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Li B, Tan K, Lao AR, Wang H, Zheng H, Zhang L. A comprehensive review of artificial intelligence for pharmacology research. Front Genet 2024; 15:1450529. [PMID: 39290983 PMCID: PMC11405247 DOI: 10.3389/fgene.2024.1450529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
With the innovation and advancement of artificial intelligence, more and more artificial intelligence techniques are employed in drug research, biomedical frontier research, and clinical medicine practice, especially, in the field of pharmacology research. Thus, this review focuses on the applications of artificial intelligence in drug discovery, compound pharmacokinetic prediction, and clinical pharmacology. We briefly introduced the basic knowledge and development of artificial intelligence, presented a comprehensive review, and then summarized the latest studies and discussed the strengths and limitations of artificial intelligence models. Additionally, we highlighted several important studies and pointed out possible research directions.
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Affiliation(s)
- Bing Li
- College of Computer Science, Sichuan University, Chengdu, China
| | - Kan Tan
- College of Computer Science, Sichuan University, Chengdu, China
| | - Angelyn R Lao
- Department of Mathematics and Statistics, De La Salle University, Manila, Philippines
| | - Haiying Wang
- School of Computing, Ulster University, Belfast, United Kingdom
| | - Huiru Zheng
- School of Computing, Ulster University, Belfast, United Kingdom
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China
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2
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Xiao M, Wei R, Yu J, Gao C, Yang F, Zhang L. CpG Island Definition and Methylation Mapping of the T2T-YAO Genome. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae009. [PMID: 39142816 DOI: 10.1093/gpbjnl/qzae009] [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: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 08/16/2024]
Abstract
Precisely defining and mapping all cytosine (C) positions and their clusters, known as CpG islands (CGIs), as well as their methylation status, are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here, we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, by mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7%-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.
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Affiliation(s)
- Ming Xiao
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Rui Wei
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chujie Gao
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Fengyi Yang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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3
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Zhang L, Xiong Z, Xiao M. A Review of the Application of Spatial Transcriptomics in Neuroscience. Interdiscip Sci 2024; 16:243-260. [PMID: 38374297 DOI: 10.1007/s12539-024-00603-4] [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: 10/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Since spatial transcriptomics can locate and distinguish the gene expression of functional genes in special regions and tissue, it is important for us to investigate the brain development, the development mechanism of brain diseases, and the relationship between brain structure and function in Neuroscience (or Brain science). While previous studies have introduced the crucial spatial transcriptomic techniques and data analysis methods, there are few studies to comprehensively overview the key methods, data resources, and technological applications of spatial transcriptomics in Neuroscience. For these reasons, we first investigate several common spatial transcriptomic data analysis approaches and data resources. Second, we introduce the applications of the spatial transcriptomic data analysis approaches in Neuroscience. Third, we summarize the integrating spatial transcriptomics with other technologies in Neuroscience. Finally, we discuss the challenges and future research directions of spatial transcriptomics in Neuroscience.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Zhenqi Xiong
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
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4
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Shi T, Zhang X, Hou Y, Jia C, Dan X, Zhang Y, Jiang Y, Lai Q, Feng J, Feng J, Ma T, Wu J, Liu S, Zhang L, Long Z, Chen L, Street NR, Ingvarsson PK, Liu J, Yin T, Wang J. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. MOLECULAR PLANT 2024; 17:725-746. [PMID: 38486452 DOI: 10.1016/j.molp.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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Affiliation(s)
- Tingting Shi
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xinxin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yukang Hou
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Lai
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jianju Feng
- College of Horticulture and Forestry, Tarim University, Alar 843300, China
| | - Tao Ma
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiali Wu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Shuyu Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Lei Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zhiqin Long
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Liyang Chen
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Västerbotten, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, Jiangsu, China.
