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An J, Brik Chaouche R, Pereyra-Bistraín LI, Zalzalé H, Wang Q, Huang Y, He X, Dias Lopes C, Antunez-Sanchez J, Bergounioux C, Boulogne C, Dupas C, Gillet C, Pérez-Pérez JM, Mathieu O, Bouché N, Fragkostefanakis S, Zhang Y, Zheng S, Crespi M, Mahfouz MM, Ariel F, Gutierrez-Marcos J, Raynaud C, Latrasse D, Benhamed M. An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution. Proc Natl Acad Sci U S A 2024; 121:e2400737121. [PMID: 38968127 DOI: 10.1073/pnas.2400737121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.
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Affiliation(s)
- Jing An
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Rim Brik Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Leonardo I Pereyra-Bistraín
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette F-91190, France
| | - Hugo Zalzalé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette F-91190, France
| | - Qingyi Wang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | | | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Claire Boulogne
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Cynthia Dupas
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Cynthia Gillet
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | | | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, Clermont-Ferrand F-63000, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | | | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | | | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette F-91190, France
- Institut Universitaire de France, Orsay, Gif-sur-Yvette 91190, France
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2
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Wang F, Xi Z, Wang M, Wang L, Wang J. Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38976378 DOI: 10.1111/tpj.16920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Linyou Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Crop and Nuclear Technology Utilization, Hangzhou, 310021, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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3
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Zhang X, Luo Z, Marand AP, Yan H, Jang H, Bang S, Mendieta JP, Minow MAA, Schmitz RJ. A spatially resolved multiomic single-cell atlas of soybean development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601616. [PMID: 39005400 PMCID: PMC11244997 DOI: 10.1101/2024.07.03.601616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cis -regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
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4
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Li T, Xu H, Teng S, Suo M, Bahitwa R, Xu M, Qian Y, Ramstein GP, Song B, Buckler ES, Wang H. Modeling 0.6 million genes for the rational design of functional cis-regulatory variants and de novo design of cis-regulatory sequences. Proc Natl Acad Sci U S A 2024; 121:e2319811121. [PMID: 38889146 PMCID: PMC11214048 DOI: 10.1073/pnas.2319811121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Rational design of plant cis-regulatory DNA sequences without expert intervention or prior domain knowledge is still a daunting task. Here, we developed PhytoExpr, a deep learning framework capable of predicting both mRNA abundance and plant species using the proximal regulatory sequence as the sole input. PhytoExpr was trained over 17 species representative of major clades of the plant kingdom to enhance its generalizability. Via input perturbation, quantitative functional annotation of the input sequence was achieved at single-nucleotide resolution, revealing an abundance of predicted high-impact nucleotides in conserved noncoding sequences and transcription factor binding sites. Evaluation of maize HapMap3 single-nucleotide polymorphisms (SNPs) by PhytoExpr demonstrates an enrichment of predicted high-impact SNPs in cis-eQTL. Additionally, we provided two algorithms that harnessed the power of PhytoExpr in designing functional cis-regulatory variants, and de novo creation of species-specific cis-regulatory sequences through in silico evolution of random DNA sequences. Our model represents a general and robust approach for functional variant discovery in population genetics and rational design of regulatory sequences for genome editing and synthetic biology.
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Affiliation(s)
- Tianyi Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Hui Xu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Shouzhen Teng
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Mingrui Suo
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Revocatus Bahitwa
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Legumes Research Program, Research and Innovation Division, Tanzania Agricultural Research Institute, Ilonga, Kilosa, Morogoro67410, Tanzania
| | - Mingchi Xu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Yiheng Qian
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
| | - Guillaume P. Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus8000, Denmark
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, People’s Republic of China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi712100, People’s Republic of China
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY14853
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY14853
| | - Hai Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing100193, People’s Republic of China
- Sanya Institute of China Agricultural University, Sanya572025, People’s Republic of China
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5
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Leduque B, Edera A, Vitte C, Quadrana L. Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing. Nucleic Acids Res 2024; 52:6285-6297. [PMID: 38676941 PMCID: PMC11194078 DOI: 10.1093/nar/gkae306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.
