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Lin Y, Huo X, Xu J, Li Y, Zhu H, Yu Y, Tang L, Wang X. A soybean bZIP transcription factor is involved in submergence resistance. Biochem Biophys Res Commun 2024; 722:150151. [PMID: 38801801 DOI: 10.1016/j.bbrc.2024.150151] [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: 03/10/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.
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Affiliation(s)
- Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China.
| | - Xing Huo
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Jing Xu
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China.
| | - Yapeng Li
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China; Sanya Research Institute of Hainan Academy of Agricultural Sciences, Sanya, 572000, China.
| | - Honglin Zhu
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China.
| | - Yongmei Yu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Liqiong Tang
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China.
| | - Xiaoning Wang
- Institute of Food Crops, Hainan Academy of Agricultural Sciences/Hainan Key Laboratory of Crop Genetics and Breeding/Hainan Scientific Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Haikou, 571100, China; Sanya Research Institute of Hainan Academy of Agricultural Sciences, Sanya, 572000, China.
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de Los Reyes P, Serrano-Bueno G, Romero-Campero FJ, Gao H, Romero JM, Valverde F. CONSTANS alters the circadian clock in Arabidopsis thaliana. MOLECULAR PLANT 2024; 17:1204-1220. [PMID: 38894538 DOI: 10.1016/j.molp.2024.06.006] [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: 07/19/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. The circadian clock strongly regulates CO expression. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments, and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily leaf rhythmic movements. We showed that CO upregulates the expression of key genes related to the circadian clock, such as CCA1, LHY, PRR5, and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a high number of PRR5-repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Taken together, our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, providing seasonal information to the circadian system.
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Affiliation(s)
- Pedro de Los Reyes
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Francisco J Romero-Campero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
| | - He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.
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Zhao L, Wei X, Chen F, Yuan L, Chen B, Li R. N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus. PLoS Pathog 2024; 20:e1012476. [PMID: 39159278 PMCID: PMC11361730 DOI: 10.1371/journal.ppat.1012476] [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: 02/01/2024] [Revised: 08/29/2024] [Accepted: 08/04/2024] [Indexed: 08/21/2024] Open
Abstract
In eukaryotic cells, N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification that plays crucial roles in multiple biological processes. Nevertheless, the functions and regulatory mechanisms of m6A in phytopathogenic fungi are poorly understood. Here, we showed that CpMTA1, an m6A methyltransferase in Cryphonectria parasitica, plays a crucial role in fungal phenotypic traits, virulence, and stress tolerance. Furthermore, the acid phosphatase gene CpAphA was implicated to be a target of CpMTA1 by integrated analysis of m6A-seq and RNA-seq, as in vivo RIP assay data confirmed that CpMTA1 directly interacts with CpAphA mRNA. Deletion of CpMTA1 drastically lowered the m6A level of CpAphA and reduced its mRNA expression. Moreover, we found that an m6A reader protein CpYTHDF1 recognizes CpAphA mRNA and increases its stability. Typically, the levels of CpAphA mRNA and protein exhibited a positive correlation with CpMTA1 and CpYTHDF1. Importantly, site-specific mutagenesis demonstrated that the m6A sites, A1306 and A1341, of CpAphA mRNA are important for fungal phenotypic traits and virulence in C. parasitica. Together, our findings demonstrate the essential role of the m6A methyltransferase CpMTA1 in C. parasitica, thereby advancing our understanding of fungal gene regulation through m6A modification.
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Affiliation(s)
- Lijiu Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiangyu Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Fengyue Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Luying Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
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Meng Y, Xiao L, Liu R, Du J, Liu N, Yu J, Li Y, Lu G. Antidepressant effect and mechanism of TMP269 on stress-induced depressive-like behavior in mice. Biochem Pharmacol 2024; 225:116320. [PMID: 38801927 DOI: 10.1016/j.bcp.2024.116320] [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: 01/10/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
TMP269, a class IIA histone deacetylase inhibitor with selectivity, that has a protective effect on the central nervous system, yet its specific mechanism of action remains ambiguous. Although major depressive disorder (MDD) is highly prevalent, its pathophysiology is poorly understood. Recent evidence suggests that histone deacetylase 5 plays a key role in the pathological process of depression and the fact that preclinical studies have shown HDAC5 to be a potential antidepressant target, the search for natural drugs or small molecule compounds that can target HDAC5 may be a potential therapeutic strategy for the treatment of depression. In addition, we examined the role of the Brain-derived neurotrophic factor (BDNF), an important neurotrophic factor for neuronal survival and growth, as a potential downstream target of HDAC5. We found downward revision of HDAC5 levels in the hippocampus ameliorated depressive-like behavior in LH (Learned helplessness) mice. Furthermore, injection of HDAC5 overexpressing adenoviral vectors in the hippocampal dentate gyrus of wild-type mice produced a somewhat depressive-like phenotype. Pharmacological, immunofluorescence and biochemical experiments showed that TMP269 could produce antidepressant effects by inhibiting mouse hippocampal HDAC5 and thus modulating its downstream BDNF. Over all, TMP269 mitigated LH-induced depressive-like behaviors and abnormalities in synapse formation and neurogenesis within the hippocampus. These findings suggest potential beneficial effects of TMP269 on depression.
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Affiliation(s)
- Yuan Meng
- Key Laboratory of Cerebrocranial Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan 750000, China; Department of Pharmacology, College of Pharmacy, Wuhan University, Wuhan 430072, China; Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan 750000, China
| | - Lifei Xiao
- Department of Anesthesiology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Ruyun Liu
- Key Laboratory of Cerebrocranial Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan 750000, China; Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan 750000, China
| | - Juan Du
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan 750000, China
| | - Ning Liu
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan 750000, China
| | - Jianqiang Yu
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yinchuan 750000, China
| | - Yanqin Li
- Department of Pharmacology, College of Pharmacy, Wuhan University, Wuhan 430072, China.
| | - Guangyuan Lu
- Key Laboratory of Cerebrocranial Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan 750000, China; Key Laboratory of Drug Creation and Generic Drug Research, Ningxia Medical University, Yinchuan 750000, China.
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Xin X, Li P, Zhao X, Yu Y, Wang W, Jin G, Wang J, Sun L, Zhang D, Zhang F, Yu S, Su T. Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa. Nat Commun 2024; 15:5470. [PMID: 38937441 PMCID: PMC11211497 DOI: 10.1038/s41467-024-49721-z] [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: 01/02/2023] [Accepted: 06/12/2024] [Indexed: 06/29/2024] Open
Abstract
Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.
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Affiliation(s)
- Xiaoyun Xin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Peirong Li
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Xiuyun Zhao
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Yangjun Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Weihong Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Guihua Jin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Liling Sun
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China
| | - Fenglan Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Shuancang Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
| | - Tongbing Su
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, China.
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing, China.
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Shen GW, Liu D, Xu HR, Hou LY, Wu JX, Xia QY, Lin P. Estrogen-related receptor, a molecular target against lepidoptera pests. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 202:105947. [PMID: 38879334 DOI: 10.1016/j.pestbp.2024.105947] [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: 03/26/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024]
Abstract
Until recently, chemical pesticides were one of the most effective means of controlling agricultural pests; therefore, the search for insecticide targets for agricultural pests has been an ongoing problem. Estrogen-related receptors (ERRs) are transcription factors that regulate cellular metabolism and energy homeostasis in animals. Silkworms are highly sensitive to chemical pesticides, making them ideal models for pesticide screening and evaluation. In this study, we detected ERR expression in key organs involved in pesticide metabolism in silkworms (Bombyx mori), including the fat body and midgut. Using ChIP-seq technology, many estrogen- related response elements were identified in the 2000-bp promoter region upstream of metabolism-related genes, almost all of which were potential ERR target genes. The ERR inhibitor, XCT-790, and the endocrine disruptor, bisphenol A, significantly inhibited expression of the ERR target genes, BmTreh-1, BmTret-1, BmPK, BmPFK, and BmHK, in the fat bodies of silkworms, resulting in pupation difficulties in silkworm larvae that ultimately lead to death. In addition, based on the clarification that the ERR can bind to XCT-790, as observed through biofilm interferometry, its three-dimensional spatial structure was predicted, and using molecular docking techniques, small-molecule compounds with a stronger affinity for the ERR were identified. In summary, utilizing the powerful metabolic regulatory function of ERR in Lepidoptera pests, the developed small molecule inhibitors of ERR can be used for future control of Lepidoptera pests.
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Affiliation(s)
- Guan Wang Shen
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Die Liu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Hao Ran Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Lu Yu Hou
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Jin Xin Wu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Qing You Xia
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Ping Lin
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
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Arčan IŠ, Kouter K, Zupanc T, Paska AV. Epigenetics and suicide: investigating altered H3K14ac unveiled differential expression in ADORA2A, B4GALT2 and MMP14. Epigenomics 2024; 16:701-714. [PMID: 38545853 PMCID: PMC11318710 DOI: 10.2217/epi-2023-0351] [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: 10/06/2023] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Background: Environmental factors make an important contribution to suicide. Histone tails are prone to different modifications, leading to changes of chromatin (de)condensation and consequently gene expression. Materials & methods: Level of H3K14ac was studied with chromatin immunoprecipitation followed by high-throughput DNA sequencing. Genes were further validated with RT-qPCR; using hippocampal tissue. Results: We showed lowered H3K14ac levels in individuals who died by suicide. The genes ADORA2A, B4GALT2 and MMP14 showed differential expression in individuals who died by suicide. Identified genetic and protein interactions among genes show interactions with suicide-related genes. Conclusion: Further investigations of histone modifications in association with DNA methylation and miRNA are needed to expand our knowledge of the genes that could significantly contribute to suicide.
