Buckler ES. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. THE PLANT GENOME 2022; 15:e20249. [PMID: 35924336 DOI: 10.1002/tpg2.20249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/20/2022] [Indexed: 06/06/2024]
Abstract
Accessible chromatin regions are critical components of gene regulation but modeling them directly from sequence remains challenging, especially within plants, whose mechanisms of chromatin remodeling are less understood than in animals. We trained an existing deep-learning architecture, DanQ, on data from 12 angiosperm species to predict the chromatin accessibility in leaf of sequence windows within and across species. We also trained DanQ on DNA methylation data from 10 angiosperms because unmethylated regions have been shown to overlap significantly with ACRs in some plants. The across-species models have comparable or even superior performance to a model trained within species, suggesting strong conservation of chromatin mechanisms across angiosperms. Testing a maize (Zea mays L.) held-out model on a multi-tissue chromatin accessibility panel revealed our models are best at predicting constitutively accessible chromatin regions, with diminishing performance as cell-type specificity increases. Using a combination of interpretation methods, we ranked JASPAR motifs by their importance to each model and saw that the TCP and AP2/ERF transcription factor (TF) families consistently ranked highly. We embedded the top three JASPAR motifs for each model at all possible positions on both strands in our sequence window and observed position- and strand-specific patterns in their importance to the model. With our publicly available across-species 'a2z' model it is now feasible to predict the chromatin accessibility and methylation landscape of any angiosperm genome.
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Affiliation(s)
- Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Peter A Crisp
- School of Agriculture and Food Sciences, Univ. of Queensland, Brisbane, QLD, 4072, Australia
| | - Nathan M Springer
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, 55108, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell Univ., Ithaca, NY, 14853, USA
- USDA-ARS, Ithaca, NY, 14853, USA
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7
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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8
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Marand AP, Schmitz RJ. Single-cell analysis of cis-regulatory elements. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102094. [PMID: 34390932 DOI: 10.1016/j.pbi.2021.102094] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Plant tissues and organs are composed of functionally discrete cell types that are all defined by the same genome sequence. Cell-type variation in part arises from differential accessibility of cis-regulatory elements that encode the blueprints for transcriptional programs underlying cell identity and function. Owing to technical limitations, the role of cis-regulatory elements in cell identity maintenance, differentiation, and functional specialization has remained relatively unexplored in plant systems. Single-cell profiling has emerged as a powerful tool to circumvent these past obstacles by enabling unbiased charting of transcriptional and cis-regulatory states at the resolution of individual cells. Here, we review state-of-the-art single-cell approaches and analytical frameworks that have paved the way for establishing the link between cellular phenotypic variation and cis-regulatory mechanisms in plants.
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Affiliation(s)
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Jain M, Garg R. Enhancers as potential targets for engineering salinity stress tolerance in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:1382-1391. [PMID: 33837536 DOI: 10.1111/ppl.13421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Enhancers represent noncoding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features. Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to nonavailability of plant-specific experimental and computational approaches for their discovery. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.
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Affiliation(s)
- Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
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Marand AP, Chen Z, Gallavotti A, Schmitz RJ. A cis-regulatory atlas in maize at single-cell resolution. Cell 2021; 184:3041-3055.e21. [PMID: 33964211 DOI: 10.1101/2020.09.27.315499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 05/22/2023]
Abstract
cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. Using single-cell genomics in six maize organs, we determined the cis- and trans-regulatory factors defining diverse cell identities and coordinating chromatin organization by profiling transcription factor (TF) combinatorics, identifying TFs with non-cell-autonomous activity, and uncovering TFs underlying higher-order chromatin interactions. Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. Moreover, we found cell-type-specific CREs are hotspots for phenotype-associated genetic variants and were targeted by selection during modern maize breeding, highlighting the biological implications of this CRE atlas. Through comparison of maize and Arabidopsis thaliana developmental trajectories, we identified TFs and CREs with conserved and divergent chromatin dynamics, showcasing extensive evolution of gene regulatory networks. In addition to this rich dataset, we developed single-cell analysis software, Socrates, which can be used to understand cis-regulatory variation in any species.