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Affiliation(s)
- Basile Leduque
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche Scientifique, Institute National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, Orsay, France
| | - Alejandro Edera
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche Scientifique, Institute National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, Orsay, France
| | - Clémentine Vitte
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Leandro Quadrana
- Institute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche Scientifique, Institute National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, Orsay, France
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6
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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7
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Galli M, Chen Z, Ghandour T, Chaudhry A, Gregory J, Li M, Zhang X, Dong Y, Song G, Walley JW, Chuck G, Whipple C, Kaeppler HF, Huang SSC, Gallavotti A. Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596834. [PMID: 38895211 PMCID: PMC11185568 DOI: 10.1101/2024.05.31.596834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.3% of the maize genome. TF binding site comparison in B73 and Mo17 inbreds reveals widespread differences, driven largely by structural variation, that correlate with gene expression changes. TF binding site presence-absence variation helps clarify complex QTL such as vgt1, an important determinant of maize flowering time, and DICE, a distal enhancer involved in herbivore resistance. Modification of TF binding regions via CRISPR-Cas9 mediated editing alters target gene expression and phenotype. Our functional catalog of maize TF binding events enables collective and comparative TF binding analysis, and highlights its value for agricultural improvement.
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Affiliation(s)
- Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Tara Ghandour
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Amina Chaudhry
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jason Gregory
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Yinxin Dong
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University; Ames, IA, 50011
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, WI, USA
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
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8
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Long Y, Wendel JF, Zhang X, Wang M. Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants. TRENDS IN PLANT SCIENCE 2024; 29:638-649. [PMID: 38061928 DOI: 10.1016/j.tplants.2023.11.009] [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: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 06/09/2024]
Abstract
Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.
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Affiliation(s)
- Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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9
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Vollen K, Zhao C, Alonso JM, Stepanova AN. Sourcing DNA parts for synthetic biology applications in plants. Curr Opin Biotechnol 2024; 87:103140. [PMID: 38723389 DOI: 10.1016/j.copbio.2024.103140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024]
Abstract
Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.
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Affiliation(s)
- Katie Vollen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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10
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Xin H, Liu X, Chai S, Yang X, Li H, Wang B, Xu Y, Lin S, Zhong X, Liu B, Lu Z, Zhang Z. Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops. THE PLANT CELL 2024; 36:2272-2288. [PMID: 38421027 PMCID: PMC11132967 DOI: 10.1093/plcell/koae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.
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Affiliation(s)
- Hongjia Xin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bowen Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuanchao Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyun Zhong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Liu
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091China
| | - Zefu Lu
- National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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11
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Hsieh JWA, Lin PY, Wang CT, Lee YJ, Chang P, Lu RJH, Chen PY, Wang CJR. Establishing an optimized ATAC-seq protocol for the maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1370618. [PMID: 38863553 PMCID: PMC11165127 DOI: 10.3389/fpls.2024.1370618] [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: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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12
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Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, Bass HW, Wendel JF. Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton. Mol Biol Evol 2024; 41:msae095. [PMID: 38758089 PMCID: PMC11140268 DOI: 10.1093/molbev/msae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
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Affiliation(s)
- Guanjing Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated, Chinese Academy of Agricultural Sciences, Institute of Cotton Research, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Emma R Miller
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shujun Ou
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Dongming Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Joseph P Gallagher
- Forage Seed and Cereal Research Unit, USDA/Agricultural Research Service, Corvallis, OR 97331, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, TX 77845, USA
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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13
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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14
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Vlad D, Zaidem M, Perico C, Sedelnikova O, Bhattacharya S, Langdale JA. The WIP6 transcription factor TOO MANY LATERALS specifies vein type in C 4 and C 3 grass leaves. Curr Biol 2024; 34:1670-1686.e10. [PMID: 38531358 DOI: 10.1016/j.cub.2024.03.007] [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] [Received: 12/20/2023] [Revised: 02/04/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Grass leaves are invariantly strap shaped with an elongated distal blade and a proximal sheath that wraps around the stem. Underpinning this shape is a scaffold of leaf veins, most of which extend in parallel along the proximo-distal leaf axis. Differences between species are apparent both in the vein types that develop and in the distance between veins across the medio-lateral leaf axis. A prominent engineering goal is to increase vein density in leaves of C3 photosynthesizing species to facilitate the introduction of the more efficient C4 pathway. Here, we discover that the WIP6 transcription factor TOO MANY LATERALS (TML) specifies vein rank in both maize (C4) and rice (C3). Loss-of-function tml mutations cause large lateral veins to develop in positions normally occupied by smaller intermediate veins, and TML transcript localization in wild-type leaves is consistent with a role in suppressing lateral vein development in procambial cells that form intermediate veins. Attempts to manipulate TML function in rice were unsuccessful because transgene expression was silenced, suggesting that precise TML expression is essential for shoot viability. This finding may reflect the need to prevent the inappropriate activation of downstream targets or, given that transcriptome analysis revealed altered cytokinin and auxin signaling profiles in maize tml mutants, the need to prevent local or general hormonal imbalances. Importantly, rice tml mutants display an increased occupancy of veins in the leaf, providing a step toward an anatomical chassis for C4 engineering. Collectively, a conserved mechanism of vein rank specification in grass leaves has been revealed.