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Affiliation(s)
- Iris Šalamon Arčan
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Kouter
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Institute of Microbiology & Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Institute of Biochemistry & Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Jue D, Li Z, Zhang W, Tang J, Xie T, Sang X, Guo Q. Identification and functional analysis of the LEAFY gene in longan flower induction. BMC Genomics 2024; 25:308. [PMID: 38528464 DOI: 10.1186/s12864-024-10229-x] [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: 01/19/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Flowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy development of the longan industry. Therefore, identifying relevant genes and analysing their regulatory mechanism are essential for scientific research and longan industry development. RESULTS DlLFY (Dimocarpus longan LEAFY) contains a 1167 bp open reading frame and encodes 388 amino acids. The amino acid sequence has a typical LFY/FLO family domain. DlLFY was expressed in all tissues tested, except for the leaf, pericarp, and pulp, with the highest expression occurring in flower buds. Expression of DlLFY was significantly upregulated at the early flower induction stage in "SX" ("Shixia"). The results of subcellular localization and transactivation analysis showed that DlLFY is a typical transcription factor acting as a transcriptional activator. Moreover, overexpression of DlLFY in Arabidopsis promoted early flowering and restrained growth, resulting in reduced plant height and rosette leaf number and area in transgenic plants. DNA affinity purification sequencing (DAP-Seq) analysis showed that 13 flower-related genes corresponding to five homologous genes of Arabidopsis may have binding sites and be putative target genes. Among these five flower-related genes, only AtTFL1 (terminal flower 1) was strongly inhibited in transgenic lines. CONCLUSION Taken together, these results indicate that DlLFY plays a pivotal role in controlling longan flowering, possibly by interacting with TFL1.
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Affiliation(s)
- Dengwei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Ting Xie
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Xuelian Sang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China.
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China.
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Mierzejewska J, Adamczak D, Smolibowski M, Kaczmarek M, Mackiewicz A. ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes. Int J Mol Sci 2023; 24:16380. [PMID: 38003570 PMCID: PMC10671213 DOI: 10.3390/ijms242216380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Julia Mierzejewska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Dominika Adamczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
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10
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Wu J, Luo J, He Q, Xia Y, Tian H, Zhu L, Li C, Loor JJ. Docosahexaenoic Acid Alters Lipid Metabolism Processes via H3K9ac Epigenetic Modification in Dairy Goat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37224334 DOI: 10.1021/acs.jafc.3c01606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Goat milk is increasingly recognized by consumers due to its high nutritional value, richness in short- and medium-chain fatty acids, and richness in polyunsaturated fatty acids (PUFA). Exogenous supplementation of docosahexaenoic acid (DHA) is an important approach to increasing the content of PUFA in goat milk. Several studies have reported benefits of dietary DHA in terms of human health, including potential against chronic diseases and tumors. However, the mechanisms whereby an increased supply of DHA regulates mammary cell function is unknown. In this study, we investigated the effect of DHA on lipid metabolism processes in goat mammary epithelial cells (GMEC) and the function of H3K9ac epigenetic modifications in this process. Supplementation of DHA promoted lipid droplet accumulation increased the DHA content and altered fatty acid composition in GMEC. Lipid metabolism processes were altered by DHA supplementation through transcriptional programs in GMEC. ChIP-seq analysis revealed that DHA induced genome-wide H3K9ac epigenetic changes in GMEC. Multiomics analyses (H3K9ac genome-wide screening and RNA-seq) revealed that DHA-induced expression of lipid metabolism genes (FASN, SCD1, FADS1, FADS2, LPIN1, DGAT1, MBOAT2), which were closely related with changes in lipid metabolism processes and fatty acid profiles, were regulated by modification of H3K9ac. In particular, DHA increased the enrichment of H3K9ac in the promoter region of PDK4 and promoted its transcription, while PDK4 inhibited lipid synthesis and activated AMPK signaling in GMEC. The activation of the expression of fatty acid metabolism-related genes FASN, FADS2, and SCD1 and their upstream transcription factor SREBP1 by the AMPK inhibitor was attenuated in PDK4-overexpressing GMEC. In conclusion, DHA alters lipid metabolism processes via H3K9ac modifications and the PDK4-AMPK-SREBP1 signaling axis in goat mammary epithelial cells, providing new insights into the mechanism through which DHA affects mammary cell function and regulates milk fat metabolism.
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Affiliation(s)
- Jiao Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Qiuya He
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Yingying Xia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Huibin Tian
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Lu Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Cong Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Juan J Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801, United States of America
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11
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Hill L, Wutz G, Jaritz M, Tagoh H, Calderón L, Peters JM, Goloborodko A, Busslinger M. Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells. Nat Commun 2023; 14:2316. [PMID: 37085514 PMCID: PMC10121685 DOI: 10.1038/s41467-023-37994-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination following downregulation of the cohesin-release factor Wapl by Pax5, resulting in global changes in the chromosomal architecture of pro-B cells. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus were insensitive to Wapl upregulation in pre-B cells. Notably, the Wapl protein was expressed at a 2.2-fold higher level in pre-B cells compared with pro-B cells, which resulted in a distinct chromosomal architecture with normal loop sizes in pre-B cells. High-resolution chromosomal contact analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igμ-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3' proximal VH genes and likely to allelic exclusion of all other VH genes in pre-B cells. These results suggest that pro-B and pre-B cells with their distinct chromosomal architectures use different chromatin folding principles for V gene recombination, thereby enabling allelic exclusion at the Igh locus, when the Igk locus is recombined.
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Affiliation(s)
- Louisa Hill
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Lesly Calderón
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, A-1030, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria.
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12
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Lafleur VN, Halim S, Choudhry H, Ratcliffe PJ, Mole DR. Multi-level interaction between HIF and AHR transcriptional pathways in kidney carcinoma. Life Sci Alliance 2023; 6:e202201756. [PMID: 36725335 PMCID: PMC9896012 DOI: 10.26508/lsa.202201756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Hypoxia-inducible factor (HIF) and aryl hydrocarbon receptor (AHR) are members of the bHLH-PAS family of transcription factors that underpin cellular responses to oxygen and to endogenous and exogenous ligands, respectively, and have central roles in the pathogenesis of renal cancer. Composed of heterodimers, they share a common HIF-1β/ARNT subunit and similar DNA-binding motifs, raising the possibility of crosstalk between the two transcriptional pathways. Here, we identify both general and locus-specific mechanisms of interaction between HIF and AHR that act both antagonistically and cooperatively. Specifically, we observe competition for the common HIF-1β/ARNT subunit, in cis synergy for chromatin binding, and overlap in their transcriptional targets. Recently, both HIF and AHR inhibitors have been developed for the treatment of solid tumours. However, inhibition of one pathway may promote the oncogenic effects of the other. Therefore, our work raises important questions as to whether combination therapy targeting both of these pro-tumourigenic pathways might show greater efficacy than targeting each system independently.
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Affiliation(s)
| | - Silvia Halim
- NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
- The Francis Crick Institute, London, UK
| | - David R Mole
- NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
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13
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Mai Y, Sun P, Suo Y, Li H, Han W, Diao S, Wang L, Yuan J, Wang Y, Ye L, Zhang Y, Li F, Fu J. Regulatory mechanism of MeGI on sexuality in Diospyros oleifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1046235. [PMID: 36909399 PMCID: PMC9994623 DOI: 10.3389/fpls.2023.1046235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Dioecy system is an important strategy for maintaining genetic diversity. The transcription factor MeGI, contributes to dioecy by promoting gynoecium development in Diospyros lotus and D. kaki. However, the function of MeGI in D. oleifera has not been identified. In this study, we confirmed that MeGI, cloned from D. oleifera, repressed the androecium development in Arabidopsis thaliana. Subsequently, chromatin immunoprecipitation-sequencing (ChIP-seq), DNA affinity purification-sequencing (DAP-seq), and RNA-seq were used to uncover the gene expression response to MeGI. The results showed that the genes upregulated and downregulated in response to MeGI were mainly enriched in the circadian rhythm-related and flavonoid biosynthetic pathways, respectively. Additionally, the WRKY DNA-binding protein 28 (WRKY28) gene, which was detected by ChIP-seq, DAP-seq, and RNA-seq, was emphasized. WRKY28 has been reported to inhibit salicylic acid (SA) biosynthesis and was upregulated in MeGI-overexpressing A. thaliana flowers, suggesting that MeGI represses the SA level by increasing the expression level of WRKY28. This was confirmed that SA level was lower in D. oleifera female floral buds than male. Overall, our findings indicate that the MeGI mediates its sex control function in D. oleifera mainly by regulating genes in the circadian rhythm, SA biosynthetic, and flavonoid biosynthetic pathways.
