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Gong H, Zhang S, Zhang X, Chen Y. A method for chromatin domain partitioning based on hypergraph clustering. Comput Struct Biotechnol J 2024; 23:1584-1593. [PMID: 38655013 PMCID: PMC11035048 DOI: 10.1016/j.csbj.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
For many years, multi-scale models of chromatin domains, such as A/B compartments, sub-compartments, topologically associated domains (TADs), sub-TADs, and loops have been popular. However, existing methods can only identify structures at a single scale and cannot partition multi-scale structures. In this paper, we proposed a method (TORNADOES) for chromatin domain partitioning based on hypergraph clustering. First, we use a density clustering algorithm to identify TADs at different scales based on Hi-C data with different resolutions. Then, by combining ChIP-seq data features and TAD results at different scales, we generate a hypergraph based on these TADs. Finally, we partition the chromatin domain structure at different scales, including A/B, A1, A2, B1, B2, and B3 based on the Laplacian matrix feature of the hypergraph. Similarity comparison experiments and ChIP-seq signal enrichment analysis are performed on the A/B region and sub-TAD levels, respectively, demonstrating that our method can identify chromatin domains with distinct features and provide a deeper understanding of the organizational patterns and functional differences in TADs at the genomic hierarchical structure. Comparative analysis of multiple cell line data shows that TORNADOES can better classify different numbers and types of compartments by changing the factors ChIP-seq data and clustering number used to characterize TAD compared to other methods. Source code for the TORNADOES method can be found at https://github.com/ghaiyan/TORNADOES.
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Affiliation(s)
- Haiyan Gong
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, Guangdong, China
| | - Sichen Zhang
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiaotong Zhang
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, Guangdong, China
| | - Yang Chen
- The State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
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2
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Wang L, Chen H, Zhuang Y, Chen K, Zhang C, Cai T, Yang Q, Fu H, Chen X, Chitkineni A, Wang X, Varshney RK, Zhuang W. Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1681-1702. [PMID: 38294334 PMCID: PMC11123434 DOI: 10.1111/pbi.14296] [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: 06/29/2023] [Revised: 11/28/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
Alternative splicing (AS), an important post-transcriptional regulation mechanism in eukaryotes, can significantly increase transcript diversity and contribute to gene expression regulation and many other complicated developmental processes. While plant gene AS events are well described, few studies have investigated the comprehensive regulation machinery of plant AS. Here, we use multi-omics to analyse peanut AS events. Using long-read isoform sequencing, 146 464 full-length non-chimeric transcripts were obtained, resulting in annotation corrections for 1782 genes and the identification of 4653 new loci. Using Iso-Seq RNA sequences, 271 776 unique splice junctions were identified, 82.49% of which were supported by transcriptome data. We characterized 50 977 polyadenylation sites for 23 262 genes, 12 369 of which had alternative polyadenylation sites. AS allows differential regulation of the same gene by miRNAs at the isoform level coupled with polyadenylation. In addition, we identified many long non-coding RNAs and fusion transcripts. There is a suppressed effect of 6mA on AS and gene expression. By analysis of chromatin structures, the genes located in the boundaries of topologically associated domains, proximal chromosomal telomere regions, inter- or intra-chromosomal loops were found to have more unique splice isoforms, higher expression, lower 6mA and more transposable elements (TEs) in their gene bodies than the other genes, indicating that chromatin interaction, 6mA and TEs play important roles in AS and gene expression. These results greatly refine the peanut genome annotation and contribute to the study of gene expression and regulation in peanuts. This work also showed AS is associated with multiple strategies for gene regulation.
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Affiliation(s)
- Lihui Wang
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Hua Chen
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Yuhui Zhuang
- Center for Legume Plant Genetics and System Biology, College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Kun Chen
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Chong Zhang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Tiecheng Cai
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Qiang Yang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Huiwen Fu
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Xiangyu Chen
- Crop Research InstituteFujian Academy of Agricultural SciencesFuzhouFujianChina
| | - Annapurna Chitkineni
- Centre for Crop & Food Innovation, State Agricultural Biotechnology CentreFood Futures Institute, Murdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiyin Wang
- North China University of Science and TechnologyTangshanChina
| | - Rajeev K. Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology CentreFood Futures Institute, Murdoch UniversityMurdochWestern AustraliaAustralia
| | - Weijian Zhuang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
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3
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Shao W, Wang J, Zhang Y, Zhang C, Chen J, Chen Y, Fei Z, Ma Z, Sun X, Jiao C. The jet-like chromatin structure defines active secondary metabolism in fungi. Nucleic Acids Res 2024; 52:4906-4921. [PMID: 38407438 PMCID: PMC11109943 DOI: 10.1093/nar/gkae131] [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: 09/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.