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Affiliation(s)
- Daniela Vlad
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Maricris Zaidem
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Chiara Perico
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Olga Sedelnikova
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Samik Bhattacharya
- Resolve BioSciences GmbH, Alfred-Nobel-Straße 10, 40789 Monheim am Rhein, Germany
| | - Jane A Langdale
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK.
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15
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Tsuji H, Sato M. The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem. PLANT & CELL PHYSIOLOGY 2024; 65:322-337. [PMID: 38179836 PMCID: PMC11020210 DOI: 10.1093/pcp/pcae001] [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: 09/10/2023] [Revised: 11/30/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.
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Affiliation(s)
- Hiroyuki Tsuji
- Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Moeko Sato
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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16
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Zhang LL, Liu JX. 3D chromatin reorganization during stress responses in plants. Sci Bull (Beijing) 2024; 69:847-849. [PMID: 38278707 DOI: 10.1016/j.scib.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Affiliation(s)
- Lin-Lin Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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17
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. PLANT PHYSIOLOGY 2024; 194:2511-2532. [PMID: 38109503 PMCID: PMC10980416 DOI: 10.1093/plphys/kiad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (Mediator of paramutation1), with that of their parents, wild-type siblings, and backcrossed progeny in maize (Zea mays). Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of these DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that both TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in most TCM DMRs in F1 plants required Mop1, initiation of a new epigenetic state of these DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is independent of RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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18
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Xu D, Zeng L, Wang L, Yang DL. Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity. PLANT PHYSIOLOGY 2024; 194:2149-2164. [PMID: 37992039 DOI: 10.1093/plphys/kiad624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.
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Affiliation(s)
- Dachao Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjun Zeng
- Institute of Crop Sciences, Yichun Academy of Sciences, Yichun, 336000 Jiangxi, China
| | - Lili Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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19
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Zhang Q, Yang Z, Yang J. Dissecting the colocalized GWAS and eQTLs with mediation analysis for high-dimensional exposures and confounders. Biometrics 2024; 80:ujae050. [PMID: 38801257 DOI: 10.1093/biomtc/ujae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/14/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
To leverage the advancements in genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping for traits and molecular phenotypes to gain mechanistic understanding of the genetic regulation, biological researchers often investigate the expression QTLs (eQTLs) that colocalize with QTL or GWAS peaks. Our research is inspired by 2 such studies. One aims to identify the causal single nucleotide polymorphisms that are responsible for the phenotypic variation and whose effects can be explained by their impacts at the transcriptomic level in maize. The other study in mouse focuses on uncovering the cis-driver genes that induce phenotypic changes by regulating trans-regulated genes. Both studies can be formulated as mediation problems with potentially high-dimensional exposures, confounders, and mediators that seek to estimate the overall indirect effect (IE) for each exposure. In this paper, we propose MedDiC, a novel procedure to estimate the overall IE based on difference-in-coefficients approach. Our simulation studies find that MedDiC offers valid inference for the IE with higher power, shorter confidence intervals, and faster computing time than competing methods. We apply MedDiC to the 2 aforementioned motivating datasets and find that MedDiC yields reproducible outputs across the analysis of closely related traits, with results supported by external biological evidence. The code and additional information are available on our GitHub page (https://github.com/QiZhangStat/MedDiC).
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Affiliation(s)
- Qi Zhang
- Department of Mathematics and Statistics, University of New Hampshire, Durham, NH 03824, United States
| | - Zhikai Yang
- Complex Biosystems Program and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
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20
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Lu Z, Xiao X, Zheng Q, Wang X, Xu L. Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578316. [PMID: 38562775 PMCID: PMC10983863 DOI: 10.1101/2024.02.01.578316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This article provides an in-depth review of computational methods for predicting transcriptional regulators with query gene sets. Identification of transcriptional regulators is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement. Key points An introduction to available computational methods for predicting functional TRs from a query gene set.A detailed walk-through along with practical concerns and limitations.A systematic benchmark of NGS-based methods in terms of accuracy, sensitivity, coverage, and usability, using 570 TR perturbation-derived gene sets.NGS-based methods outperform motif-based methods. Among NGS methods, those utilizing larger databases and adopting region-centric approaches demonstrate favorable performance. BART, ChIP-Atlas, and Lisa are recommended as these methods have overall better performance in evaluated scenarios.