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Affiliation(s)
- Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Liyuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Chinese Academy of Sciences (CAS) Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lingshuai Ye
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
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14
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Goruppi S, Clocchiatti A, Bottoni G, Di Cicco E, Ma M, Tassone B, Neel V, Demehri S, Simon C, Paolo Dotto G. The ULK3 kinase is a determinant of keratinocyte self-renewal and tumorigenesis targeting the arginine methylome. Nat Commun 2023; 14:887. [PMID: 36797248 PMCID: PMC9935893 DOI: 10.1038/s41467-023-36410-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Epigenetic mechanisms oversee epidermal homeostasis and oncogenesis. The identification of kinases controlling these processes has direct therapeutic implications. We show that ULK3 is a nuclear kinase with elevated expression levels in squamous cell carcinomas (SCCs) arising in multiple body sites, including skin and Head/Neck. ULK3 loss by gene silencing or deletion reduces proliferation and clonogenicity of human keratinocytes and SCC-derived cells and affects transcription impinging on stem cell-related and metabolism programs. Mechanistically, ULK3 directly binds and regulates the activity of two histone arginine methyltransferases, PRMT1 and PRMT5 (PRMT1/5), with ULK3 loss compromising PRMT1/5 chromatin association to specific genes and overall methylation of histone H4, a shared target of these enzymes. These findings are of translational significance, as downmodulating ULK3 by RNA interference or locked antisense nucleic acids (LNAs) blunts the proliferation and tumorigenic potential of SCC cells and promotes differentiation in two orthotopic models of skin cancer.
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Affiliation(s)
- Sandro Goruppi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA.
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.
| | - Andrea Clocchiatti
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | - Giulia Bottoni
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | - Emery Di Cicco
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | - Min Ma
- Personalized Cancer Prevention Research Unit and Head and Neck Surgery Division, Centre Hospitalier Universitaire Vaudois, Lausanne, 1011, Switzerland
- Department of Immunobiology, University of Lausanne, Epalinges, 1066, Switzerland
| | - Beatrice Tassone
- Personalized Cancer Prevention Research Unit and Head and Neck Surgery Division, Centre Hospitalier Universitaire Vaudois, Lausanne, 1011, Switzerland
- Department of Immunobiology, University of Lausanne, Epalinges, 1066, Switzerland
| | - Victor Neel
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | - Shadhmer Demehri
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | - Christian Simon
- Personalized Cancer Prevention Research Unit and Head and Neck Surgery Division, Centre Hospitalier Universitaire Vaudois, Lausanne, 1011, Switzerland
- Department of Immunobiology, University of Lausanne, Epalinges, 1066, Switzerland
- International Cancer Prevention Institute, Epalinges, 1066, Switzerland
| | - G Paolo Dotto
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, 02129, MA, USA.
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.
- Personalized Cancer Prevention Research Unit and Head and Neck Surgery Division, Centre Hospitalier Universitaire Vaudois, Lausanne, 1011, Switzerland.
- Department of Immunobiology, University of Lausanne, Epalinges, 1066, Switzerland.
- International Cancer Prevention Institute, Epalinges, 1066, Switzerland.
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15
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Ma J, You D, Chen S, Fang N, Yi X, Wang Y, Lu X, Li X, Zhu M, Xue M, Tang Y, Wei X, Huang J, Zhu Y. Epigenetic association study uncovered H3K27 acetylation enhancers and dysregulated genes in high-fat-diet-induced nonalcoholic fatty liver disease in rats. Epigenomics 2022; 14:1523-1540. [PMID: 36851897 DOI: 10.2217/epi-2022-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Aim: To evaluate the regulatory landscape underlying the active enhancer marked by H3K27ac in high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in rats. Materials & methods: H3K27ac chromatin immunoprecipitation and high-throughput RNA sequencing to construct regulatory profiles and transcriptome of liver from NAFLD rat model induced by HFD. De novo motif analysis for differential H3K27ac peaks. Functional enrichment, Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction network were examined for differential peak-genes. The mechanism was further verified by western blot, chromatin immunoprecipitation-quantitative PCR and real-time PCR. Results: A total of 1831 differential H3K27ac peaks were identified significantly correlating with transcription factors and target genes (CYP8B1, PLA2G12B, SLC27A5, CYP7A1 and APOC3) involved in lipid and energy homeostasis. Conclusion: Altered acetylation induced by HFD leads to the dysregulation of gene expression, further elucidating the epigenetic mechanism in the etiology of NAFLD.
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Affiliation(s)
- Jinhu Ma
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Dandan You
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Shuwen Chen
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Nana Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xinrui Yi
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Yi Wang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xuejin Lu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xinyu Li
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Meizi Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Min Xue
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Yunshu Tang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xiaohui Wei
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Jianzhen Huang
- College of Animal Science & Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yaling Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
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16
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Maghsoudi Z, Nguyen H, Tavakkoli A, Nguyen T. A comprehensive survey of the approaches for pathway analysis using multi-omics data integration. Brief Bioinform 2022; 23:6761962. [PMID: 36252928 PMCID: PMC9677478 DOI: 10.1093/bib/bbac435] [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: 04/28/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 02/07/2023] Open
Abstract
Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method's practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.
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Affiliation(s)
- Zeynab Maghsoudi
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Ha Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Alireza Tavakkoli
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Tin Nguyen
- Corresponding author: Tin Nguyen, Department of Computer Science and Engineering, University of Nevada, Reno, NV, USA. Tel.: +1-775-784-6619;
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Veiga DFT, Tremblay M, Gerby B, Herblot S, Haman A, Gendron P, Lemieux S, Zúñiga-Pflücker JC, Hébert J, Cohen JP, Hoang T. Monoallelic Heb/Tcf12 Deletion Reduces the Requirement for NOTCH1 Hyperactivation in T-Cell Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:867443. [PMID: 35401501 PMCID: PMC8987207 DOI: 10.3389/fimmu.2022.867443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 12/21/2022] Open
Abstract
Early T-cell development is precisely controlled by E proteins, that indistinguishably include HEB/TCF12 and E2A/TCF3 transcription factors, together with NOTCH1 and pre-T cell receptor (TCR) signalling. Importantly, perturbations of early T-cell regulatory networks are implicated in leukemogenesis. NOTCH1 gain of function mutations invariably lead to T-cell acute lymphoblastic leukemia (T-ALL), whereas inhibition of E proteins accelerates leukemogenesis. Thus, NOTCH1, pre-TCR, E2A and HEB functions are intertwined, but how these pathways contribute individually or synergistically to leukemogenesis remain to be documented. To directly address these questions, we leveraged Cd3e-deficient mice in which pre-TCR signaling and progression through β-selection is abrogated to dissect and decouple the roles of pre-TCR, NOTCH1, E2A and HEB in SCL/TAL1-induced T-ALL, via the use of Notch1 gain of function transgenic (Notch1ICtg) and Tcf12+/- or Tcf3+/- heterozygote mice. As a result, we now provide evidence that both HEB and E2A restrain cell proliferation at the β-selection checkpoint while the clonal expansion of SCL-LMO1-induced pre-leukemic stem cells in T-ALL is uniquely dependent on Tcf12 gene dosage. At the molecular level, HEB protein levels are decreased via proteasomal degradation at the leukemic stage, pointing to a reversible loss of function mechanism. Moreover, in SCL-LMO1-induced T-ALL, loss of one Tcf12 allele is sufficient to bypass pre-TCR signaling which is required for Notch1 gain of function mutations and for progression to T-ALL. In contrast, Tcf12 monoallelic deletion does not accelerate Notch1IC-induced T-ALL, indicating that Tcf12 and Notch1 operate in the same pathway. Finally, we identify a tumor suppressor gene set downstream of HEB, exhibiting significantly lower expression levels in pediatric T-ALL compared to B-ALL and brain cancer samples, the three most frequent pediatric cancers. In summary, our results indicate a tumor suppressor function of HEB/TCF12 in T-ALL to mitigate cell proliferation controlled by NOTCH1 in pre-leukemic stem cells and prevent NOTCH1-driven progression to T-ALL.
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Affiliation(s)
- Diogo F. T. Veiga
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- Department of Translational Medicine, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Mathieu Tremblay
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
| | - Bastien Gerby
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1037, Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | - Sabine Herblot
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- Unité de recherche en hémato-oncologie Charles-Bruneau, Centre de Recherche du CHU Sainte-Justine, Montréal, Canada
| | - André Haman
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
| | - Patrick Gendron
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
| | - Sébastien Lemieux
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | | | - Josée Hébert
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- Institut universitaire d’hémato-oncologie et de thérapie cellulaire, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
- Quebec Leukemia Cell Bank, Centre de recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Joseph Paul Cohen
- Department of Computer Science and Operations Research, Université de Montréal, Montreal, QC, Canada
- Université de Montréal, Montreal, QC, Canada
| | - Trang Hoang
- Department of Pharmacology and Physiology, Université de Montréal, Institute for Research in Immunology and Cancer, QC, Canada
- *Correspondence: Trang Hoang,
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18
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Zheng Y, He S, Cai W, Shen L, Huang X, Yang S, Huang Y, Lu Q, Wang H, Guan D, He S. CaAIL1 Acts Positively in Pepper Immunity against Ralstonia solanacearum by Repressing Negative Regulators. PLANT & CELL PHYSIOLOGY 2021; 62:1702-1717. [PMID: 34463342 DOI: 10.1093/pcp/pcab125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/09/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
APETALA2 (AP2) subfamily transcription factors participate in plant growth and development, but their roles in plant immunity remain unclear. Here, we discovered that the AP2 transcription factor CaAIL1 functions in immunity against Ralstonia solanacearum infection (RSI) in pepper (Capsicum annuum). CaAIL1 expression was upregulated by RSI, and loss- and gain-of-function assays using virus-induced gene silencing and transient overexpression, respectively, revealed that CaAIL1 plays a positive role in immunity to RSI in pepper. Chromatin immunoprecipitation sequencing (ChIP-seq) uncovered a subset of transcription-factor-encoding genes, including CaRAP2-7, CaGATA17, CaGtf3a and CaTCF25, that were directly targeted by CaAIL1 via their cis-elements, such as GT or AGGCA motifs. ChIP-qPCR and electrophoretic mobility shift assays confirmed these findings. These genes, encoding transcription factors with negative roles in immunity, were repressed by CaAIL1 during pepper response to RSI, whereas genes encoding positive immune regulators such as CaEAS were derepressed by CaAIL1. Importantly, we showed that the atypical EAR motif (LXXLXXLXX) in CaAIL1 is indispensable for its function in immunity. These findings indicate that CaAIL1 enhances the immunity of pepper against RSI by repressing a subset of negative immune regulators during the RSI response through its binding to several cis-elements in their promoters.