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Affiliation(s)
- Wenyong Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jingrui Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yueqi Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chaofan Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Jie Chen
- National Joint Engineering Laboratory of Biopesticide Preparation, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Chen Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
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Li Z, Sun L, Xu X, Liu Y, He H, Deng XW. Light control of three-dimensional chromatin organization in soybean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38762905 DOI: 10.1111/pbi.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
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Affiliation(s)
- Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiao Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Yutong Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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5
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [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: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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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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7
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Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, Swarbreck D, Collins J, Yao E, Sen TZ, Wilson M, Yant L, King IP, King J. Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii. Sci Data 2024; 11:420. [PMID: 38653999 PMCID: PMC11039740 DOI: 10.1038/s41597-024-03260-w] [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: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.
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Affiliation(s)
- Surbhi Grewal
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.
| | - Cai-Yun Yang
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Duncan Scholefield
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Stephen Ashling
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Sreya Ghosh
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Joanna Collins
- Genome Reference Informatics Team, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Eric Yao
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA
| | - Taner Z Sen
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA
| | - Michael Wilson
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Ian P King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Julie King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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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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Zheng YY, Chen LH, Fan BL, Xu Z, Wang Q, Zhao BY, Gao M, Yuan MH, Tahir Ul Qamar M, Jiang Y, Yang L, Wang L, Li W, Cai W, Ma C, Lu L, Song JM, Chen LL. Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma. PLANT PHYSIOLOGY 2024; 194:2491-2510. [PMID: 38039148 DOI: 10.1093/plphys/kiad640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023]
Abstract
Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.
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Affiliation(s)
- Yu-Yu Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin-Hua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhenni Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiuxia Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyuan Jiang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Liu Yang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Hongshan Laboratory, Wuhan 430071, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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10
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Kim J, Wang H, Ercan S. Cohesin mediated loop extrusion from active enhancers form chromatin jets in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558239. [PMID: 37786717 PMCID: PMC10541618 DOI: 10.1101/2023.09.18.558239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
In mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication between cis-regulatory elements. However, many organisms, including S. cerevisiae , C. elegans , and A. thaliana lack CTCF. Here, we use C. elegans as a model to investigate the function of cohesin in 3D genome organization in an animal without CTCF. We use auxin-inducible degradation to acutely deplete SMC-3 or its negative regulator WAPL-1 from somatic cells. Using Hi-C data, we identify a cohesin-dependent 3D genome organization feature called chromatin jets (aka fountains). These are population average reflections of DNA loops that are ∼20-40 kb in scale and often cover a few transcribed genes. The jets emerge from NIPBL occupied segments, and the trajectory of the jets coincides with cohesin binding. Cohesin translocation from jet origins depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C results support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. The location of putative loading sites coincide with active enhancers and the strength of chromatin jet pattern correlates with transcription. Hi-C analyses upon WAPL-1 depletion reveal unequal loop extrusion processivity on each side and stalling due to cohesin molecules colliding. Compared to mammalian systems, average processivity of C. elegans cohesin is ∼10-fold shorter and NIPBL binding does not depend on cohesin. We conclude that the processivity of cohesin scales with genome size; and regardless of CTCF presence, preferential loading of cohesin at enhancers is a conserved mechanism of genome organization that regulates the interaction of gene regulatory elements in 3D.
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11
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Li H, Playter C, Das P, McCord RP. Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends Cell Biol 2024:S0962-8924(24)00021-7. [PMID: 38395734 DOI: 10.1016/j.tcb.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
The spatial segregation of the genome into compartments is a major feature of 3D genome organization. New data on mammalian chromosome organization across different conditions reveal important information about how and why these compartments form and change. A combination of epigenetic state, nuclear body tethering, physical forces, gene expression, and replication timing (RT) can all influence the establishment and alteration of chromosome compartments. We review the causes and implications of genomic regions undergoing a 'compartment switch' that changes their physical associations and spatial location in the nucleus. About 20-30% of genomic regions change compartment during cell differentiation or cancer progression, whereas alterations in response to a stimulus within a cell type are usually much more limited. However, even a change in 1-2% of genomic bins may have biologically relevant implications. Finally, we review the effects of compartment changes on gene regulation, DNA damage repair, replication, and the physical state of the cell.
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Affiliation(s)
- Heng Li
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Christopher Playter
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Priyojit Das
- University of Tennessee-Oak Ridge National Laboratory (UT-ORNL) Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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12
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Nolan B, Harris HL, Kalluchi A, Reznicek TE, Cummings CT, Rowley MJ. HiCrayon reveals distinct layers of multi-state 3D chromatin organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579821. [PMID: 38405883 PMCID: PMC10888951 DOI: 10.1101/2024.02.11.579821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The co-visualization of chromatin conformation with 1D 'omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization. Local version: https://github.com/JRowleyLab/HiCrayon Web version: https://jrowleylab.com/HiCrayon.
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Affiliation(s)
- Ben Nolan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Timothy E Reznicek
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Christopher T Cummings
- Department of Pediatrics, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
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13
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Gao Z, Su Y, Chang L, Jiao G, Ou Y, Yang M, Xu C, Liu P, Wang Z, Qi Z, Liu W, Sun L, He G, Deng XW, He H. Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:208-227. [PMID: 38326968 DOI: 10.1111/jipb.13620] [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: 06/16/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.