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Affiliation(s)
| | - Zongliang Chen
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Fan X, Liu L, Qian K, Chen J, Zhang Y, Xie P, Xu M, Hu Z, Yan W, Wu Y, Xu G, Fan X. Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice. BMC PLANT BIOLOGY 2021; 21:211. [PMID: 33975546 PMCID: PMC8111971 DOI: 10.1186/s12870-021-02953-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress. RESULTS Our results showed that external N deficiency could decrease seed N content and plant growth of the overexpression line. During the filial growth, we found that the low parent seed nitrogen (LPSN) in the overexpression line could lead to a decrease in the filial seed nitrogen content, total plant nitrogen content, yield, and OsNAR2.1 expression (28, 35, 23, and 55%, respectively) compared with high parent seed nitrogen (HPSN) in high nitrogen external supply. However, such decreases were not observed in wild type. Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type. CONCLUSIONS We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1, resulting in a heritable phenotype of N deficiency over two generations of the overexpression line.
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Affiliation(s)
- Xiaoru Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Laihua Liu
- Vazyme Biotech Co Ltd, Nanjing, 210033, China
| | - Kaiyun Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingguang Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- School of Agriculture, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuyue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Man Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - WenKai Yan
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufeng Wu
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China.
- College of Resource and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China.
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12
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A cis-regulatory atlas in maize at single-cell resolution. Cell 2021; 184:3041-3055.e21. [PMID: 33964211 DOI: 10.1016/j.cell.2021.04.014] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. Using single-cell genomics in six maize organs, we determined the cis- and trans-regulatory factors defining diverse cell identities and coordinating chromatin organization by profiling transcription factor (TF) combinatorics, identifying TFs with non-cell-autonomous activity, and uncovering TFs underlying higher-order chromatin interactions. Cell-type-specific CREs were enriched for enhancer activity and within unmethylated long terminal repeat retrotransposons. Moreover, we found cell-type-specific CREs are hotspots for phenotype-associated genetic variants and were targeted by selection during modern maize breeding, highlighting the biological implications of this CRE atlas. Through comparison of maize and Arabidopsis thaliana developmental trajectories, we identified TFs and CREs with conserved and divergent chromatin dynamics, showcasing extensive evolution of gene regulatory networks. In addition to this rich dataset, we developed single-cell analysis software, Socrates, which can be used to understand cis-regulatory variation in any species.
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13
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Lin Y, Zhao H, Kotlarz M, Jiang J. Enhancer-mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:661-671. [PMID: 33547831 DOI: 10.1111/tpj.15189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Gene expression is controlled and regulated by interactions between cis-regulatory DNA elements (CREs) and regulatory proteins. Enhancers are one of the most important classes of CREs in eukaryotes. Eukaryotic genes, especially those related to development or responses to environmental cues, are often regulated by multiple enhancers in different tissues and/or at different developmental stages. Remarkably, little is known about the molecular mechanisms by which enhancers regulate gene expression in plants. We identified a distal enhancer, CREβ, which regulates the expression of AtDGK7, which encodes a diacylglycerol kinase in Arabidopsis. We developed a transgenic line containing the luciferase reporter gene (LUC) driven by CREβ fused with a minimal cauliflower mosaic virus (CaMV) 35S promoter. The CREβ enhancer was shown to play a role in the response to osmotic pressure of the LUC reporter gene. A forward genetic screen pipeline based on the transgenic line was established to generate mutations associated with altered expression of the LUC reporter gene. We identified a suite of mutants with variable LUC expression levels as well as different segregation patterns of the mutations in populations. We demonstrate that this pipeline will allow us to identify trans-regulatory factors associated with CREβ function as well as those acting in the regulation of the endogenous AtDGK7 gene.