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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Hao Y, Yan X, Li Q. Genome-Wide Identification and Expression Profiling of Velvet Complex Transcription Factors in Populus alba × Populus glandulosa. Int J Mol Sci 2024; 25:3926. [PMID: 38612736 PMCID: PMC11011700 DOI: 10.3390/ijms25073926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The discovery of new genes with novel functions is a major driver of adaptive evolutionary innovation in plants. Especially in woody plants, due to genome expansion, new genes evolve to regulate the processes of growth and development. In this study, we characterized the unique VeA transcription factor family in Populus alba × Populus glandulosa, which is associated with secondary metabolism. Twenty VeA genes were characterized systematically on their phylogeny, genomic distribution, gene structure and conserved motif, promoter binding site, and expression profiling. Furthermore, through ChIP-qPCR, Y1H, and effector-reporter assays, it was demonstrated that PagMYB128 directly regulated PagVeA3 to influence the biosynthesis of secondary metabolites. These results provide a basis for further elucidating the function of VeAs gene in poplar and its genetic regulation mechanism.
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Affiliation(s)
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (Y.H.); (Q.L.)
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Zhang L, Zhao R, Liang J, Cai X, Zhang L, Guo H, Zhang Z, Wu J, Wang X. BL-Hi-C reveals the 3D genome structure of Brassica crops with high sensitivity. HORTICULTURE RESEARCH 2024; 11:uhae017. [PMID: 38464474 PMCID: PMC10923644 DOI: 10.1093/hr/uhae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/03/2024] [Indexed: 03/12/2024]
Abstract
High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.
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Affiliation(s)
- Lupeng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Cai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiling Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhicheng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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7
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Qu K, Liu A, Yin M, Mu W, Wu S, Hu H, Chen J, Su X, Dou Q, Ren G. A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera. Commun Biol 2023; 6:1223. [PMID: 38042963 PMCID: PMC10693610 DOI: 10.1038/s42003-023-05620-5] [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: 02/22/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.
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Affiliation(s)
- Kunjing Qu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Guangpeng Ren
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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Lallemand T, Leduc M, Desmazières A, Aubourg S, Rizzon C, Landès C, Celton JM. Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica. Genome Biol Evol 2023; 15:evad178. [PMID: 37847638 PMCID: PMC10601995 DOI: 10.1093/gbe/evad178] [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: 06/02/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.
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Affiliation(s)
- Tanguy Lallemand
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Martin Leduc
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Adèle Desmazières
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sébastien Aubourg
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d’Evry Val d’Essonne, Evry, France
| | - Claudine Landès
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Jean-Marc Celton
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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Wang W, Chen K, Chen N, Gao J, Zhang W, Gong J, Tong S, Chen Y, Li Y, Feng Y, Jiang Y, Ma T. Chromatin accessibility dynamics insight into crosstalk between regulatory landscapes in poplar responses to multiple treatments. TREE PHYSIOLOGY 2023; 43:1023-1041. [PMID: 36851850 DOI: 10.1093/treephys/tpad023] [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: 12/09/2022] [Accepted: 01/22/2023] [Indexed: 06/11/2023]
Abstract
Perennial trees develop and coordinate endogenous response signaling pathways, including their crosstalk and convergence, to cope with various environmental stresses which occur simultaneously in most cases. These processes are involved in gene transcriptional regulations that depend on dynamic interactions between regulatory proteins and corresponding chromatin regions, but the mechanisms remain poorly understood in trees. In this study, we detected chromatin regulatory landscapes of poplar under abscisic acid, methyl jasmonate, salicylic acid and sodium chloride (NaCl) treatment, through integrating ATAC-seq and RNA-seq data. Our results showed that the degree of chromatin accessibility for a given gene is closely related to its expression level. However, unlike the gene expression that shows treatment-specific response patterns, changes in chromatin accessibility exhibit high similarities under these treatments. We further proposed and experimentally validated that a homologous gene copy of RESPONSIVE TO DESICCATION 26 mediates the crosstalk between jasmonic acid and NaCl signaling pathways by directly regulating the stress-responsive genes and that circadian clock-related transcription factors like REVEILLE8 play a central role in response of poplar to these treatments. Overall, our study provides a chromatin insight into the molecular mechanism of transcription regulatory networks in response to different environmental stresses and raises the key roles of the circadian clock of poplar to adapt to adverse environments.