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Affiliation(s)
- Zhaoxu Gao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yanning Su
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Le Chang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guanzhong Jiao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yang Ou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Mei Yang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Chao Xu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Pengtao Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zejia Wang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Wenwen Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guangming He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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14
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [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: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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15
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Zhang L, Liu L, Li H, He J, Chao H, Yan S, Yin Y, Zhao W, Li M. 3D genome structural variations play important roles in regulating seed oil content of Brassica napus. PLANT COMMUNICATIONS 2024; 5:100666. [PMID: 37496273 PMCID: PMC10811347 DOI: 10.1016/j.xplc.2023.100666] [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: 03/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan 430075, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Yontai Yin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China.
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16
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Luo B, Zhang Z, Li B, Zhang H, Ma J, Li J, Han Z, Zhang C, Zhang S, Yu T, Zhang G, Ma P, Lan Y, Zhang X, Liu D, Wu L, Gao D, Gao S, Su S, Zhang X, Gao S. Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:33-52. [PMID: 37731059 DOI: 10.1111/tpj.16468] [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: 03/29/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.
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Affiliation(s)
- Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ziqi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Binyang Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Junchi Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Zheng Han
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Chong Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shuhao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ting Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Guidi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Peng Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, Sichuan, China
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Yuzhou Lan
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422, Lomma, Sweden
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shunzong Su
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
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17
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Manosalva Pérez N, Ferrari C, Engelhorn J, Depuydt T, Nelissen H, Hartwig T, Vandepoele K. MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:280-301. [PMID: 37788349 DOI: 10.1111/tpj.16483] [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: 05/23/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023]
Abstract
Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
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Affiliation(s)
- Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Julia Engelhorn
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Thomas Hartwig
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
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18
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Junaid A, Singh B, Bhatia S. Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo. Life Sci Alliance 2024; 7:e202302074. [PMID: 37923361 PMCID: PMC10624639 DOI: 10.26508/lsa.202302074] [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: 04/04/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
Eukaryotic genomes show an intricate three-dimensional (3D) organization within the nucleus that regulates multiple biological processes including gene expression. Contrary to animals, understanding of 3D genome organization in plants remains at a nascent stage. Here, we investigate the evolution of 3D chromatin architecture in legumes. By using cutting-edge PacBio, Illumina, and Hi-C contact reads, we report a gap-free, chromosome-scale reference genome assembly of Vigna mungo, an important minor legume cultivated in Southeast Asia. We spatially resolved V. mungo chromosomes into euchromatic, transcriptionally active A compartment and heterochromatic, transcriptionally-dormant B compartment. We report the presence of TAD-like-regions throughout the diagonal of the HiC matrix that resembled transcriptional quiescent centers based on their genomic and epigenomic features. We observed high syntenic breakpoints but also high coverage of syntenic sequences and conserved blocks in boundary regions than in the TAD-like region domains. Our findings present unprecedented evolutionary insights into spatial 3D genome organization and epigenetic patterns and their interaction within the V. mungo genome. This will aid future genomics and epigenomics research and breeding programs of V. mungo.
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Affiliation(s)
- Alim Junaid
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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19
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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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20
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [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: 02/23/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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21
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Das JR, Mathur S. HSFA1a: the quarterback of heat stress response and 3D-chromatin organization. TRENDS IN PLANT SCIENCE 2023; 28:1198-1200. [PMID: 37544818 DOI: 10.1016/j.tplants.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023]
Abstract
In eukaryotes, the highly complex chromatin exhibits structural dynamism to modulate cellular responses. Recently, Huang et al. have shown a novel role of the heat stress master regulator, HSFA1a, in transiently reorganizing the 3D chromatin to promote distal and proximal enhancer-promoter contacts to regulate stress-responsive genes in tomato.
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Affiliation(s)
- Jaishri Rubina Das
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi - 110 067, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi - 110 067, India.
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22
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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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23
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Sakamoto T, Matsunaga S. Chromatin dynamics and subnuclear gene positioning for transcriptional regulation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102431. [PMID: 37562088 DOI: 10.1016/j.pbi.2023.102431] [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: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
Plants have been found to exhibit diverse characteristics and functions of chromatin organization, showing both similarities and differences to animals. It is becoming clear how chromatin organization is linked to transcriptional regulation in response to environmental stresses. Regulation of specific chromatin positions in the nuclear space is important for transcription, and the mechanisms that enable such chromatin dynamics are gradually being unveiled. Genes move between subdomains responsible for transcriptional activation or suppression in the subnuclear space in a gene repositioning cycle. We propose a model of localized chromatin interaction in nuclear subdomains, in which the dynamics of local chromatin interactions have a more important impact on the regulation of gene expression than large-scale chromatin organization. In this mini-review, we highlight recent findings on chromatin dynamics, particularly involving transcriptional regulation, and discuss future directions in the study of chromatin organization in plants.