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21
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Höfer M, Schäfer M, Wang Y, Wink S, Xu S. Genetic Mechanism of Non-Targeted-Site Resistance to Diquat in Spirodela polyrhiza. PLANTS (BASEL, SWITZERLAND) 2024; 13:845. [PMID: 38592881 PMCID: PMC10975167 DOI: 10.3390/plants13060845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/27/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Understanding non-target-site resistance (NTSR) to herbicides represents a pressing challenge as NTSR is widespread in many weeds. Using giant duckweed (Spirodela polyrhiza) as a model, we systematically investigated genetic and molecular mechanisms of diquat resistance, which can only be achieved via NTSR. Quantifying the diquat resistance of 138 genotypes, we revealed an 8.5-fold difference in resistance levels between the most resistant and most susceptible genotypes. Further experiments suggested that diquat uptake and antioxidant-related processes jointly contributed to diquat resistance in S. polyrhiza. Using a genome-wide association approach, we identified several candidate genes, including a homolog of dienelactone hydrolase, that are associated with diquat resistance in S. polyrhiza. Together, these results provide new insights into the mechanisms and evolution of NTSR in plants.
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Affiliation(s)
- Martin Höfer
- Institute for Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55128 Mainz, Germany (M.S.)
| | - Martin Schäfer
- Institute for Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55128 Mainz, Germany (M.S.)
| | - Yangzi Wang
- Institute for Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55128 Mainz, Germany (M.S.)
| | - Samuel Wink
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Shuqing Xu
- Institute for Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55128 Mainz, Germany (M.S.)
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22
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genet 2024; 20:e1011174. [PMID: 38437180 PMCID: PMC10911594 DOI: 10.1371/journal.pgen.1011174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis-regulatory sequences. It remains unclear how such drastic cis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 (CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis-regulatory sequences. Our results demonstrate remarkable malleability in cis-regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis-regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis-regulation to effectively engineer trait variation from conserved productivity genes in crops.
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Affiliation(s)
- Danielle Ciren
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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Gomez-Cano F, Rodriguez J, Zhou P, Chu YH, Magnusson E, Gomez-Cano L, Krishnan A, Springer NM, de Leon N, Grotewold E. Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582075. [PMID: 38464086 PMCID: PMC10925184 DOI: 10.1101/2024.02.26.582075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks. In total, we analyzed ~4.6M interactions to generate four distinct types of TF-target networks: co-expression, protein-DNA interaction (PDI), trans-expression quantitative loci (trans-eQTL), and cis-eQTL combined with PDIs. To improve the functional annotation of TFs based on its target genes, we implemented three different strategies to integrate these four types of networks. We subsequently evaluated the effectiveness of our method through loss-of function mutant and random networks. The multi-network integration allowed us to identify transcriptional regulators of hormone-, metabolic- and development-related processes. Finally, using the topological properties of the fully integrated network, we identified potentially functional redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jonas Rodriguez
- Department of Plant and Agroecosystem Sciences, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
| | - Arjun Krishnan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
- Current address: Global Breeding, Bayer Crop Sciences, Chesterfield MO 63017, USA
| | - Natalia de Leon
- Department of Plant and Agroecosystem Sciences, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-6473, USA
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24
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Yan H, Mendieta JP, Zhang X, Marand AP, Liang Y, Luo Z, Minow MAA, Roulé T, Wagner D, Tu X, Wang Y, Zhong S, Wessler SR, Schmitz RJ. Evolution of plant cell-type-specific cis -regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574753. [PMID: 38260561 PMCID: PMC10802394 DOI: 10.1101/2024.01.08.574753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet our understanding of CRE evolution remains a challenge. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum , and Urochloa fusca ). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1 epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially critical silencer CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of cell-type-specific CRE evolution in plants.
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25
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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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26
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Shaw DE, Naftaly AS, White MA. Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome. Mol Biol Evol 2024; 41:msae020. [PMID: 38306314 PMCID: PMC10899008 DOI: 10.1093/molbev/msae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.
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Affiliation(s)
- Daniel E Shaw
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Michael A White
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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27
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Li F, Xi K, Li Y, Ming T, Huang Y, Zhang L. Genome-wide analysis of transmembrane 9 superfamily genes in wheat ( Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions. FRONTIERS IN PLANT SCIENCE 2024; 14:1324974. [PMID: 38259936 PMCID: PMC10800943 DOI: 10.3389/fpls.2023.1324974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Introduction Transmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments. Methods TraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1. Results and discussion Forty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses. Conclusion These findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.
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Affiliation(s)
- Fei Li
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Kuanling Xi
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yuke Li
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Tang Ming
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yufeng Huang
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Lijun Zhang
- Science and Technology Division, Guizhou Normal University, Guiyang, China
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28
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Yuan Y, Huo Q, Zhang Z, Wang Q, Wang J, Chang S, Cai P, Song KM, Galbraith DW, Zhang W, Huang L, Song R, Ma Z. Decoding the gene regulatory network of endosperm differentiation in maize. Nat Commun 2024; 15:34. [PMID: 38167709 PMCID: PMC10762121 DOI: 10.1038/s41467-023-44369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene-expression pattern from 6 to 7 days after pollination. We profile the genomic DNA-binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.