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Affiliation(s)
- Yutong Zheng
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Shicong He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Weiwei Cai
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Lei Shen
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Xueying Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Yu Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Qiaoling Lu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Hui Wang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Deyi Guan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15, Shang xia dian Road, Jianxin Town, Cangshan District, Fuzhou, Fujian 350002, China
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19
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Ren C, Li H, Wang Z, Dai Z, Lecourieux F, Kuang Y, Xin H, Li S, Liang Z. Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis. PLANT & CELL PHYSIOLOGY 2021; 62:1615-1629. [PMID: 34279666 PMCID: PMC8643690 DOI: 10.1093/pcp/pcab115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 05/29/2023]
Abstract
Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Zemin Wang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Fatma Lecourieux
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, 210 chemin de Leysotte, Villenave d’Ornon 33882, France
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 1 Lumo Rd, Wuhan 430074, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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20
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Rogers D, Sood A, Wang H, van Beek JJP, Rademaker TJ, Artusa P, Schneider C, Shen C, Wong DC, Bhagrath A, Lebel MÈ, Condotta SA, Richer MJ, Martins AJ, Tsang JS, Barreiro LB, François P, Langlais D, Melichar HJ, Textor J, Mandl JN. Pre-existing chromatin accessibility and gene expression differences among naive CD4 + T cells influence effector potential. Cell Rep 2021; 37:110064. [PMID: 34852223 DOI: 10.1016/j.celrep.2021.110064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/26/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.
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Affiliation(s)
- Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Aditi Sood
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Microbiology, Immunology, and Infectious Disease, Université de Montréal, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Jasper J P van Beek
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Patricio Artusa
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Caitlin Schneider
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Connie Shen
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Dylan C Wong
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Aanya Bhagrath
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Paul François
- Department of Physics, McGill University, Montreal, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University Genome Centre, Montreal, QC, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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21
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Girgis J, Yang D, Chakroun I, Liu Y, Blais A. Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter. Skelet Muscle 2021; 11:26. [PMID: 34809717 PMCID: PMC8607597 DOI: 10.1186/s13395-021-00281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Six1 transcription factor is implicated in controlling the development of several tissue types, notably skeletal muscle. Six1 also contributes to muscle metabolism and its activity is associated with the fast-twitch, glycolytic phenotype. Six1 regulates the expression of certain genes of the fast muscle program by directly stimulating their transcription or indirectly acting through a long non-coding RNA. We hypothesized that additional mechanisms of action of Six1 might be at play. METHODS A combined analysis of gene expression profiling and genome-wide location analysis data was performed. Results were validated using in vivo RNA interference loss-of-function assays followed by measurement of gene expression by RT-PCR and transcriptional reporter assays. RESULTS The Slc16a10 gene, encoding the thyroid hormone transmembrane transporter MCT10, was identified as a gene with a transcriptional enhancer directly bound by Six1 and requiring Six1 activity for full expression in adult mouse tibialis anterior, a predominantly fast-twitch muscle. Of the various thyroid hormone transporters, MCT10 mRNA was found to be the most abundant in skeletal muscle, and to have a stronger expression in fast-twitch compared to slow-twitch muscle groups. Loss-of-function of MCT10 in the tibialis anterior recapitulated the effect of Six1 on the expression of fast-twitch muscle genes and led to lower activity of a thyroid hormone receptor-dependent reporter gene. CONCLUSIONS These results shed light on the molecular mechanisms controlling the tissue expression profile of MCT10 and identify modulation of the thyroid hormone signaling pathway as an additional mechanism by which Six1 influences skeletal muscle metabolism.
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Affiliation(s)
- John Girgis
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dabo Yang
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Imane Chakroun
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Yubing Liu
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alexandre Blais
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada. .,University of Ottawa Centre for Inflammation, Immunity and Infection (CI3), Ottawa, Ontario, Canada.
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22
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Zhang G, Lv Z, Diao S, Liu H, Duan A, He C, Zhang J. Unique features of the m 6A methylome and its response to drought stress in sea buckthorn ( Hippophae rhamnoides Linn.). RNA Biol 2021; 18:794-803. [PMID: 34806556 DOI: 10.1080/15476286.2021.1992996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In plants, recent studies have revealed that N6-methyladenosine (m6A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m6A methyltransferase, m6A demethylase and m6A-binding proteins can cause differential phenotypes, indicating that m6A may have critical roles in the plant. In this study, we depicted the m6A map of sea buckthorn (Hippophae rhamnoides Linn.) transcriptome. Similar to A. thaliana, m6A sites of sea buckthorn transcriptome is significantly enriched around the stop codon and within 3'-untranslated regions (3'UTR). Gene ontology analysis shows that the m6A modification genes are associated with metabolic biosynthesis. In addition, we identified 13,287 different m6A peaks (DMPs) between leaf under drought (TR) and control (CK) treatment. It reveals that m6A has a high level of conservation and has a positive correlation with mRNA abundance in plants. GO and KEGG enrichment results showed that DMP modification DEGs in TR were particularly associated with ABA biosynthesis. Interestingly, our results showed three m6A demethylase (HrALKBH10B, HrALKBH10C and HrALKBH10D) genes were significantly increased following drought stress, which indicated that it may contributed the decreased m6A levels. This exhaustive m6A map provides a basis and resource for the further functional study of mRNA m6A modification in abiotic stress.
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Affiliation(s)
- Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zhongrui Lv
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Songfeng Diao
- Non-timber Forestry Research and Development Center, Chinese Academy of Forestry & Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Hong Liu
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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23
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He Y, Li L, Yao Y, Li Y, Zhang H, Fan M. Transcriptome-wide N6-methyladenosine (m 6A) methylation in watermelon under CGMMV infection. BMC PLANT BIOLOGY 2021; 21:516. [PMID: 34749644 PMCID: PMC8574010 DOI: 10.1186/s12870-021-03289-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 10/22/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon. RESULTS We measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity. CONCLUSIONS Our study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.
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Affiliation(s)
- Yanjun He
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Lili Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Yixiu Yao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Yulin Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Huiqing Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Min Fan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China.
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24
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Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep 2021; 11:15463. [PMID: 34326396 PMCID: PMC8322331 DOI: 10.1038/s41598-021-94805-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.
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Affiliation(s)
- Arno Meiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Manuela Weitkunat
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.
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25
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Song X, Zhao Y, Wang J, Lu MZ. The transcription factor KNAT2/6b mediates changes in plant architecture in response to drought via down-regulating GA20ox1 in Populus alba × P. glandulosa. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5625-5637. [PMID: 33987654 DOI: 10.1093/jxb/erab201] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 05/11/2023]
Abstract
Plant architecture is genetically controlled, but is influenced by environmental factors. Plants have evolved adaptive mechanisms that allow changes in their architecture under stress, in which phytohormones play a central role. However, the gene regulators that connect growth and stress signals are rarely reported. Here, we report that a class I KNOX gene, PagKNAT2/6b, can directly inhibit the synthesis of gibberellin (GA), altering plant architecture and improving drought resistance in Populus. Expression of PagKNAT2/6b was significantly induced under drought conditions, and transgenic poplars overexpressing PagKNAT2/6b exhibited shorter internode length and smaller leaf size with short or even absent petioles. Interestingly, these transgenic plants showed improved drought resistance under both short- and long-term drought stress. Histological observations indicated that decreased internode length and leaf size were mainly caused by the inhibition of cell elongation and expansion. GA content was reduced, and the GA20-oxidase gene PagGA20ox1 was down-regulated in overexpressing plants. Expression of PagGA20ox1 was negatively related to that of PagKNAT2/6b under drought stress. ChIP and transient transcription activity assays revealed that PagGA20ox1 was directly targeted by PagKNAT2/6b. Therefore, this study provides evidence that PagKNAT2/6b mediates stress signals and changes in plant architecture via GA signaling by down-regulating PagGA20ox1.