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Affiliation(s)
- Takuya Sakamoto
- Department of Science, Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-0802, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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24
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Liao X, Guo S, Liao B, Shen X, He W, Meng Y, Liang C, Pei J, Liu J, Zhang Y, Xu J, Chen S. Chromatin architecture of two different strains of Artemisia annua reveals the alterations in interaction and gene expression. PLANTA 2023; 258:74. [PMID: 37668722 DOI: 10.1007/s00425-023-04223-y] [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: 04/21/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
MAIN CONCLUSION The hierarchical architecture of chromatins affects the gene expression level of glandular secreting trichomes and the artemisinin biosynthetic pathway-related genes, consequently bringing on huge differences in the content of artemisinin and its derivatives of A. annua. The plant of traditional Chinese medicine "Qinghao" is called Artemisia annua L. in Chinese Pharmacopoeia. High content and the total amount of artemisinin is the main goal of A. annua breeding, nevertheless, the change of chromatin organization during the artemisinin synthesis process has not been discovered yet. This study intended to find the roles of chromatin structure in the production of artemisinin through bioinformatics and experimental validation. Chromosome conformation capture analysis was used to scrutinize the interactions among chromosomes and categorize various scales of chromatin during artemisinin synthesis in A. annua. To confirm the effect of the changes in chromatin structure, Hi-C and RNA-sequencing were performed on two different strains to find the correlation between chromatin structure and gene expression levels on artemisinin synthesis progress and regulation. Our results revealed that the frequency of intra-chromosomal interactions was higher in the inter-chromosomal interactions between the root and leaves on a high artemisinin production strain (HAP) compared to a low artemisinin production strain (LAP). We found that compartmental transition was connected with interactions among different chromatins. Interestingly, glandular secreting trichomes (GSTs) and the artemisinin biosynthetic pathway (ABP) related genes were enriched in the areas which have the compartmental transition, reflecting the regulation of artemisinin synthesis. Topologically associated domain boundaries were associated with various distributions of genes and expression levels. Genes associated with ABP and GST in the adjacent loop were highly expressed, suggesting that epigenetic regulation plays an important role during artemisinin synthesis and glandular secreting trichomes production process. Chromatin structure could show an important status in the mechanisms of artemisinin synthesis process in A. annua.
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Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wenrui He
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ying Meng
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Conglian Liang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193, China
| | - Yongqing Zhang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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25
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Ranawaka B, An J, Lorenc MT, Jung H, Sulli M, Aprea G, Roden S, Llaca V, Hayashi S, Asadyar L, LeBlanc Z, Ahmed Z, Naim F, de Campos SB, Cooper T, de Felippes FF, Dong P, Zhong S, Garcia-Carpintero V, Orzaez D, Dudley KJ, Bombarely A, Bally J, Winefield C, Giuliano G, Waterhouse PM. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology. NATURE PLANTS 2023; 9:1558-1571. [PMID: 37563457 PMCID: PMC10505560 DOI: 10.1038/s41477-023-01489-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Jiyuan An
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
| | - Michał T Lorenc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Hyungtaek Jung
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Victor Llaca
- Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Leila Asadyar
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Zuba Ahmed
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Fatima Naim
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Samanta Bolzan de Campos
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tal Cooper
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Felipe F de Felippes
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- QUT Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
- Università degli Studi di Milano, Milan, Italy
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Christopher Winefield
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
- Department of Wine Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
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26
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Zhu W, Li H, Dong P, Ni X, Fan M, Yang Y, Xu S, Xu Y, Qian Y, Chen Z, Lü P. Low temperature-induced regulatory network rewiring via WRKY regulators during banana peel browning. PLANT PHYSIOLOGY 2023; 193:855-873. [PMID: 37279567 PMCID: PMC10469544 DOI: 10.1093/plphys/kiad322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Banana (Musa spp.) fruits, as typical tropical fruits, are cold sensitive, and lower temperatures can disrupt cellular compartmentalization and lead to severe browning. How tropical fruits respond to low temperature compared to the cold response mechanisms of model plants remains unknown. Here, we systematically characterized the changes in chromatin accessibility, histone modifications, distal cis-regulatory elements, transcription factor binding, and gene expression levels in banana peels in response to low temperature. Dynamic patterns of cold-induced transcripts were generally accompanied by concordant chromatin accessibility and histone modification changes. These upregulated genes were enriched for WRKY binding sites in their promoters and/or active enhancers. Compared to banana peel at room temperature, large amounts of banana WRKYs were specifically induced by cold and mediated enhancer-promoter interactions regulating critical browning pathways, including phospholipid degradation, oxidation, and cold tolerance. This hypothesis was supported by DNA affinity purification sequencing, luciferase reporter assays, and transient expression assay. Together, our findings highlight widespread transcriptional reprogramming via WRKYs during banana peel browning at low temperature and provide an extensive resource for studying gene regulation in tropical plants in response to cold stress, as well as potential targets for improving cold tolerance and shelf life of tropical fruits.