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Affiliation(s)
- Yue Yuan
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Qiang Huo
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ziru Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qun Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Juanxia Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuaikang Chang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Peng Cai
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Karen M Song
- Department of Biology, Trinity College of Arts and Sciences, Duke University, Durham, NC, 27708, USA
| | - David W Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Weixiao Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Long Huang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
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29
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Yu G, Sun B, Zhu Z, Mehareb EM, Teng A, Han J, Zhang H, Liu J, Liu X, Raza G, Zhang B, Zhang Y, Wang K. Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:573-589. [PMID: 37897092 DOI: 10.1111/tpj.16513] [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: 03/06/2023] [Revised: 09/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
The characterization of cis-regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome-wide identification of DNase I-hypersensitive sites (DHSs) in leaf and stem tissues of the auto-octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf- and stem-dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue-specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene-responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue-specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Bo Sun
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Eid M Mehareb
- Sugar Crops Research Institute (SRCI), Agricultural Research Center (ARC), Giza, 12619, Egypt
| | - Ailing Teng
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jiayong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Xinlong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Yuebin Zhang
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China
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30
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis -regulatory regions controlling a deeply conserved plant stem cell regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572550. [PMID: 38187729 PMCID: PMC10769289 DOI: 10.1101/2023.12.20.572550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis -regulatory sequences. It remains unclear how such drastic cis -regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis- regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ∼125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 ( CLV3 ) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis -regulatory sequences. Our results demonstrate remarkable malleability in cis -regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis -regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis -regulation to effectively engineer trait variation from conserved productivity genes in crops. Author summary We investigated the evolution of cis -regulatory elements (CREs) and their interactions in the regulation of a plant stem cell regulator gene, CLAVATA3 (CLV3) , in Arabidopsis and tomato. Despite diverging ∼125 million years ago, the function and expression of CLV3 is conserved in these species; however, cis -regulatory sequences upstream and downstream have drastically diverged, preventing identification of conserved non-coding sequences between them. We used CRISPR-Cas9 to engineer dozens of mutations within the cis -regulatory regions of Arabidopsis and tomato CLV3. In tomato, our results show that tomato CLV3 function primarily relies on interactions among CREs in the 5' non-coding region, unlike Arabidopsis CLV3 , which depends on a more balanced distribution of functional CREs between the 5' and 3' regions. Therefore, despite a high degree of functional conservation, our study demonstrates divergent regulatory strategies between two distantly related CLV3 orthologs, with substantial alterations in regulatory sequences, their spatial arrangement, and their relative effects on CLV3 regulation. These results suggest that regulatory regions are not only extremely robust to mutagenesis, but also that the sequences underlying this robustness can be lineage-specific for conserved genes, due to the complex and often redundant interactions among CREs that ensure proper gene function amidst large-scale sequence turnover.
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31
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Zhang H, Jin Z, Cui F, Zhao L, Zhang X, Chen J, Zhang J, Li Y, Li Y, Niu Y, Zhang W, Gao C, Fu X, Tong Y, Wang L, Ling HQ, Li J, Xiao J. Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat. Nat Commun 2023; 14:8238. [PMID: 38086830 PMCID: PMC10716289 DOI: 10.1038/s41467-023-44003-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyuan Jin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Long Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yongpeng Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CICMCP, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China.
| | - Junming Li
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China.
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, China.
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Mammarella MF, Lucero L, Hussain N, Muñoz‐Lopez A, Huang Y, Ferrero L, Fernandez‐Milmanda GL, Manavella P, Benhamed M, Crespi M, Ballare CL, Gutiérrez Marcos J, Cubas P, Ariel F. Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis. EMBO J 2023; 42:e113941. [PMID: 38054357 PMCID: PMC10711646 DOI: 10.15252/embj.2023113941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.