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Affiliation(s)
- Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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26
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Salisbury DA, Casero D, Zhang Z, Wang D, Kim J, Wu X, Vergnes L, Mirza AH, Leon-Mimila P, Williams KJ, Huertas-Vazquez A, Jaffrey SR, Reue K, Chen J, Sallam T. Transcriptional regulation of N 6-methyladenosine orchestrates sex-dimorphic metabolic traits. Nat Metab 2021; 3:940-953. [PMID: 34282353 PMCID: PMC8422857 DOI: 10.1038/s42255-021-00427-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Males and females exhibit striking differences in the prevalence of metabolic traits including hepatic steatosis, a key driver of cardiometabolic morbidity and mortality. RNA methylation is a widespread regulatory mechanism of transcript turnover. Here, we show that presence of the RNA modification N6-methyladenosine (m6A) triages lipogenic transcripts for degradation and guards against hepatic triglyceride accumulation. In male but not female mice, this protective checkpoint stalls under lipid-rich conditions. Loss of m6A control in male livers increases hepatic triglyceride stores, leading to a more 'feminized' hepatic lipid composition. Crucially, liver-specific deletion of the m6A complex protein Mettl14 from male and female mice significantly diminishes sex-specific differences in steatosis. We further surmise that the m6A installing machinery is subject to transcriptional control by the sex-responsive BCL6-STAT5 axis in response to dietary conditions. These data show that m6A is essential for precise and synchronized control of lipogenic enzyme activity and provide insights into the molecular basis for the existence of sex-specific differences in hepatic lipid traits.
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Affiliation(s)
- David A Salisbury
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zhengyi Zhang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dan Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jason Kim
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiaohui Wu
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aashiq H Mirza
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Paola Leon-Mimila
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kevin J Williams
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Huertas-Vazquez
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Karen Reue
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, The Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.
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27
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Zhou L, Tang R, Li X, Tian S, Li B, Qin G. N 6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner. Genome Biol 2021; 22:168. [PMID: 34078442 PMCID: PMC8173835 DOI: 10.1186/s13059-021-02385-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/21/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits. RESULTS Here we show that m6A methylation displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3' untranslated regions is generally negatively correlated with the abundance of associated mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those of NCED5, ABAR, and AREB1 in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrate that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability of NCED5 and AREB1, while facilitating translation of ABAR. CONCLUSION Our findings uncover that m6A methylation regulates ripening of the non-climacteric strawberry fruit by targeting the ABA pathway, which is distinct from that in the climacteric tomato fruit.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renkun Tang
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojing Li
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingbing Li
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Zhang Q, Xing C, Kong X, Wang C, Chen X. ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol Agent Pseudomonas protegens FD6. Front Microbiol 2021; 12:667637. [PMID: 34054776 PMCID: PMC8160232 DOI: 10.3389/fmicb.2021.667637] [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: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Many Pseudomonas protegens strains produce the antibiotics pyoluteorin (PLT) and 2,4-diacetylphloroglucinol (2,4-DAPG), both of which have antimicrobial properties. The biosynthesis of these metabolites is typically controlled by multiple regulatory factors. Virulence factor regulator (Vfr) is a multifunctional DNA-binding regulator that modulates 2,4-DAPG biosynthesis in P. protegens FD6. However, the mechanism by which Vfr regulates this process remains unclear. In the present study, chromatin immunoprecipitation of FLAG-tagged Vfr and nucleotide sequencing analysis were used to identify 847 putative Vfr binding sites in P. protegens FD6. The consensus P. protegens Vfr binding site predicted from nucleotide sequence alignment is TCACA. The qPCR data showed that Vfr positively regulates the expression of phlF and phlG, and the expression of these genes was characterized in detail. The purified recombinant Vfr bound to an approximately 240-bp fragment within the phlF and phlG upstream regions that harbor putative Vfr consensus sequences. Using electrophoretic mobility shift assays, we localized Vfr binding to a 25-bp fragment that contains part of the Vfr binding region. Vfr binding was eliminated by mutating the TACG and CACA sequences in phlF and phlG, respectively. Taken together, our results show that Vfr directly regulates the expression of the 2,4-DAPG operon by binding to the upstream regions of both the phlF and phlG genes. However, unlike other Vfr-targeted genes, Vfr binding to P. protegens FD6 does not require an intact binding consensus motif. Furthermore, we demonstrated that vfr expression is autoregulated in this bacterium. These results provide novel insights into the regulatory role of Vfr in the biocontrol agent P. protegens.
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Affiliation(s)
- Qingxia Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chenglin Xing
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiangwei Kong
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Cheng Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xijun Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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29
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Zou X, Du M, Liu Y, Wu L, Xu L, Long Q, Peng A, He Y, Andrade M, Chen S. CsLOB1 regulates susceptibility to citrus canker through promoting cell proliferation in citrus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1039-1057. [PMID: 33754403 DOI: 10.1111/tpj.15217] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 05/25/2023]
Abstract
Citrus sinensis lateral organ boundary 1 (CsLOB1) was previously identified as a critical disease susceptibility gene for citrus bacterial canker, which is caused by Xanthomonas citri subsp. citri (Xcc). However, the molecular mechanisms of CsLOB1 in citrus response to Xcc are still elusive. Here, we constructed transgenic plants overexpressing and RNAi-silencing of CsLOB1 using the canker-disease susceptible 'wanjincheng' orange (C. sinensis Osbeck) as explants. CsLOB1-overexpressing plants exhibited dwarf phenotypes with smaller and thicker leaf, increased branches and adventitious buds clustered on stems. These phenotypes were followed by a process of pustule- and canker-like development that exhibited enhanced cell proliferation. Pectin depolymerization and expansin accumulation were enhanced by CsLOB1 overexpression, while cellulose and hemicellulose synthesis were increased by CsLOB1 silence. Whilst overexpression of CsLOB1 increased susceptibility, RNAi-silencing of CsLOB1 enhanced resistance to canker disease without impairing pathogen entry. Transcriptome analysis revealed that CsLOB1 positively regulated cell wall degradation and modification processes, cytokinin metabolism, and cell division. Additionally, 565 CsLOB1-targeted genes were identified in chromatin immunoprecipitation-sequencing (ChIP-seq) experiments. Motif discovery analysis revealed that the most highly overrepresented binding sites had a conserved 6-bp 'GCGGCG' consensus DNA motif. RNA-seq and ChIP-seq data suggested that CsLOB1 directly activates the expression of four genes involved in cell wall remodeling, and three genes that participate in cytokinin and brassinosteroid hormone pathways. Our findings indicate that CsLOB1 promotes cell proliferation by mechanisms depending on cell wall remodeling and phytohormone signaling, which may be critical to citrus canker development and bacterial growth in citrus.
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Affiliation(s)
- Xiuping Zou
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Meixia Du
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Yunuo Liu
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Liu Wu
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Lanzhen Xu
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Qin Long
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Aihong Peng
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Yongrui He
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
| | - Maxuel Andrade
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Shanchun Chen
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing, 400712, P. R. China
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30
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Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature 2021; 593:440-444. [PMID: 33767446 PMCID: PMC9827709 DOI: 10.1038/s41586-021-03468-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023]
Abstract
Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.
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Affiliation(s)
- Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.,Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kenta Shinoda
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raffaella De Pace
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Han-Yu Shih
- National Eye Institute, NIH, Bethesda, MD, USA
| | - Steve Coon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Maia Parsadanian
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Solji Park
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Seol Kyoung Jung
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andres Canela
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic. .,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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31
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Monteiro FA, Miranda RM, Samina MC, Dias AF, Raposo AASF, Oliveira P, Reguenga C, Castro DS, Lima D. Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord. Front Cell Dev Biol 2021; 9:642697. [PMID: 33996801 PMCID: PMC8117147 DOI: 10.3389/fcell.2021.642697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/30/2021] [Indexed: 11/28/2022] Open
Abstract
The spinal cord dorsal horn is a major station for integration and relay of somatosensory information and comprises both excitatory and inhibitory neuronal populations. The homeobox gene Tlx3 acts as a selector gene to control the development of late-born excitatory (dILB) neurons by specifying glutamatergic transmitter fate in dorsal spinal cord. However, since Tlx3 direct transcriptional targets remain largely unknown, it remains to be uncovered how Tlx3 functions to promote excitatory cell fate. Here we combined a genomics approach based on chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and expression profiling, with validation experiments in Tlx3 null embryos, to characterize the transcriptional program of Tlx3 in mouse embryonic dorsal spinal cord. We found most dILB neuron specific genes previously identified to be directly activated by Tlx3. Surprisingly, we found Tlx3 also directly represses many genes associated with the alternative inhibitory dILA neuronal fate. In both cases, direct targets include transcription factors and terminal differentiation genes, showing that Tlx3 directly controls cell identity at distinct levels. Our findings provide a molecular frame for the master regulatory role of Tlx3 in developing glutamatergic dILB neurons. In addition, they suggest a novel function for Tlx3 as direct repressor of GABAergic dILA identity, pointing to how generation of the two alternative cell fates being tightly coupled.
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Affiliation(s)
- Filipe A Monteiro
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rafael M Miranda
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Marta C Samina
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana F Dias
- Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Alexandre A S F Raposo
- Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Diagnostics, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Carlos Reguenga
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Diogo S Castro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Stem Cells & Neurogenesis Group, Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Deolinda Lima
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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32
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A neural m 6A/Ythdf pathway is required for learning and memory in Drosophila. Nat Commun 2021; 12:1458. [PMID: 33674589 PMCID: PMC7935873 DOI: 10.1038/s41467-021-21537-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Epitranscriptomic modifications can impact behavior. Here, we used Drosophila melanogaster to study N6-methyladenosine (m6A), the most abundant modification of mRNA. Proteomic and functional analyses confirm its nuclear (Ythdc1) and cytoplasmic (Ythdf) YTH domain proteins as major m6A binders. Assays of short term memory in m6A mutants reveal neural-autonomous requirements of m6A writers working via Ythdf, but not Ythdc1. Furthermore, m6A/Ythdf operate specifically via the mushroom body, the center for associative learning. We map m6A from wild-type and Mettl3 mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites that are highly enriched in 5' UTRs. Genomic analyses indicate that Drosophila m6A is preferentially deposited on genes with low translational efficiency and that m6A does not affect RNA stability. Nevertheless, functional tests indicate a role for m6A/Ythdf in translational activation. Altogether, our molecular genetic analyses and tissue-specific m6A maps reveal selective behavioral and regulatory defects for the Drosophila Mettl3/Ythdf pathway.