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Affiliation(s)
- Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Kai Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ningning Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jinwen Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenyan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jue Gong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yanlin Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Bai Q, Niu Z, Chen Q, Gao C, Zhu M, Bai J, Liu M, He L, Liu J, Jiang Y, Wan D. The C 2 H 2 -type zinc finger transcription factor OSIC1 positively regulates stomatal closure under osmotic stress in poplar. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:943-960. [PMID: 36632734 PMCID: PMC10106854 DOI: 10.1111/pbi.14007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 12/23/2022] [Indexed: 05/04/2023]
Abstract
Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C2 H2 transcription factor gene OSMOTIC STRESS INDUCED C2 H2 1 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up-regulates PalCuAOζ in vitro and in vivo, encoding a copper-containing polyamine oxidase, to enhance H2 O2 accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA-, drought- and salt-induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H2 O2 production in guard cells mediated by the OSIC1-PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding.
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Affiliation(s)
- Qiuxian Bai
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
- Department of PharmacologyNingxia Medical UniversityYinchuanChina
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Qingyuan Chen
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Chengyu Gao
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Jiexian Bai
- College of Computer Information Engineering,Shanxi Technology and Business CollegeTaiyuanChina
| | - Meijun Liu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Ling He
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
| | - Yuanzhong Jiang
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro‐Ecosystem, College of EcologyLanzhou UniversityLanzhouChina
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11
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Zhang L, Badai J, Wang G, Ru X, Song W, You Y, He J, Huang S, Feng H, Chen R, Zhao Y, Chen Y. Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis. Front Immunol 2023; 14:1123652. [PMID: 36825001 PMCID: PMC9941151 DOI: 10.3389/fimmu.2023.1123652] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Introduction Central nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important, yet challenging to study due to disease lesion locations and other complexities. Methods Utilizing the powerful method of spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular hemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications. Results Our data identified three main 3D global pseudospace-time trajectory bundles that represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex affected by experimental IVH stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH stimulation. Discussion These results are informative for understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injury, strategizing more effective clinical management regimens, and developing novel bioinformatics strategies for the study of other CNS diseases. The algorithm strategies used in this study are searchable via a web service (www.combio-lezhang.online/3dstivh/home).
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China,Innovation Center of Nursing Research, West China Hospital, Sichuan University, Chengdu, China
| | - Jiayidaer Badai
- College of Computer Science, Sichuan University, Chengdu, China
| | - Guan Wang
- College of Computer Science, Sichuan University, Chengdu, China,Innovation Center of Nursing Research, West China Hospital, Sichuan University, Chengdu, China
| | - Xufang Ru
- Chinese Academy of Sciences (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China,Department of Neurosurgery and State Key Laboratory of Trauma, Burn and Combined Injury, Southwest Hospital, Army Medical University, Chongqing, China
| | - Wenkai Song
- College of Computer Science, Sichuan University, Chengdu, China
| | - Yujie You
- College of Computer Science, Sichuan University, Chengdu, China
| | - Jiaojiao He
- College of Computer Science, Sichuan University, Chengdu, China
| | - Suna Huang
- Department of Neurosurgery and State Key Laboratory of Trauma, Burn and Combined Injury, Southwest Hospital, Army Medical University, Chongqing, China
| | - Hua Feng
- Department of Neurosurgery and State Key Laboratory of Trauma, Burn and Combined Injury, Southwest Hospital, Army Medical University, Chongqing, China
| | - Runsheng Chen
- College of Computer Science, Sichuan University, Chengdu, China,Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Runsheng Chen, ; Yi Zhao, ; Yujie Chen, ;
| | - Yi Zhao
- College of Computer Science, Sichuan University, Chengdu, China,West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China,Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Runsheng Chen, ; Yi Zhao, ; Yujie Chen, ;
| | - Yujie Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China,Department of Neurosurgery and State Key Laboratory of Trauma, Burn and Combined Injury, Southwest Hospital, Army Medical University, Chongqing, China,*Correspondence: Runsheng Chen, ; Yi Zhao, ; Yujie Chen, ;
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12