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Affiliation(s)
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | | | - Aitor Muñoz‐Lopez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Ying Huang
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Lucia Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Guadalupe L Fernandez‐Milmanda
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
| | - Pablo Manavella
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Carlos L Ballare
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
- Instituto de Investigaciones Biotecnológicas (IIBIO), CONICETUniversidad Nacional de San MartínBuenos AiresArgentina
| | | | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
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Laspisa D, Illa-Berenguer E, Bang S, Schmitz RJ, Parrott W, Wallace J. Mining the Utricularia gibba genome for insulator-like elements for genetic engineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1279231. [PMID: 38023853 PMCID: PMC10663240 DOI: 10.3389/fpls.2023.1279231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. Methods To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. Results We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Discussion Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
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Affiliation(s)
- Daniel Laspisa
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Jason Wallace
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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34
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Sen S, Woodhouse MR, Portwood JL, Andorf CM. Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Database (Oxford) 2023; 2023:baad078. [PMID: 37935586 PMCID: PMC10634621 DOI: 10.1093/database/baad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 09/16/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The big-data analysis of complex data associated with maize genomes accelerates genetic research and improves agronomic traits. As a result, efforts have increased to integrate diverse datasets and extract meaning from these measurements. Machine learning models are a powerful tool for gaining knowledge from large and complex datasets. However, these models must be trained on high-quality features to succeed. Currently, there are no solutions to host maize multi-omics datasets with end-to-end solutions for evaluating and linking features to target gene annotations. Our work presents the Maize Feature Store (MFS), a versatile application that combines features built on complex data to facilitate exploration, modeling and analysis. Feature stores allow researchers to rapidly deploy machine learning applications by managing and providing access to frequently used features. We populated the MFS for the maize reference genome with over 14 000 gene-based features based on published genomic, transcriptomic, epigenomic, variomic and proteomics datasets. Using the MFS, we created an accurate pan-genome classification model with an AUC-ROC score of 0.87. The MFS is publicly available through the maize genetics and genomics database. Database URL https://mfs.maizegdb.org/.
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Affiliation(s)
- Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Dr, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Atanasoff Hall, 2434 Osborn Dr, Ames, IA 50011, USA
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35
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Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B. Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. FRONTIERS IN PLANT SCIENCE 2023; 14:1288826. [PMID: 37965014 PMCID: PMC10642751 DOI: 10.3389/fpls.2023.1288826] [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: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.
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Affiliation(s)
- C. Robin Buell
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Christopher Dardick
- Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Breeanna Urbanowicz
- Center for Complex Carbohydrate Research, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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36
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Lee H, Seo P. Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis. Nucleic Acids Res 2023; 51:10261-10277. [PMID: 37884483 PMCID: PMC10602878 DOI: 10.1093/nar/gkad710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 10/28/2023] Open
Abstract
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.
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Affiliation(s)
- Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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37
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Tan Y, Yan X, Sun J, Wan J, Li X, Huang Y, Li L, Niu L, Hou C. Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:234-250. [PMID: 37387536 DOI: 10.1111/tpj.16373] [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: 11/29/2022] [Revised: 05/29/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Enhancers are critical cis-regulatory elements controlling gene expression during cell development and differentiation. However, genome-wide enhancer characterization has been challenging due to the lack of a well-defined relationship between enhancers and genes. Function-based methods are the gold standard for determining the biological function of cis-regulatory elements; however, these methods have not been widely applied to plants. Here, we applied a massively parallel reporter assay on Arabidopsis to measure enhancer activities across the genome. We identified 4327 enhancers with various combinations of epigenetic modifications distinctively different from animal enhancers. Furthermore, we showed that enhancers differ from promoters in their preference for transcription factors. Although some enhancers are not conserved and overlap with transposable elements forming clusters, enhancers are generally conserved across thousand Arabidopsis accessions, suggesting they are selected under evolution pressure and could play critical roles in the regulation of important genes. Moreover, comparison analysis reveals that enhancers identified by different strategies do not overlap, suggesting these methods are complementary in nature. In sum, we systematically investigated the features of enhancers identified by functional assay in A. thaliana, which lays the foundation for further investigation into enhancers' functional mechanisms in plants.
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Affiliation(s)
- Yongjun Tan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaohao Yan
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jialei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jing Wan
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Li
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yingzhang Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Li
- Department of Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longjian Niu
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunhui Hou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
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38
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Jores T, Hamm M, Cuperus JT, Queitsch C. Frontiers and techniques in plant gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102403. [PMID: 37331209 DOI: 10.1016/j.pbi.2023.102403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/20/2023]
Abstract
Understanding plant gene regulation has been a priority for generations of plant scientists. However, due to its complex nature, the regulatory code governing plant gene expression has yet to be deciphered comprehensively. Recently developed methods-often relying on next-generation sequencing technology and state-of-the-art computational approaches-have started to further our understanding of the gene regulatory logic used by plants. In this review, we discuss these methods and the insights into the regulatory code of plants that they can yield.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Morgan Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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39
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Cui Y, Cao Q, Li Y, He M, Liu X. Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5441-5457. [PMID: 37402253 DOI: 10.1093/jxb/erad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
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Affiliation(s)
- Yue Cui
- College of Teacher Education, Molecular and Cellular Postdoctoral Research Station, Hebei Normal University, Shijiazhuang 050024, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiao Cao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Yongpeng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Mingqi He
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei Province 050041, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Research Center of the Basic Discipline Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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40
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Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating ("nascent") transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many "distal" elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer "enhancers" or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
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Affiliation(s)
- Bayley R. Mcdonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Colette Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M. Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | | | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H. Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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41
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Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1486-1499. [PMID: 37309871 PMCID: PMC10598807 DOI: 10.1111/tpj.16351] [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: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/14/2023]
Abstract
Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single-cell epigenomics have revolutionized the field of identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single-cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges, and common pitfalls in the analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.