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33
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Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat Genet 2021; 53:354-366. [PMID: 33603233 PMCID: PMC8812996 DOI: 10.1038/s41588-021-00782-6] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin immunoprecipitation (ChIP)-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions. Strikingly, Nanog preferentially binds with helical periodicity, and TFs often cooperate in a directional manner, which we validate using clustered regularly interspaced short palindromic repeat (CRISPR)-induced point mutations. Our model represents a powerful general approach to uncover the motifs and syntax of cis-regulatory sequences in genomics data.
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Affiliation(s)
- Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany,Currently at DeepMind, London, UK
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Amr Alexandari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Khyati Dalal
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA
| | - Robin Fropf
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Charles McAnany
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA,Department of Genetics, Stanford University, Stanford, CA, USA,correspondence: ,
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA,correspondence: ,
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34
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Ji Z, Li Y, Liu SX, Sharrocks AD. The forkhead transcription factor FOXK2 premarks lineage-specific genes in human embryonic stem cells for activation during differentiation. Nucleic Acids Res 2021; 49:1345-1363. [PMID: 33434264 PMCID: PMC7897486 DOI: 10.1093/nar/gkaa1281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers play important roles in controlling gene expression in a choreographed spatial and temporal manner during development. However, it is unclear how these regulatory regions are established during differentiation. Here we investigated the genome-wide binding profile of the forkhead transcription factor FOXK2 in human embryonic stem cells (ESCs) and downstream cell types. This transcription factor is bound to thousands of regulatory regions in human ESCs, and binding at many sites is maintained as cells differentiate to mesendodermal and neural precursor cell (NPC) types, alongside the emergence of new binding regions. FOXK2 binding is generally associated with active histone marks in any given cell type. Furthermore newly acquired, or retained FOXK2 binding regions show elevated levels of activating histone marks following differentiation to NPCs. In keeping with this association with activating marks, we demonstrate a role for FOXK transcription factors in gene activation during NPC differentiation. FOXK2 occupancy in ESCs is therefore an early mark for delineating the regulatory regions, which become activated in later lineages.
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Affiliation(s)
- Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Sean X Liu
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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35
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Zhu Y, Zeng Q, Li F, Fang H, Zhou Z, Jiang T, Yin C, Wei Q, Wang Y, Ruan J, Huang J. Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens. Front Genet 2021; 11:574167. [PMID: 33505421 PMCID: PMC7831272 DOI: 10.3389/fgene.2020.574167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/23/2020] [Indexed: 12/29/2022] Open
Abstract
Epigenetic regulation of gene expression has been reported in the pathogenesis of metabolic disorders such as diabetes and liver steatosis in humans. However, the molecular mechanisms of fatty liver hemorrhagic syndrome (FLHS) in chickens have been rarely studied. H3K27ac chromatin immunoprecipitation coupled with high-throughput sequencing and high-throughput RNA sequencing was performed to compare genome-wide H3K27ac profiles and transcriptomes of liver tissue between healthy and FLHS chickens. In total, 1,321 differential H3K27ac regions and 443 differentially expressed genes were identified (| log2Fold change| ≥ 1 and P-value ≤ 0.05) between the two groups. Binding motifs for transcription factors involved in immune processes and metabolic homeostasis were enriched among those differential H3K27ac regions. Differential H3K27ac peaks were associated with multiple known FLHS risk genes, involved in lipid and energy metabolism (PCK1, APOA1, ANGPTL4, and FABP1) and the immune system (FGF7, PDGFRA, and KIT). Previous studies and our current results suggested that the high-energy, low-protein (HELP) diet might have an impact on histone modification and chromatin structure, leading to the dysregulation of candidate genes and the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which causes excessive accumulation of fat in the liver tissue and induces the development of FLHS. These findings highlight that epigenetic modifications contribute to the regulation of gene expression and play a central regulatory role in FLHS. The PPAR signaling pathway and other genes implicated in FLHS are of great importance for the development of novel and specific therapies for FLHS-susceptible commercial laying hens.
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Affiliation(s)
- Yaling Zhu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.,Department of Pathophysiology, Anhui Medical University, Hefei, China.,Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Fang Li
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, China.,Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Zhimin Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Chao Yin
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qing Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yujie Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jiming Ruan
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jianzhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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36
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Panahi R, Ebrahimie E, Niazi A, Afsharifar A. Integration of meta-analysis and supervised machine learning for pattern recognition in breast cancer using epigenetic data. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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37
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Fukusumi T, Guo TW, Ren S, Haft S, Liu C, Sakai A, Ando M, Saito Y, Sadat S, Califano JA. Reciprocal activation of HEY1 and NOTCH4 under SOX2 control promotes EMT in head and neck squamous cell carcinoma. Int J Oncol 2020; 58:226-237. [PMID: 33491747 PMCID: PMC7864008 DOI: 10.3892/ijo.2020.5156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Several comprehensive studies have demonstrated that the NOTCH pathway is altered in a bimodal manner in head and neck squamous cell carcinoma (HNSCC). In a previous study, it was found that the NOTCH4/HEY1 pathway was specifically upregulated in HNSCC and promoted epithelial-mesenchymal transition (EMT), and that HEY1 activation supported SOX2 expression. However, the interactions in this pathway have not yet been fully elucidated. The present study investigated the NOTCH4/HEY1/SOX2 axis in HNSCC using in vitro models and the Cancer Genome Atlas (TCGA) database. To explore the association, reporter and ChIP RT-qPCR assays using SOX2-overexpressing (SOX2-OE) cells were performed. The association between NOTCH4 and HEY1 was examined in the same manner using HEY1-overexpressing (HEY1-OE) cells. The results of the in vitro experiments indicated that HEY1 promoted EMT in the HNSCC cells. Furthermore, the overexpression of HEY1 also promoted sphere formation and increased murine xenograft tumorigenicity. Reporter assays and ChIP RT-qPCR experiments indicated that SOX2 regulated HEY1 expression via direct binding of the HEY1 promoter. HEY1 expression significantly correlated with SOX2 expression in primary lung SCC and other SCCs using the TCGA database. HEY1 also regulated NOTCH4 expression to create a positive reciprocal feedback loop. On the whole, the present study demonstrates that HEY1 expression in HNSCC is regulated via the promotion of SOX2 and promotes EMT. The NOTCH4/HEY1 pathway is specifically upregulated via a positive reciprocal feedback loop mediated by the HEY1-medaited regulation of NOTCH4 transcription, and SOX2 correlates with HEY1 expression in SCC from other primary sites.
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Affiliation(s)
- Takahito Fukusumi
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Theresa W Guo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shuling Ren
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sunny Haft
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chao Liu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Akihiro Sakai
- Department of Otolaryngology‑Head and Neck Surgery, Tokai University, School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Mizuo Ando
- Department of Otolaryngology‑Head and Neck Surgery, University of Tokyo, Tokyo 113‑8655, Japan
| | - Yuki Saito
- Department of Otolaryngology‑Head and Neck Surgery, University of Tokyo, Tokyo 113‑8655, Japan
| | - Sayed Sadat
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Califano
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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38
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Czipa E, Schiller M, Nagy T, Kontra L, Steiner L, Koller J, Pálné-Szén O, Barta E. ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5700342. [PMID: 31942977 PMCID: PMC6964213 DOI: 10.1093/database/baz141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 01/15/2023]
Abstract
ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein–protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.
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Affiliation(s)
- Erik Czipa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Mátyás Schiller
- Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Levente Kontra
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
| | - László Steiner
- UD-GenoMed Medical Genomic Technologies Research & Development Services Ltd., Nagyerdei krt. 98, Debrecen H-4032, Hungary
| | - Júlia Koller
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Semmelweis University, Institute of Genomic Medicines and Rare Disorders, Üllői út 78/B, Budapest, H-1082, Hungary
| | - Orsolya Pálné-Szén
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary
| | - Endre Barta
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen H-4032, Hungary.,Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Györgyi Albert út 4, Gödöllő H-2100, Hungary
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39
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Tan Z, Wen X, Wang Y. Betula platyphylla BpHOX2 transcription factor binds to different cis-acting elements and confers osmotic tolerance. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1762-1779. [PMID: 32681705 DOI: 10.1111/jipb.12994] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/16/2020] [Indexed: 05/22/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) proteins play crucial roles in plant developmental and environmental responses. However, how they mediate gene expression to facilitate abiotic stress tolerance remains unknown. In the present study, we characterized BpHOX2 (encoding a HD-Zip I family protein) from birch (Betula platyphylla). BpHOX2 is predominately expressed in mature stems and leaves, but expressed at a low level in apical buds and roots, suggesting that it has tissue-specific characteristics. BpHOX2 expression was highly induced by osmotic and salt, but only slightly induced by abscisic acid. Overexpression of BpHOX2 markedly improved osmotic tolerance, while knockdown of BpHOX2 increased sensitivity to osmotic stress. BpHOX2 could induce the expression of pyrroline-5-carboxylate synthase, peroxidase, and superoxide dismutase genes to improve proline levels and the reactive oxygen species scavenging capability. Chromatin immunoprecipitation sequencing combined with RNA sequencing showed that BpHOX2 could bind to at least four cis-acting elements, including dehydration-responsive element "RCCGAC", Myb-p binding box "CCWACC," and two novel cis-acting elements with the sequences of "AAGAAG" and "TACGTG" (termed HBS1 and HBS2, respectively) to regulate gene expression. Our results suggested that BpHOX2 is a transcription factor that binds to different cis-acting elements to regulate gene expression, ultimately improving osmotic tolerance in birch.