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Chen N, Tong S, Yang J, Qin J, Wang W, Chen K, Shi W, Li J, Liu J, Jiang Y. PtoWRKY40 interacts with PtoPHR1-LIKE3 while regulating the phosphate starvation response in poplar. PLANT PHYSIOLOGY 2022; 190:2688-2705. [PMID: 36040189 PMCID: PMC9706449 DOI: 10.1093/plphys/kiac404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/03/2022] [Indexed: 05/27/2023]
Abstract
Plants usually suffer from phosphorus starvation because of the low inorganic phosphate (Pi) status of most soils. To cope with this, plants have evolved an adaptive phosphate starvation response (PSR) which involves both developmental and metabolic changes regulated mainly by PHOSPHATE STARVATION RESPONSE1 (PHR1) and its homologs. Here, we elucidated how perennial woody plants, such as poplars (Populus spp.), respond to low-Pi stress. We first performed RNA-seq analysis of low-Pi-treated poplars and identified PtoWRKY40 is rapidly downregulated and protein degraded after stress. Overexpressing and knocking-down PtoWRKY40 downregulated and upregulated the expression of Pi starvation signaling genes, respectively, such as PHOSPHATE TRANSPORTER1 (PHT1)-type genes and PURPLE ACID PHOSPHATASE genes. PtoWRKY40 bound to the W box in the promoter of several PtoPHT1s and repressed their expression. Moreover, PtoWRKY40 interacted with PtoPHR1-LIKE3 (PtoPHL3), a PHR1 homolog in poplar, to inhibit the latter binding to the P1BS element and thus reduced PtoPHT1s' transcription under Pi-sufficient conditions. However, Pi deficiency decreased PtoWRKY40 abundance and therefore released its inhibition on PHT1s. In conclusion, we have uncovered a PSR mechanism mediated by PtoWRKY40 and PtoPHL3 which regulates Pi content in poplars, deepening our understanding of how poplars adapt to diverse Pi conditions and regulate appropriate responses to maintain Pi homeostasis.
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Affiliation(s)
- Ningning Chen
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Shaofei Tong
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jian Yang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiajia Qin
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Weiwei Wang
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Kai Chen
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Wensen Shi
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jiacong Li
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
- College of Ecology, State Key Laboratory of Grassland Agro-Ecosystem, Lanzhou University, Lanzhou, 730000, China
| | - Yuanzhong Jiang
- College of Life Science, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, 610065, China
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13
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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14
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Tong S, Wang Y, Chen N, Wang D, Liu B, Wang W, Chen Y, Liu J, Ma T, Jiang Y. PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar. Genome Biol 2022; 23:148. [PMID: 35799188 PMCID: PMC9264554 DOI: 10.1186/s13059-022-02718-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/25/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations. RESULTS We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar. CONCLUSION Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.
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Affiliation(s)
- Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yubo Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Deyan Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Weiwei Wang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
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15
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You Y, Lai X, Pan Y, Zheng H, Vera J, Liu S, Deng S, Zhang L. Artificial intelligence in cancer target identification and drug discovery. Signal Transduct Target Ther 2022; 7:156. [PMID: 35538061 PMCID: PMC9090746 DOI: 10.1038/s41392-022-00994-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 02/08/2023] Open
Abstract
Artificial intelligence is an advanced method to identify novel anticancer targets and discover novel drugs from biology networks because the networks can effectively preserve and quantify the interaction between components of cell systems underlying human diseases such as cancer. Here, we review and discuss how to employ artificial intelligence approaches to identify novel anticancer targets and discover drugs. First, we describe the scope of artificial intelligence biology analysis for novel anticancer target investigations. Second, we review and discuss the basic principles and theory of commonly used network-based and machine learning-based artificial intelligence algorithms. Finally, we showcase the applications of artificial intelligence approaches in cancer target identification and drug discovery. Taken together, the artificial intelligence models have provided us with a quantitative framework to study the relationship between network characteristics and cancer, thereby leading to the identification of potential anticancer targets and the discovery of novel drug candidates.
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Affiliation(s)
- Yujie You
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Xin Lai
- Laboratory of Systems Tumor Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, 91052, Germany
| | - Yi Pan
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Room D513, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China
| | - Huiru Zheng
- School of Computing, Ulster University, Belfast, BT15 1ED, UK
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, 91052, Germany
| | - Suran Liu
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Senyi Deng
- Institute of Thoracic Oncology, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610065, China.