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Affiliation(s)
- Wenjun Zhu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hua Li
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xueting Ni
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minlei Fan
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yingjie Yang
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shiyao Xu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanbing Xu
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yangwen Qian
- WIMI Biotechnology Co., Ltd., Changzhou 213000, China
| | - Zhuo Chen
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peitao Lü
- Fujian Agriculture and Forestry University, Fuzhou 350002, China
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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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Yan T, Wang K, Feng K, Gao X, Jin Y, Wu H, Zhang W, Wei L. Remodeling of the 3D chromatin architecture in the marine microalga Nannochloropsis oceanica during lipid accumulation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:129. [PMID: 37592325 PMCID: PMC10436460 DOI: 10.1186/s13068-023-02378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized. RESULTS Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the 'fatty acid metabolism', 'response to stress', 'carbon fixation' and 'photosynthesis' functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression. CONCLUSIONS Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.
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Affiliation(s)
- Tongtong Yan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China
| | - Kexin Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Kexin Feng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Xiangchen Gao
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Yinghong Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China
| | - Hongping Wu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China
| | - Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China.
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29
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Deng L, Zhou Q, Zhou J, Zhang Q, Jia Z, Zhu G, Cheng S, Cheng L, Yin C, Yang C, Shen J, Nie J, Zhu JK, Li G, Zhao L. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis. Genome Biol 2023; 24:181. [PMID: 37550699 PMCID: PMC10405511 DOI: 10.1186/s13059-023-03018-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants. RESULTS Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression. CONCLUSION The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangfeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lulu Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caijun Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Nie
- Vazyme Biotech Co., Ltd., Nanjing, 210000, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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31
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Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev 2023; 81:102064. [PMID: 37390583 PMCID: PMC10547022 DOI: 10.1016/j.gde.2023.102064] [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: 03/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/02/2023]
Abstract
3D genome folding enables the physical storage of chromosomes into the compact volume of a cell's nucleus, allows for the accurate segregation of chromatin to daughter cells, and has been shown to be tightly coupled to the way in which genetic information is converted into transcriptional programs [1-3]. Importantly, this link between chromatin architecture and gene regulation is a selectable feature in which modifications to chromatin organization accompany, or perhaps even drive the establishment of new regulatory strategies with enduring impacts on animal body plan complexity. Here, we discuss the nature of different 3D genome folding systems found across the tree of life, with particular emphasis on metazoans, and the relative influence of these systems on gene regulation. We suggest how the properties of these folding systems have influenced regulatory strategies employed by different lineages and may have catalyzed the partitioning and specialization of genetic programs that enabled multicellularity and organ-grade body plan complexity.
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Affiliation(s)
- Jenks Hehmeyer
- Department of Organismal Biology and Anatomy, The University of Chicago, USA
| | - François Spitz
- Department of Human Genetics, The University of Chicago, USA
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, USA.
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32
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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: 4] [Impact Index Per Article: 4.0] [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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33
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Shivnauth V, Pretheepkumar S, Marchetta EJR, Rossi CAM, Amani K, Castroverde CDM. Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato). Funct Integr Genomics 2023; 23:236. [PMID: 37439880 DOI: 10.1007/s10142-023-01172-3] [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: 01/19/2023] [Revised: 06/23/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Cellular signaling generates calcium (Ca2+) ions, which are ubiquitous secondary messengers decoded by calcium-dependent protein kinases, calcineurins, calreticulin, calmodulins (CAMs), and CAM-binding proteins. Previous studies in the model plant Arabidopsis thaliana have shown the critical roles of the CAM-BINDING PROTEIN 60 (CBP60) protein family in plant growth, stress responses, and immunity. Certain CBP60 factors can regulate plant immune responses, like pattern-triggered immunity, effector-triggered immunity, and synthesis of major plant immune-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). Although homologous CBP60 sequences have been identified in the plant kingdom, their function and regulation in most species remain unclear. In this paper, we specifically characterized 11 members of the CBP60 family in the agriculturally important crop tomato (Solanum lycopersicum). Protein sequence analyses revealed that three CBP60 homologs have the closest amino acid identity to Arabidopsis CBP60g and SARD1, master transcription factors involved in plant immunity. Strikingly, AlphaFold deep learning-assisted prediction of protein structures highlighted close structural similarity between these tomato and Arabidopsis CBP60 homologs. Conserved domain analyses revealed that they possess CAM-binding domains and DNA-binding domains, reflecting their potential involvement in linking Ca2+ signaling and transcriptional regulation in tomato plants. In terms of their gene expression profiles under biotic (Pseudomonas syringae pv. tomato DC3000 pathogen infection) and/or abiotic stress (warming temperatures), five tomato CBP60 genes were pathogen-responsive and temperature-sensitive, reminiscent of Arabidopsis CBP60g and SARD1. Overall, we present a genome-wide identification of the CBP60 gene/protein family in tomato plants, and we provide evidence on their regulation and potential function as Ca2+-sensing transcriptional regulators.