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Affiliation(s)
- Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agriculture University, Changsha, 410128, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Magdalena Kotlarz
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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14
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Huang MK, Zhang L, Zhou LM, Yung WS, Li MW, Lam HM. Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions. Genes (Basel) 2021; 12:640. [PMID: 33923056 PMCID: PMC8146116 DOI: 10.3390/genes12050640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.
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Affiliation(s)
- Ming-Kun Huang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; (M.-K.H.); (L.-M.Z.); (W.-S.Y.); (M.-W.L.)
| | - Ling Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518055, China
| | - Li-Meng Zhou
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; (M.-K.H.); (L.-M.Z.); (W.-S.Y.); (M.-W.L.)
| | - Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; (M.-K.H.); (L.-M.Z.); (W.-S.Y.); (M.-W.L.)
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; (M.-K.H.); (L.-M.Z.); (W.-S.Y.); (M.-W.L.)
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; (M.-K.H.); (L.-M.Z.); (W.-S.Y.); (M.-W.L.)
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15
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Lin Y, Jiang J. Rapid Validation of Transcriptional Enhancers Using a Transient Reporter Assay. Methods Mol Biol 2021; 2328:253-259. [PMID: 34251631 DOI: 10.1007/978-1-0716-1534-8_16] [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: 12/17/2023]
Abstract
Enhancers are one of the main classes of cis-regulatory elements (CREs) in the regulation of plant gene expression. Plant enhancers can be predicted based on genomic signatures associated with open chromatin. However, predicted enhancers need to be validated experimentally. We developed an experimental system for rapid enhancer validation. Predicted enhancer candidates are cloned into a vector containing a minimal 35S promoter and a luciferase reporter gene. The construct is then agroinfiltrated into Nicotiana benthamiana leaves followed by bioluminescence signal detection and analysis. Positive bioluminescence signals indicate the enhancer function of each candidate, and the relative signal strength from different enhancers can be quantitatively measured and compared. In summary, we have developed an efficient and rapid plant enhancer validation assay based on a bioluminescent luciferase reporter and agroinfiltration-based N. benthamiana leaf transient expression. This assay can be used for the initial screening of candidate enhancers that are active in leaf tissue. The system can potentially be used to examine the activity of candidate enhancers under different environmental conditions.
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Affiliation(s)
- Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
- Michigan State University AgBioResearch, East Lansing, MI, USA.
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16
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Galli M, Feng F, Gallavotti A. Mapping Regulatory Determinants in Plants. Front Genet 2020; 11:591194. [PMID: 33193733 PMCID: PMC7655918 DOI: 10.3389/fgene.2020.591194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Fan Feng
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
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17
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Jores T, Tonnies J, Dorrity MW, Cuperus JT, Fields S, Queitsch C. Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves. THE PLANT CELL 2020; 32:2120-2131. [PMID: 32409318 PMCID: PMC7346570 DOI: 10.1105/tpc.20.00155] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 05/04/2023]
Abstract
Genetic engineering of cis-regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis-regulatory elements. Here, we adapted self-transcribing active regulatory region sequencing (STARR-seq)-a technology for the high-throughput identification of enhancers-for its use in transiently transformed tobacco (Nicotiana benthamiana) leaves. We demonstrate that the optimal placement in the reporter construct of enhancer sequences from a plant virus, pea (Pisum sativum) and wheat (Triticum aestivum), was just upstream of a minimal promoter and that none of these four known enhancers was active in the 3' untranslated region of the reporter gene. The optimized assay sensitively identified small DNA regions containing each of the four enhancers, including two whose activity was stimulated by light. Furthermore, we coupled the assay to saturation mutagenesis to pinpoint functional regions within an enhancer, which we recombined to create synthetic enhancers. Our results describe an approach to define enhancer properties that can be performed in potentially any plant species or tissue transformable by Agrobacterium and that can use regulatory DNA derived from any plant genome.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Graduate Program in Biology, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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18
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Jones DM, Vandepoele K. Identification and evolution of gene regulatory networks: insights from comparative studies in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:42-48. [PMID: 32062128 DOI: 10.1016/j.pbi.2019.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
The availability of genome sequences, genome-wide assays of transcription factor binding, and accessible chromatin maps have unveiled gene regulatory landscapes in plants. This understanding has ushered in comparative gene regulatory network studies that assess network rewiring between species, across time, and between biological tissues. Comparisons of cis-regulatory elements across the plant kingdom have uncovered examples of conserved sequences, but also of divergence, indicating that selective pressures can vary in different plant families. Transcription factor duplication, followed by spatiotemporal expression divergence of the duplicates, also appears to be a key mechanism of network evolution. Here, we review recent literature describing the regulation of gene expression in plants, and how comparative studies provide insights into how these regulatory interactions change and lead to gene regulatory network rewiring.