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Affiliation(s)
- Zilong Tan
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Graduate School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuejing Wen
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Yucheng Wang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
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40
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Yu C, Qi X, Lin Y, Li Y, Shen B. iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J Biomed Inform 2020; 112:103605. [PMID: 33096244 DOI: 10.1016/j.jbi.2020.103605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 02/05/2023]
Abstract
The latest advances in the next generation sequencing technology have greatly facilitated the extensive research of genomics and transcriptomics, thereby promoting the decoding of carcinogenesis with unprecedented resolution. Considering the contribution of analyzing high-throughput multi-omics data to the exploration of cancer molecular mechanisms, an integrated tool for heterogeneous multi-omics data analysis (iODA) is proposed for the systems-level interpretation of multi-omics data, i.e., transcriptomic profiles (mRNA or miRNA expression data) and protein-DNA interactions (ChIP-Seq data). Considering the data heterogeneity, iODA can compare six statistical algorithms in differential analysis for the selected sample data and assist users in choosing the globally optimal one for dysfunctional mRNA or miRNA identification. Since molecular signatures are more consistent at the pathway level than at the gene level, the tool is able to enrich the identified dysfunctional molecules onto the KEGG pathways and extracted the consistent items as key components for further pathogenesis investigation. Compared with other tools, iODA is multi-functional for the systematic analysis of different level of omics data, and its analytical power was demonstrated through case studies of single and cross-level prostate cancer omics data. iODA is open source under GNU GPL and can be downloaded from http://www.sysbio.org.cn/iODA.
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Affiliation(s)
- Chunjiang Yu
- School of Biotechnology, Suzhou Industrial Park Institute of Service Outsourcing, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Xin Qi
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Yin Li
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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41
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Hill L, Ebert A, Jaritz M, Wutz G, Nagasaka K, Tagoh H, Kostanova-Poliakova D, Schindler K, Sun Q, Bönelt P, Fischer M, Peters JM, Busslinger M. Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion. Nature 2020; 584:142-147. [PMID: 32612238 PMCID: PMC7116900 DOI: 10.1038/s41586-020-2454-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
Nuclear processes, such as V(D)J recombination, are orchestrated by the three-dimensional organization of chromosomes at multiple levels, including compartments1 and topologically associated domains (TADs)2,3 consisting of chromatin loops4. TADs are formed by chromatin-loop extrusion5-7, which depends on the loop-extrusion function of the ring-shaped cohesin complex8-12. Conversely, the cohesin-release factor Wapl13,14 restricts loop extension10,15. The generation of a diverse antibody repertoire, providing humoral immunity to pathogens, requires the participation of all V genes in V(D)J recombination16, which depends on contraction of the 2.8-Mb-long immunoglobulin heavy chain (Igh) locus by Pax517,18. However, how Pax5 controls Igh contraction in pro-B cells remains unknown. Here we demonstrate that locus contraction is caused by loop extrusion across the entire Igh locus. Notably, the expression of Wapl is repressed by Pax5 specifically in pro-B and pre-B cells, facilitating extended loop extrusion by increasing the residence time of cohesin on chromatin. Pax5 mediates the transcriptional repression of Wapl through a single Pax5-binding site by recruiting the polycomb repressive complex 2 to induce bivalent chromatin at the Wapl promoter. Reduced Wapl expression causes global alterations in the chromosome architecture, indicating that the potential to recombine all V genes entails structural changes of the entire genome in pro-B cells.
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Affiliation(s)
- Louisa Hill
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Anja Ebert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | | | - Karina Schindler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Qiong Sun
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Peter Bönelt
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Maria Fischer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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42
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Falcão AM, Meijer M, Scaglione A, Rinwa P, Agirre E, Liang J, Larsen SC, Heskol A, Frawley R, Klingener M, Varas-Godoy M, Raposo AASF, Ernfors P, Castro DS, Nielsen ML, Casaccia P, Castelo-Branco G. PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination. Cell Rep 2020; 27:1090-1102.e10. [PMID: 31018126 PMCID: PMC6486480 DOI: 10.1016/j.celrep.2019.03.108] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/13/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022] Open
Abstract
Citrullination, the deimination of peptidylarginine residues into peptidylcitrulline, has been implicated in the etiology of several diseases. In multiple sclerosis, citrullination is thought to be a major driver of pathology through hypercitrullination and destabilization of myelin. As such, inhibition of citrullination has been suggested as a therapeutic strategy for MS. Here, in contrast, we show that citrullination by peptidylarginine deiminase 2 (PAD2) contributes to normal oligodendrocyte differentiation, myelination, and motor function. We identify several targets for PAD2, including myelin and chromatin-related proteins, implicating PAD2 in epigenomic regulation. Accordingly, we observe that PAD2 inhibition and its knockdown affect chromatin accessibility and prevent the upregulation of oligodendrocyte differentiation genes. Moreover, mice lacking PAD2 display motor dysfunction and a decreased number of myelinated axons in the corpus callosum. We conclude that citrullination contributes to proper oligodendrocyte lineage progression and myelination. PAD2 is increased upon OL differentiation OL differentiation is facilitated by PAD2-mediated chromatin remodeling in myelin genes PAD2 contributes to efficient myelination and motor and cognitive functions Nuclear and myelin proteins interact and are citrullinated by PAD2
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Affiliation(s)
- Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Antonella Scaglione
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Puneet Rinwa
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jialiang Liang
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Sara C Larsen
- Department of Proteomics, the Novo Nordisk Foundation Center for Protein Research, Faculty of Heath Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Abeer Heskol
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Rebecca Frawley
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Michael Klingener
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Manuel Varas-Godoy
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Cancer Cell Biology Lab, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile
| | | | - Patrik Ernfors
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Michael L Nielsen
- Department of Proteomics, the Novo Nordisk Foundation Center for Protein Research, Faculty of Heath Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Patrizia Casaccia
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 171 77 Stockholm, Sweden.
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43
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Divoux A, Sandor K, Bojcsuk D, Yi F, Hopf ME, Smith JS, Balint BL, Osborne TF, Smith SR. Fat Distribution in Women Is Associated With Depot-Specific Transcriptomic Signatures and Chromatin Structure. J Endocr Soc 2020; 4:bvaa042. [PMID: 32500109 PMCID: PMC7261146 DOI: 10.1210/jendso/bvaa042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Preferential accumulation of fat in the upper body (apple shape) is associated with higher risk of developing metabolic syndrome relative to lower body fat (pear shape). We previously discovered that chromatin openness partially defined the transcriptome of preadipocytes isolated from abdominal and gluteofemoral fat. However, the molecular mechanisms underlying interindividual variation in body shape are unknown. METHODS Adipocyte fraction was isolated from abdominal and gluteofemoral fat biopsies of premenopausal women (age and body mass index matched) segregated initially only by their waist-to-hip ratio. We evaluated transcriptomic and chromatin accessibility using RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq) along with key clinical parameters. RESULTS Our data showed that higher lower body fat mass was associated with better lipid profile and free fatty acid decrease after glucose administration. Lipid and glucose metabolic pathways genes were expressed at higher levels in gluteofemoral adipocyte fraction in pears, whereas genes associated with inflammation were higher both in abdominal and gluteofemoral apple adipocyte fraction. Gluteofemoral adipocyte chromatin from pear-shaped women contained a significantly higher number of differentially open ATAC-seq peaks relative to chromatin from the apple-shaped gluteofemoral adipocytes. In contrast, abdominal adipocyte chromatin openness showed few differences between apple- and pear-shaped women. We revealed a correlation between gene transcription and open chromatin at the proximity of the transcriptional start site of some of the differentially expressed genes. CONCLUSIONS Integration of data from all 3 approaches suggests that chromatin openness partially governs the transcriptome of gluteofemoral adipocytes and may be involved in the early metabolic syndrome predisposition associated with body shape.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Katalin Sandor
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Dora Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Fanchao Yi
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Meghan E Hopf
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Joshua S Smith
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
| | - Balint L Balint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Timothy F Osborne
- Department of Medicine, Johns Hopkins University School of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, USA
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44
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Yang L, Chen Z, Stout ES, Delerue F, Ittner LM, Wilkins MR, Quinlan KGR, Crossley M. Methylation of a CGATA element inhibits binding and regulation by GATA-1. Nat Commun 2020; 11:2560. [PMID: 32444652 PMCID: PMC7244756 DOI: 10.1038/s41467-020-16388-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alterations in DNA methylation occur during development, but the mechanisms by which they influence gene expression remain uncertain. There are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding and regulation of a target gene in vivo. Here, we show that the erythroid transcription factor GATA-1 — that typically binds T/AGATA sites — can also recognise CGATA elements, but only if the CpG dinucleotide is unmethylated. We focus on a single CGATA site in the c-Kit gene which progressively becomes unmethylated during haematopoiesis. We observe that methylation attenuates GATA-1 binding and gene regulation in cell lines. In mice, converting the CGATA element to a TGATA site that cannot be methylated leads to accumulation of megakaryocyte-erythroid progenitors. Thus, the CpG dinucleotide is essential for normal erythropoiesis and this study illustrates how a single methylated CpG can directly affect transcription factor binding and cellular regulation. While DNA methylation is thought to play a regulatory role, there are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding. Here the authors show that methylation of a single CGATA element within the c-Kit gene inhibits binding and regulation by erythroid transcription factor GATA-1, both in cells and in mice, suggesting that methylation at this site plays an essential role in erythropoiesis.