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Affiliation(s)
- Vanessa Shivnauth
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Sonya Pretheepkumar
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Eric J R Marchetta
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Christina A M Rossi
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Keaun Amani
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
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34
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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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35
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Yin X, Romero-Campero FJ, Yang M, Baile F, Cao Y, Shu J, Luo L, Wang D, Sun S, Yan P, Gong Z, Mo X, Qin G, Calonje M, Zhou Y. Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome. THE PLANT CELL 2023; 35:2484-2503. [PMID: 37070946 PMCID: PMC10291032 DOI: 10.1093/plcell/koad112] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.
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Affiliation(s)
- Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
- Department of Computer Science and Artificial Intelligence, University of Sevilla, Avenida Reina Mercedes s/n, Seville 41012, Spain
| | - Minqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiayue Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lingxiao Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dingyue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shang Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Peng Yan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Zhiyun Gong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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36
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Krasikova A, Kulikova T, Rodriguez Ramos JS, Maslova A. Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes. Epigenetics Chromatin 2023; 16:24. [PMID: 37322523 DOI: 10.1186/s13072-023-00499-2] [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: 04/07/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The three-dimensional configuration of the eukaryotic genome is an emerging area of research. Chromosome conformation capture outlined genome segregation into large scale A and B compartments corresponding mainly to transcriptionally active and repressive chromatin. It remains unknown how the compartmentalization of the genome changes in growing oocytes of animals with hypertranscriptional type of oogenesis. Such oocytes are characterized by highly elongated chromosomes, called lampbrush chromosomes, which acquire a typical chromomere-loop appearance, representing one of the classical model systems for exploring the structural and functional organization of chromatin domains. RESULTS Here, we compared the distribution of A/B compartments in chicken somatic cells with chromatin domains in lampbrush chromosomes. We found that in lampbrush chromosomes, the extended chromatin domains, restricted by compartment boundaries in somatic cells, disintegrate into individual chromomeres. Next, we performed FISH-mapping of the genomic loci, which belong to A or B chromatin compartments as well as to A/B compartment transition regions in embryonic fibroblasts on isolated lampbrush chromosomes. We found, that in chicken lampbrush chromosomes, clusters of dense compact chromomeres bearing short lateral loops and enriched with repressive epigenetic modifications generally correspond to constitutive B compartments in somatic cells. A compartments align with lampbrush chromosome segments with smaller, less compact chromomeres, longer lateral loops, and a higher transcriptional status. Clusters of small loose chromomeres with relatively long lateral loops show no obvious correspondence with either A or B compartment identity. Some genes belonging to facultative B (sub-) compartments can be tissue-specifically transcribed during oogenesis, forming distinct lateral loops. CONCLUSIONS Here, we established a correspondence between the A/B compartments in somatic interphase nucleus and chromatin segments in giant lampbrush chromosomes from diplotene stage oocytes. The chromomere-loop structure of the genomic regions corresponding to interphase A and B compartments reveals the difference in how they are organized at the level of chromatin domains. The results obtained also suggest that gene-poor regions tend to be packed into chromomeres.
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Affiliation(s)
- Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia.
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37
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Harris HL, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL, Rowley MJ. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nat Commun 2023; 14:3303. [PMID: 37280210 PMCID: PMC10244318 DOI: 10.1038/s41467-023-38429-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023] Open
Abstract
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
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Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Huiya Gu
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Moshe Olshansky
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ailun Wang
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BISB), 17 08028, Barcelona, Spain
- Integrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Yossi Eliaz
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Akshay Krishna
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mozes Jacobs
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Gesine Cauer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melanie Pham
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina Omer
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Michael H Nichols
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimos Gkountaroulis
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Devika Udupa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aviva Presser Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - William Stafford Noble
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jeong-Sun Seo
- Macrogen Inc, Seoul, Republic of Korea
- Asian Genome Institute, Seoul National University Bundang Hospital, Gyeonggi-do, Republic of Korea
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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39