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Affiliation(s)
- D Marc Jones
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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19
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Abstract
Enhancers are cis-acting elements with many sites bound by transcription factors and activate transcription over long distance. Histone modifications are critical for enhancer activity and utilized as hallmarks for the identification of putative enhancers. Monomethylation of histone H3 lysine 4 (H3K4me1) is the mark for enhancer priming; acetylation of histone H3 lysine 27 (H3K27ac) for active enhancers and trimethylation of histone H3 lysine 27 (H3K27me3) for silent enhancers. Recent studies from multiple groups have provided evidence that enhancer reprogramming, especially gain of enhancer activity, is closely related to tumorigenesis and cancer development. In this review, we will summarize the recent discoveries about enhancer regulation and the mechanisms of enhancer reprogramming in tumorigenesis, and discuss the potential application of enhancer manipulation in precision medicine.
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Affiliation(s)
- Jie Yao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Ji Chen
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Lian-Yun Li
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
| | - Min Wu
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, Hubei, China
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20
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Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X. Widespread long-range cis-regulatory elements in the maize genome. NATURE PLANTS 2019; 5:1237-1249. [PMID: 31740773 PMCID: PMC6904520 DOI: 10.1038/s41477-019-0547-0] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Abstract
Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the widespread existence of gene-distal (hereafter, distal) loci that act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Putative CREs also display elevated transcriptional enhancer activities, as measured by self-transcribing active regulatory region sequencing. These results provide functional support for the widespread existence of CREs that act over large genomic distances to control gene expression.
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Affiliation(s)
- William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | | | | | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | | | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Plant Science, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Department of Plant Science, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | | | | | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- US Department of Agriculture-Agricultural Research Service, Robert Holley Center, Ithaca, NY, USA
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA.
- Institute for Advanced Study, Technical University of Munich, Garching, Germany.
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
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21
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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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22
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Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N. The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Res 2019; 46:2380-2397. [PMID: 29365184 PMCID: PMC5861414 DOI: 10.1093/nar/gky025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, WI 53705, USA.,State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Georgia C Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR 72160, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
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23
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Wu Z, Tang J, Zhuo J, Tian Y, Zhao F, Li Z, Yan Y, Yang R. Chromatin Signature and Transcription Factor Binding Provide a Predictive Basis for Understanding Plant Gene Expression. PLANT & CELL PHYSIOLOGY 2019; 60:1471-1486. [PMID: 31038680 DOI: 10.1093/pcp/pcz051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Chromatin accessibility and post-transcriptional histone modifications play important roles in gene expression regulation. However, little is known about the joint effect of multiple chromatin modifications on the gene expression level in plants, despite that the regulatory roles of individual histone marks such as H3K4me3 in gene expression have been well-documented. By using machine-learning methods, we systematically performed gene expression level prediction based on multiple chromatin modifications data in Arabidopsis and rice. We found that as few as four histone modifications were sufficient to yield good prediction performance, and H3K4me3 and H3K36me3 being the top two predictors with known functions related to transcriptional initiation and elongation, respectively. We demonstrated that the predictive powers differed between protein-coding and non-coding genes as well as between CpG-enriched and CpG-depleted genes. We also showed that the predictive model trained in one tissue or species could be applied to another tissue or species, suggesting shared underlying mechanisms. More interestingly, the gene expression levels of conserved orthologs are easier to predict than the species-specific genes. In addition, chromatin state of distal enhancers was moderately correlated to gene expression but was dispensable if given the chromatin features of the proximal regions of genes. We further extended the analysis to transcription factor (TF) binding data. Strikingly, the combinatorial effects of only a few TFs were roughly fit to gene expression levels in Arabidopsis. Overall, by using quantitative modeling, we provide a comprehensive and unbiased perspective on the epigenetic and TF-mediated regulation of gene expression in plants.