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Affiliation(s)
| | - Ankush Sangra
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Mark A A Minow
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, 30602, Georgia, USA
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Chen Y, Xie D, Ma X, Xue X, Liu M, Xiao X, Lai C, Xu X, Chen X, Chen Y, Zhang Z, XuHan X, Lai Z, Lin Y. Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis. PLANT PHYSIOLOGY 2023; 193:555-577. [PMID: 37313777 DOI: 10.1093/plphys/kiad348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
Somatic embryogenesis (SE), like zygotic embryo development, is a progressive process. Early SE is the beginning of a switch from a somatic to an embryogenic state and is an important stage for initiating chromatin reprogramming of SE. Previous studies suggest that changes in chromatin accessibility occur during early SE, although information on the 3D structure of chromatin is not yet available. Here, we present a chromosome-level genome assembly of longan (Dimocarpus longan) using PacBio combined with high-through chromosome conformation capture scaffolding, which resulted in a 446 Mb genome assembly anchored onto 15 scaffolds. During early SE, chromatin was concentrated and then decondensed, and a large number of long terminal repeat retrotransposons (LTR-RTs) were enriched in the local chromatin interaction region, suggesting LTR-RTs were involved in chromatin reorganization. Early SE was accompanied by the transformation from A to B compartments, and the interactions between B compartments were enhanced. Results from chromatin accessibility, monomethylation of histone H3 at lysine 4 (H3K4me1) modification, and transcription analyses further revealed a gene regulatory network for cell wall thickening during SE. Particularly, we found that the H3K4me1 differential peak binding motif showed abnormal activation of ethylene response factor transcription factors and participation in SE. The chromosome-level genomic and multiomics analyses revealed the 3D conformation of chromatin during early SE, providing insight into the molecular mechanisms underlying cell wall thickening and the potential regulatory networks of TFs during early SE in D. longan. These results provide additional clues for revealing the molecular mechanisms of plant SE.
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Affiliation(s)
- Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dejian Xie
- Beijing Research Center, Wuhan Frasergen Bioinformatics Co., Ltd, Beijing 100081, China
| | - Xiangwei Ma
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mengyu Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xuechen Xiao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, Toulouse 31300, France
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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43
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [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: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
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Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
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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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Ouyang K, Liang Q, Miao L, Zhang Z, Li Z. Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves. Front Genet 2023; 14:1086554. [PMID: 37470036 PMCID: PMC10352800 DOI: 10.3389/fgene.2023.1086554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Pineapple [Ananas comosus (L.) Merr.] is the most economically important crop possessing crassulacean acid metabolism (CAM) photosynthesis which has a higher water use efficiency by control of nocturnal opening and diurnal closure of stomata. To provide novel insights into the diel regulatory landscape in pineapple leaves, we performed genome-wide mapping of DNase I hypersensitive sites (DHSs) in pineapple leaves at day (2a.m.) and night (10a.m.) using a simplified DNase-seq method. As a result, totally 33340 and 28753 DHSs were found in green-tip tissue, and 29597 and 40068 were identified in white-base tissue at 2a.m. and 10a.m., respectively. We observed that majority of the pineapple genes occupied less than two DHSs with length shorter than 1 kb, and the promotor DHSs showed a proximal trend to the transcription start site (>77% promotor DHSs within 1 kb). In addition, more intergenic DHSs were identified around transcription factors or transcription co-regulators (TFs/TCs) than other functional genes, indicating complex regulatory contexts around TFs/TCs. Through combined analysis of tissue preferential DHSs and genes, we respectively found 839 and 888 coordinately changed genes in green-tip at 2a.m. and 10a.m. (AcG2 and AcG10). Furthermore, AcG2-specific, AcG10-specific and common accessible DHSs were dissected from the total photosynthetic preferential DHSs, and the regulatory networks indicated dynamic regulations with multiple cis-regulatory elements occurred to genes preferentially expressed in photosynthetic tissues. Interestingly, binding motifs of several cycling TFs were identified in the DHSs of key CAM genes, revealing a circadian regulation to CAM coordinately diurnal expression. Our results provide a chromatin regulatory landscape in pineapple leaves during the day and night. This will provide important information to assist with deciphering the circadian regulation of CAM photosynthesis.