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Shen F, He H, Huang X, Deng Y, Yang X. Insights into the convergent evolution of fructan biosynthesis in angiosperms from the highly characteristic chicory genome. THE NEW PHYTOLOGIST 2023; 238:1245-1262. [PMID: 36751914 DOI: 10.1111/nph.18796] [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: 09/22/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Fructans in angiosperms play essential roles in physiological functions and environmental adaptations. As a major source of industrial fructans (especially inulin-type), chicory (Cichorium intybus L.) is a model species for studying fructan biosynthesis. However, the genes underlying this process and their evolutionary history in angiosperms remain elusive. We combined multiple sequencing technologies to assemble and annotate the chicory genome and scan its (epi)genomic features, such as genomic components, DNA methylation, and three-dimensional (3D) structure. We also performed a comparative genomics analysis to uncover the associations between key traits and gene families. We achieved a nearly complete chicory genome assembly and found that continuous bursts of a few highly active retrotransposon families largely shaped the (epi)genomic characteristics. The highly methylated genome with its unique 3D structure potentially influences critical biological processes. Our comprehensive comparative genomics analysis deciphered the genetic basis for the rich sesquiterpene content in chicory and indicated that the fructan-accumulating trait resulted from convergent evolution in angiosperms due to shifts in critical sites of fructan-active enzymes. The highly characterized chicory genome provides insight into Asteraceae evolution and fructan biosynthesis in angiosperms.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hao He
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Huang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yang Deng
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaozeng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
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40
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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41
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Kalluchi A, Harris HL, Reznicek TE, Rowley MJ. Considerations and caveats for analyzing chromatin compartments. Front Mol Biosci 2023; 10:1168562. [PMID: 37091873 PMCID: PMC10113542 DOI: 10.3389/fmolb.2023.1168562] [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: 02/17/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
Genomes are organized into nuclear compartments, separating active from inactive chromatin. Chromatin compartments are readily visible in a large number of species by experiments that map chromatin conformation genome-wide. When analyzing these maps, a common step is the identification of genomic intervals that interact within A (active) and B (inactive) compartments. It has also become increasingly common to identify and analyze subcompartments. We review different strategies to identify A/B and subcompartment intervals, including a discussion of various machine-learning approaches to predict these features. We then discuss the strengths and limitations of current strategies and examine how these aspects of analysis may have impacted our understanding of chromatin compartments.
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Affiliation(s)
| | | | | | - M. Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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42
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Ni L, Tian Z. Toward cis-regulation in soybean: a 3D genome scope. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:28. [PMID: 37313524 PMCID: PMC10248674 DOI: 10.1007/s11032-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
In eukaryotic cells, 3D genome plays an important role in the regulation of gene spatiotemporal expression, which is essential for the biological and developmental processes in a life cycle. In the past decade, the development of high-throughput technologies greatly enhances our ability to map the 3D genome organization, identifies multiple 3D genome structures, and investigates the functional role of 3D genome organization in gene regulation, which facilitates our understandings of cis-regulatory landscape and biological development. Comparing with the comprehensive analyses of 3D genome in mammals and model plants, the progress in soybean is much less. Future development and application of tools to precisely manipulate 3D genome structure at different levels will significantly strengthen the functional genome study and molecular breeding in soybean. Here, we review the recent progresses in 3D genome study and discuss future directions, which may help to improve soybean 3D functional genome study and molecular breeding.
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Affiliation(s)
- Lingbin Ni
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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43
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Li X, Wang J, Yu Y, Li G, Wang J, Li C, Zeng Z, Li N, Zhang Z, Dong Q, Yu Y, Wang X, Wang T, Grover CE, Wang B, Liu B, Wendel JF, Gong L. Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae). BMC Biol 2023; 21:56. [PMID: 36941615 PMCID: PMC10029228 DOI: 10.1186/s12915-023-01560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species. RESULTS Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), including Gossypium arboreum, Gossypium raimondii, and Gossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved in Gossypioides and Gossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestral in-cis interactions. CONCLUSIONS Our findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.
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Affiliation(s)
- Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yanan Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Changping Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zixian Zeng
- Department of Biological Science, College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yiyang Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, Hainan, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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Sievers A, Sauer L, Bisch M, Sprengel J, Hausmann M, Hildenbrand G. Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes. Genes (Basel) 2023; 14:genes14030755. [PMID: 36981025 PMCID: PMC10048725 DOI: 10.3390/genes14030755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other's influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.