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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16
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Li A, Liu A, Wu S, Qu K, Hu H, Yang J, Shrestha N, Liu J, Ren G. Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108. BMC PLANT BIOLOGY 2022; 22:77. [PMID: 35193491 PMCID: PMC8862580 DOI: 10.1186/s12870-022-03469-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes-Jemalong A17 and R108- that have been extensively used in various legume biology studies. RESULTS To catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis. CONCLUSIONS Our results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future.
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Affiliation(s)
- Ao Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Kunjing Qu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jinli Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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17
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ASTM: Developing the web service for anthrax related spatiotemporal characteristics and meteorology study. QUANTITATIVE BIOLOGY 2022. [DOI: 10.15302/j-qb-022-0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Chen Y, Tong S, Jiang Y, Ai F, Feng Y, Zhang J, Gong J, Qin J, Zhang Y, Zhu Y, Liu J, Ma T. Transcriptional landscape of highly lignified poplar stems at single-cell resolution. Genome Biol 2021; 22:319. [PMID: 34809675 PMCID: PMC8607660 DOI: 10.1186/s13059-021-02537-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. RESULTS Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes' expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. CONCLUSIONS These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanzhong Jiang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fandi Ai
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Junlin Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jue Gong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiajia Qin
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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19
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Liu S, You Y, Tong Z, Zhang L. Developing an Embedding, Koopman and Autoencoder Technologies-Based Multi-Omics Time Series Predictive Model (EKATP) for Systems Biology research. Front Genet 2021; 12:761629. [PMID: 34764986 PMCID: PMC8576451 DOI: 10.3389/fgene.2021.761629] [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: 08/20/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
It is very important for systems biologists to predict the state of the multi-omics time series for disease occurrence and health detection. However, it is difficult to make the prediction due to the high-dimensional, nonlinear and noisy characteristics of the multi-omics time series data. For this reason, this study innovatively proposes an Embedding, Koopman and Autoencoder technologies-based multi-omics time series predictive model (EKATP) to predict the future state of a high-dimensional nonlinear multi-omics time series. We evaluate this EKATP by using a genomics time series with chaotic behavior, a proteomics time series with oscillating behavior and a metabolomics time series with flow behavior. The computational experiments demonstrate that our proposed EKATP can substantially improve the accuracy, robustness and generalizability to predict the future state of a time series for multi-omics data.
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Affiliation(s)
- Suran Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Yujie You
- College of Computer Science, Sichuan University, Chengdu, China
| | - Zhaoqi Tong
- College of Software Engineering, Sichuan University, Chengdu, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China
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MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. Acta Pharm Sin B 2021; 11:3092-3104. [PMID: 34729303 PMCID: PMC8546929 DOI: 10.1016/j.apsb.2021.05.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 02/05/2023] Open
Abstract
Mitotic catastrophe (MC) is a form of programmed cell death induced by mitotic process disorders, which is very important in tumor prevention, development, and drug resistance. Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study, it is urgent for us to develop a professional and comprehensive database to curate MC-related data. Mitotic Catastrophe Database (MCDB) consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles. Also, MCDB defines the confidence level, classification criteria, and uniform naming rules for MC-related data, which greatly improves data reliability and retrieval convenience. Moreover, MCDB develops protein sequence alignment and target prediction functions. The former can be used to predict new potential MC-related genes and proteins, and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds. In short, MCDB is such a proprietary, standard, and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry, molecular biology, bioinformatics, oncology and so on. The MCDB is distributed on http://www.combio-lezhang.online/MCDB/index_html/.
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Key Words
- Data mining
- Database
- GO, Gene Ontology
- IUPAC, International Union of Pure and Applied Chemistry
- InChI Key, International Chemical Identifier hash
- InChI, International Chemical Identifier
- MC, Mitotic Catastrophe
- MCDB, Mitotic Catastrophe Database
- Mitotic catastrophe
- PDB, Protein Data Bank
- PMID, PubMed identifier
- Protein sequence analysis
- PubChem, Public Chemistry
- PubMed, Public Medicine
- SMILES, Simplified Molecular Input Line Entry Specification
- Target prediction
- UniProt, Universal Protein Resource
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