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Affiliation(s)
- Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jing Tang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Junjie Zhuo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhan Tian
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Feiyang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhaohong Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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24
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Long-range interactions between proximal and distal regulatory regions in maize. Nat Commun 2019; 10:2633. [PMID: 31201330 PMCID: PMC6572780 DOI: 10.1038/s41467-019-10603-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 05/20/2019] [Indexed: 12/30/2022] Open
Abstract
Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal–distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize. Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.
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25
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Global Quantitative Mapping of Enhancers in Rice by STARR-seq. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:140-153. [PMID: 31201999 PMCID: PMC6624190 DOI: 10.1016/j.gpb.2018.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/21/2022]
Abstract
Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5′ untranslated regions (5′UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.
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26
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Wang H, Li S, Li Y, Xu Y, Wang Y, Zhang R, Sun W, Chen Q, Wang XJ, Li C, Zhao J. MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling. NATURE PLANTS 2019; 5:616-625. [PMID: 31182849 DOI: 10.1038/s41477-019-0441-449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/08/2019] [Indexed: 05/26/2023]
Abstract
The lipid-derived hormone jasmonate (JA) regulates plant immunity and adaptive growth by triggering a genome-wide transcriptional programme. In Arabidopsis thaliana, JA-triggered transcriptional programming is largely orchestrated by the master transcription factor MYC2. The function of MYC2 is dependent on its physical interaction with the MED25 subunit of the Mediator transcriptional co-activator complex. Here we report the identification of JA enhancers (JAEs) through profiling the occupancy pattern of MYC2 and MED25. JA regulates the dynamic chromatin looping between JAEs and their promoters in a MED25-dependent manner, while MYC2 auto-regulates itself through JAEs. Interestingly, the JAE of the MYC2 locus (named ME2) positively regulates MYC2 expression during short-term JA responses but negatively regulates it during constant JA responses. We demonstrate that new gene editing tools open up new avenues to elucidate the in vivo function of enhancers. Our work provides a paradigm for functional study of plant enhancers in the regulation of specific physiological processes.
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Affiliation(s)
- Hang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Shuyu Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan'an Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiran Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Yunhao Wang
- Key Laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ruoxi Zhang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenjing Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Qian Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiu-Jie Wang
- Key Laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jiuhai Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China.
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Wang H, Li S, Li Y, Xu Y, Wang Y, Zhang R, Sun W, Chen Q, Wang XJ, Li C, Zhao J. MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling. NATURE PLANTS 2019; 5:616-625. [PMID: 31182849 DOI: 10.1038/s41477-019-0441-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/08/2019] [Indexed: 05/19/2023]
Abstract
The lipid-derived hormone jasmonate (JA) regulates plant immunity and adaptive growth by triggering a genome-wide transcriptional programme. In Arabidopsis thaliana, JA-triggered transcriptional programming is largely orchestrated by the master transcription factor MYC2. The function of MYC2 is dependent on its physical interaction with the MED25 subunit of the Mediator transcriptional co-activator complex. Here we report the identification of JA enhancers (JAEs) through profiling the occupancy pattern of MYC2 and MED25. JA regulates the dynamic chromatin looping between JAEs and their promoters in a MED25-dependent manner, while MYC2 auto-regulates itself through JAEs. Interestingly, the JAE of the MYC2 locus (named ME2) positively regulates MYC2 expression during short-term JA responses but negatively regulates it during constant JA responses. We demonstrate that new gene editing tools open up new avenues to elucidate the in vivo function of enhancers. Our work provides a paradigm for functional study of plant enhancers in the regulation of specific physiological processes.