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Affiliation(s)
- Lu Yang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Elizabeth S Stout
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Fabien Delerue
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Mark Wainwright Analytical Centre, Transgenic Animal Unit, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Lars M Ittner
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Mark Wainwright Analytical Centre, Transgenic Animal Unit, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
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45
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Song J, Henry H, Tian L. Drought-inducible changes in the histone modification H3K9ac are associated with drought-responsive gene expression in Brachypodium distachyon. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:433-440. [PMID: 31628708 DOI: 10.1111/plb.13057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
H3K9ac, an epigenetic marker, is widely distributed in plant genomes. H3K9ac enhances gene expression, which is highly conserved in eukaryotes. However, genome-wide studies of H3K9ac in monocot species are limited, and the changes in H3K9ac under drought stress for individual genes are still not clear. We analysed changes in the H3K9ac level of Brachypodium distachyon under 20% PEG-6000-simulated drought stress conditions. We also performed chromatin immunoprecipitation, followed by next generation sequencing (ChIP-seq) on H3K9ac to reveal changes in H3K9ac for individual genes at the genome-wide level. Our study showed that H3K9ac was mainly enriched in gene exon regions. Drought increased or decreased the H3K9ac level at specific genomic loci. We identified 40 genes associated with increased H3K9ac levels and 36 genes associated with decreased H3K9ac levels under drought stress. Further, RT-qPCR analyses showed that H3K9ac was positively associated with gene expression of those drought-responsive genes. We conclude that H3K9ac enhances the expression level of a large number of drought-responsive genes under drought stress in B. distachyon. The data presented here will help to reveal the correlation of some specific drought-responsive genes and their enriched H3K9ac levels in the model plant B. distachyon.
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Affiliation(s)
- J Song
- Department of Biology, Western University, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - H Henry
- Department of Biology, Western University, London, ON, Canada
| | - L Tian
- Department of Biology, Western University, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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46
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Bojcsuk D, Nagy G, Bálint BL. Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines. Int J Mol Sci 2020; 21:E1630. [PMID: 32120995 PMCID: PMC7084573 DOI: 10.3390/ijms21051630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 01/07/2023] Open
Abstract
Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators, which together establish a chromatin environment conducting to effective transcription. While cells with distinct TF profiles can have different functions, how different cells control overlapping genetic programs remains a question. In this paper, we show that the construction of estrogen receptor alpha-driven SEs is tissue-specific, both collaborating TFs and the active SE components greatly differ between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell lines have similar transcriptional outputs. These results delineate that despite the existence of a combinatorial code allowing alternative SE construction, a single master regulator might be able to determine the overall activity of SEs.
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Affiliation(s)
- Dóra Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Bálint László Bálint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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47
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Paiano J, Wu W, Yamada S, Sciascia N, Callen E, Paola Cotrim A, Deshpande RA, Maman Y, Day A, Paull TT, Nussenzweig A. ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis. Nat Commun 2020; 11:857. [PMID: 32051414 PMCID: PMC7016097 DOI: 10.1038/s41467-020-14654-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 12/22/2022] Open
Abstract
Meiotic recombination is initiated by SPO11-induced double-strand breaks (DSBs). In most mammals, the methyltransferase PRDM9 guides SPO11 targeting, and the ATM kinase controls meiotic DSB numbers. Following MRE11 nuclease removal of SPO11, the DSB is resected and loaded with DMC1 filaments for homolog invasion. Here, we demonstrate the direct detection of meiotic DSBs and resection using END-seq on mouse spermatocytes with low sample input. We find that DMC1 limits both minimum and maximum resection lengths, whereas 53BP1, BRCA1 and EXO1 play surprisingly minimal roles. Through enzymatic modifications to END-seq, we identify a SPO11-bound meiotic recombination intermediate (SPO11-RI) present at all hotspots. We propose that SPO11-RI forms because chromatin-bound PRDM9 asymmetrically blocks MRE11 from releasing SPO11. In Atm-/- spermatocytes, trapped SPO11 cleavage complexes accumulate due to defective MRE11 initiation of resection. Thus, in addition to governing SPO11 breakage, ATM and PRDM9 are critical local regulators of mammalian SPO11 processing.
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Affiliation(s)
- Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Nicholas Sciascia
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ana Paola Cotrim
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rajashree A Deshpande
- The Howard Hughes Medical Institute and The University of Texas at Austin, Austin, TX, 78712, USA
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tanya T Paull
- The Howard Hughes Medical Institute and The University of Texas at Austin, Austin, TX, 78712, USA
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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48
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Mishra GP, Ghosh A, Jha A, Raghav SK. BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets. Front Genet 2020; 11:3. [PMID: 32117432 PMCID: PMC7013082 DOI: 10.3389/fgene.2020.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022] Open
Abstract
A large number of genomic regions, such as transcription factor binding sites (TFBSs) captured from next generation sequencing (NGS) data analyses or those available from the public resource database ENCODE, are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such an analysis, there is a notable lack of an integrated webserver application with which to identify genomic region intersections, generate publication-ready plots depicting subsets of the overlapped regions, and perform functional annotation. Thus, there is an ardent need for a comprehensive and user-friendly webserver application that allows the users to either upload multiple datasets or select from the integrated Gene Transcription Regulation Database (GTRD). We thus introduce BedSect (http://imgsb.org/bedsect/.), which not only fulfils the above criteria but also performs intersection analysis along with visualization of the intersection regions as an UpSet and correlation plot using the integrated Shiny application. Moreover, analyses, including functional annotation, gene ontology, and biological pathways enrichment for the identified unique and intersected genomic regions, can also be performed using the integrated GREAT tool. To view the genomic regions in the genome browser, the inbuilt hyperlink for UCSC can redirect the user to visualize the results as custom tracks.
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Affiliation(s)
- Gyan Prakash Mishra
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Arup Ghosh
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Atimukta Jha
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sunil Kumar Raghav
- Immunogenomics and Systems Biology Laboratory, Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
- Manipal Academy of Higher Education, Manipal, India
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49
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Fu J, Liu L, Liu Q, Shen Q, Wang C, Yang P, Zhu C, Wang Q. ZmMYC2 exhibits diverse functions and enhances JA signaling in transgenic Arabidopsis. PLANT CELL REPORTS 2020; 39:273-288. [PMID: 31741037 DOI: 10.1007/s00299-019-02490-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/23/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
ZmMYC2 was identified as the key regulator of JA signaling in maize and exhibited diverse functions through binding to many gene promoters as well as enhanced JA signaling in transgenic Arabidopsis. The plant hormone jasmonate (JA) extensively coordinates plant growth, development and defensive responses. MYC2 is the master regulator of JA signaling and has been widely studied in many plant species. However, little is known about this transcription factor in maize. Here, we identified one maize transcription factor with amino acid identity of 47% to the well-studied Arabidopsis AtMYC2, named as ZmMYC2. Gene expression analysis demonstrated inducible expression patterns of ZmMYC2 in response to multiple plant hormone treatments, as well as biotic and abiotic stresses. The yeast two-hybrid assay indicated physical interaction among ZmMYC2 and JA signal repressors ZmJAZ14, ZmJAZ17, AtJAZ1 and AtJAZ9. ZmMYC2 overexpression in Arabidopsis myc2myc3myc4 restored the sensitivity to JA treatment, resulting in shorter root growth and inducible anthocyanin accumulation. Furthermore, overexpression of ZmMYC2 in Arabidopsis elevated resistance to Botrytis cinerea. Further ChIP-Seq analysis revealed diverse regulatory roles of ZmMYC2 in maize, especially in the signaling crosstalk between JA and auxin. Hence, we identified ZmMYC2 and characterized its roles in regulating JA-mediated growth, development and defense responses.
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Affiliation(s)
- Jingye Fu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lijun Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qin Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qinqin Shen
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Panpan Yang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chenying Zhu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China.
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50
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Chen C, Shu J, Li C, Thapa RK, Nguyen V, Yu K, Yuan ZC, Kohalmi SE, Liu J, Marsolais F, Huang S, Cui Y. RNA polymerase II-independent recruitment of SPT6L at transcription start sites in Arabidopsis. Nucleic Acids Res 2020; 47:6714-6725. [PMID: 31127286 PMCID: PMC6648355 DOI: 10.1093/nar/gkz465] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 01/20/2023] Open
Abstract
SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.
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Affiliation(s)
- Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Jie Shu
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Chenlong Li
- School of Life Sciences, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Raj K Thapa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada
| | - Kangfu Yu
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, Ontario N0R 1G0, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Jun Liu
- Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Shangzhi Huang
- School of Life Sciences, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
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