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Affiliation(s)
- Kai Ouyang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qifu Liang
- Fujian Key Laboratory of Agro-Products Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Li Miao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiliang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhanjie Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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47
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Han J, Wang S, Wu H, Zhao T, Guan X, Fang L. An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223591. [PMID: 37469786 PMCID: PMC10353440 DOI: 10.3389/fpls.2023.1223591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
High-throughput chromosome conformation capture (Hi-C) technology has been applied to explore the chromatin interactions and shed light on the biological functions of three-dimensional genomic features. However, it remains challenging to guarantee the high quality of Hi-C library in plants and hence the reliable capture of chromatin structures, especially loops, due to insufficient fragmentation and low efficiency of proximity ligations. To overcome these deficiencies, we optimized the parameters of the Hi-C protocol, principally the cross-linking agents and endonuclease fragmentation strategy. The double cross-linkers (FA+DSG) and double restriction enzymes (DpnII+DdeI) were utilized. Thus, a systematic in situ Hi-C protocol was designed using plant tissues embedded with comprehensive quality controls to monitor the library construction. This upgraded method, termed Hi-C 3.0, was applied to cotton leaves for trial. In comparison with the conventional Hi-C 2.0, Hi-C 3.0 can obtain more than 50% valid contacts at a given sequencing depth to improve the signal-to-noise ratio. Hi-C 3.0 can furthermore enhance the capturing of loops almost as twice as that of Hi-C 2.0. In addition, Hi-C 3.0 showed higher efficiency of compartment detection and identified compartmentalization more accurately. In general, Hi-C 3.0 contributes to the advancement of the Hi-C method in plants by promoting its capability on decoding the chromatin organization.
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Affiliation(s)
- Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
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Hong L, Rusnak B, Ko CS, Xu S, He X, Qiu D, Kang SE, Pruneda-Paz JL, Roeder AHK. Enhancer activation via TCP and HD-ZIP and repression by Dof transcription factors mediate giant cell-specific expression. THE PLANT CELL 2023; 35:2349-2368. [PMID: 36814410 PMCID: PMC10226562 DOI: 10.1093/plcell/koad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 05/30/2023]
Abstract
Proper cell-type identity relies on highly coordinated regulation of gene expression. Regulatory elements such as enhancers can produce cell type-specific expression patterns, but the mechanisms underlying specificity are not well understood. We previously identified an enhancer region capable of driving specific expression in giant cells, which are large, highly endoreduplicated cells in the Arabidopsis thaliana sepal epidermis. In this study, we use the giant cell enhancer as a model to understand the regulatory logic that promotes cell type-specific expression. Our dissection of the enhancer revealed that giant cell specificity is mediated primarily through the combination of two activators and one repressor. HD-ZIP and TCP transcription factors are involved in the activation of expression throughout the epidermis. High expression of HD-ZIP transcription factor genes in giant cells promoted higher expression driven by the enhancer in giant cells. Dof transcription factors repressed the activity of the enhancer such that only giant cells maintained enhancer activity. Thus, our data are consistent with a conceptual model whereby cell type-specific expression emerges from the combined activities of three transcription factor families activating and repressing expression in epidermal cells.
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Affiliation(s)
- Lilan Hong
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Byron Rusnak
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Clint S Ko
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shouling Xu
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi He
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dengying Qiu
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - S Earl Kang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jose L Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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49
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537008. [PMID: 37131670 PMCID: PMC10153178 DOI: 10.1101/2023.04.15.537008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (mediator of paramutation1) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of the CHH DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in F1 plants did require Mop1, initiation of the changes in the epigenetic state of TCM DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is not dependent on RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
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50
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Kong C, Zhao G, Gao L, Kong X, Wang D, Liu X, Jia J. Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii. Int J Mol Sci 2023; 24:ijms24119349. [PMID: 37298301 DOI: 10.3390/ijms24119349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Transposons (TEs) account for more than 80% of the wheat genome, the highest among all known crop species. They play an important role in shaping the elaborate genomic landscape, which is the key to the speciation of wheat. In this study, we analyzed the association between TEs, chromatin states, and chromatin accessibility in Aegilops tauschii, the D genome donor of bread wheat. We found that TEs contributed to the complex but orderly epigenetic landscape as chromatin states showed diverse distributions on TEs of different orders or superfamilies. TEs also contributed to the chromatin state and openness of potential regulatory elements, affecting the expression of TE-related genes. Some TE superfamilies, such as hAT-Ac, carry active/open chromatin regions. In addition, the histone mark H3K9ac was found to be associated with the accessibility shaped by TEs. These results suggest the role of diversiform TEs in shaping the epigenetic landscape and in gene expression regulation in Aegilops tauschii. This has positive implications for understanding the transposon roles in Aegilops tauschii or the wheat D genome.
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Affiliation(s)
- Chuizheng Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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