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Affiliation(s)
- Hang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Shuyu Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan'an Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiran Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Yunhao Wang
- Key Laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ruoxi Zhang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenjing Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Qian Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiu-Jie Wang
- Key Laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jiuhai Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China.
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Colinas M, Goossens A. Combinatorial Transcriptional Control of Plant Specialized Metabolism. TRENDS IN PLANT SCIENCE 2018; 23:324-336. [PMID: 29395832 DOI: 10.1016/j.tplants.2017.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 05/23/2023]
Abstract
Plants produce countless specialized compounds of diverse chemical nature and biological activities. Their biosynthesis often exclusively occurs either in response to environmental stresses or is limited to dedicated anatomical structures. In both scenarios, regulation of biosynthesis appears to be mainly controlled at the transcriptional level, which is generally dependent on a combined interplay of DNA-related mechanisms and the activity of transcription factors that may act in a combinatorial manner. How environmental and developmental cues are integrated into a coordinated cell type-specific stress response has only partially been unraveled so far. Building on the available examples from (metabolic) gene expression, here we propose theoretical models of how this integration of signals may occur at the level of transcriptional control.
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Affiliation(s)
- Maite Colinas
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium.
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Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
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Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
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Sheshukova EV, Komarova TV, Ershova NM, Shindyapina AV, Dorokhov YL. An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene. FRONTIERS IN PLANT SCIENCE 2017; 8:2137. [PMID: 29312392 PMCID: PMC5742262 DOI: 10.3389/fpls.2017.02137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.
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Affiliation(s)
- Ekaterina V. Sheshukova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Komarova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia M. Ershova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia V. Shindyapina
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri L. Dorokhov
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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31
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Jamge S, Stam M, Angenent GC, Immink RGH. A cautionary note on the use of chromosome conformation capture in plants. PLANT METHODS 2017; 13:101. [PMID: 29177001 PMCID: PMC5691870 DOI: 10.1186/s13007-017-0251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants. RESULTS Here we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth. CONCLUSIONS The 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution.
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Affiliation(s)
- Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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32
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Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol 2017; 18:137. [PMID: 28732548 PMCID: PMC5522596 DOI: 10.1186/s13059-017-1273-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant. Result To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes. Conclusions Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1273-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Johan Zicola
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Sarah N Anderson
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, 40 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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Banf M, Rhee SY. Computational inference of gene regulatory networks: Approaches, limitations and opportunities. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:41-52. [PMID: 27641093 DOI: 10.1016/j.bbagrm.2016.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Gene regulatory networks lie at the core of cell function control. In E. coli and S. cerevisiae, the study of gene regulatory networks has led to the discovery of regulatory mechanisms responsible for the control of cell growth, differentiation and responses to environmental stimuli. In plants, computational rendering of gene regulatory networks is gaining momentum, thanks to the recent availability of high-quality genomes and transcriptomes and development of computational network inference approaches. Here, we review current techniques, challenges and trends in gene regulatory network inference and highlight challenges and opportunities for plant science. We provide plant-specific application examples to guide researchers in selecting methodologies that suit their particular research questions. Given the interdisciplinary nature of gene regulatory network inference, we tried to cater to both biologists and computer scientists to help them engage in a dialogue about concepts and caveats in network inference. Specifically, we discuss problems and opportunities in heterogeneous data integration for eukaryotic organisms and common caveats to be considered during network model evaluation. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
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