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Affiliation(s)
- Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Liane Sauer
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Marc Bisch
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Jan Sprengel
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Faculty of Engeneering, University of Applied Science Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
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45
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Huang YF, Liu L, Wang F, Yuan XW, Chen HC, Liu ZF. High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases. Microbiol Spectr 2023; 11:e0429022. [PMID: 36847551 PMCID: PMC10100373 DOI: 10.1128/spectrum.04290-22] [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: 10/20/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
The three-dimensional (3D) genome structure of an organism or cell is highly relevant to its biological activities, but the availability of 3D genome information for bacteria, especially intracellular pathogens, is still limited. Here, we used Hi-C (high-throughput chromosome conformation capture) technology to determine the 3D chromosome structures of exponential- and stationary-phase Brucella melitensis at a 1-kb resolution. We observed that the contact heat maps of the two B. melitensis chromosomes contain a prominent diagonal and a secondary diagonal. Then, 79 chromatin interaction domains (CIDs) were detected at an optical density at 600 nm (OD600) of 0.4 (exponential phase), with the longest CID being 106 kb and the shortest being 12 kb. Moreover, we obtained 49,363 significant cis-interaction loci and 59,953 significant trans-interaction loci. Meanwhile, 82 CIDs of B. melitensis at an OD600 of 1.5 (stationary phase) were detected, with the longest CID being 94 kb and the shortest being 16 kb. In addition, 25,965 significant cis-interaction loci and 35,938 significant trans-interaction loci were obtained in this phase. Furthermore, we found that as the B. melitensis cells grew from the logarithmic to the plateau phase, the frequency of short-range interactions increased, while that of long-range interactions decreased. Finally, combined analysis of 3D genome and whole-genome transcriptome (RNA-seq) data revealed that the strength of short-range interactions in Chr1 is specifically and strongly correlated with gene expression. Overall, our study provides a global view of the chromatin interactions in the B. melitensis chromosomes, which will serve as a resource for further study of the spatial regulation of gene expression in Brucella. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and in the regulation of gene expression. Three-dimensional genome sequencing has been performed in many mammals and plants, but the availability of such data for bacteria, especially intracellular pathogens, is still limited. Approximately 10% of sequenced bacterial genomes contain more than one replicon. However, how multiple replicons are organized within bacterial cells, how they interact, and whether these interactions help to maintain or segregate these multipartite genomes are unresolved issues. Brucella is a Gram-negative, facultative intracellular, and zoonotic bacterium. Except for Brucella suis biovar 3, Brucella species have two chromosomes. Here, we applied Hi-C technology to determine the 3D genome structures of exponential- and stationary-phase Brucella melitensis chromosomes at a 1-kb resolution. Combined analysis of the 3D genome and RNA-seq data indicated that the strength of short-range interactions in B. melitensis Chr1 is specifically and strongly correlated with gene expression. Our study provides a resource to achieve a deeper understanding of the spatial regulation of gene expression in Brucella.
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Affiliation(s)
- Yong-Fang Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Fei Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xin-Wei Yuan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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Acemel RD, Lupiáñez DG. Evolution of 3D chromatin organization at different scales. Curr Opin Genet Dev 2023; 78:102019. [PMID: 36603519 DOI: 10.1016/j.gde.2022.102019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 01/04/2023]
Abstract
Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evolution. In the light of recent studies that profile TADs in disparate animal lineages, we discuss their phylogenetic distribution and the mechanisms that underlie their formation. We present evidence indicating that TADs are plastic entities composed of genomic strata of different ages: ancient cores are combined with newer regions and brought into extant TADs through genomic rearrangements. We highlight that newly incorporated TAD strata enable the establishment of new CRE-promoter interactions and in turn new expression patterns that can drive phenotypical innovation. We further highlight how subtle changes in chromatin folding may fine-tune the expression levels of developmental genes and hold a potential for evolutionary significance.
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HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions. Nat Commun 2023; 14:469. [PMID: 36709329 PMCID: PMC9884265 DOI: 10.1038/s41467-023-36227-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/19/2023] [Indexed: 01/30/2023] Open
Abstract
The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding the control of gene expression challenging, but also opens up possible ways to epigenetically modulate gene expression. Because plants are sessile, they evolved sophisticated ways to rapidly modulate gene expression in response to environmental stress, that are thought to be coordinated by changes in chromatin conformation to mediate specific cellular and physiological responses. However, to what extent and how stress induces dynamic changes in chromatin reorganization remains poorly understood. Here, we comprehensively investigated genome-wide chromatin changes associated with transcriptional reprogramming response to heat stress in tomato. Our data show that heat stress induces rapid changes in chromatin architecture, leading to the transient formation of promoter-enhancer contacts, likely driving the expression of heat-stress responsive genes. Furthermore, we demonstrate that chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato. In light of our findings, we propose that TFs play a key role in controlling dynamic transcriptional responses through 3D reconfiguration of promoter-enhancer contacts.
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Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes. Genome Biol 2023; 24:12. [PMID: 36658660 PMCID: PMC9850592 DOI: 10.1186/s13059-023-02854-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported. RESULTS Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication. CONCLUSION Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.
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Méteignier LV, Nützmann HW, Papon N, Osbourn A, Courdavault V. Emerging mechanistic insights into the regulation of specialized metabolism in plants. NATURE PLANTS 2023; 9:22-30. [PMID: 36564633 DOI: 10.1038/s41477-022-01288-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Plants biosynthesize a broad range of natural products through specialized and species-specific metabolic pathways that are fuelled by core metabolism, together forming a metabolic network. Specialized metabolites have important roles in development and adaptation to external cues, and they also have invaluable pharmacological properties. A growing body of evidence has highlighted the impact of translational, transcriptional, epigenetic and chromatin-based regulation and evolution of specialized metabolism genes and metabolic networks. Here we review the forefront of this research field and extrapolate to medicinal plants that synthetize rare molecules. We also discuss how this new knowledge could help in improving strategies to produce useful plant-derived pharmaceuticals.
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Affiliation(s)
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Nicolas Papon
- IRF, SFR ICAT, Université Angers and Université de Bretagne-Occidentale, Angers, France
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK.
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
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