Huaizhi Tian , Yuanhang Mu , Shasha Yang , Jv Zhang , Xiaolian Yang , Qingqin Zhang , Guangdong Geng , Suqin Zhang
{"title":"ATAC 测序和转录组学揭示了盐胁迫条件下染色质可及性对三尖杉基因表达的影响","authors":"Huaizhi Tian , Yuanhang Mu , Shasha Yang , Jv Zhang , Xiaolian Yang , Qingqin Zhang , Guangdong Geng , Suqin Zhang","doi":"10.1016/j.envexpbot.2024.106014","DOIUrl":null,"url":null,"abstract":"<div><div>Plants have evolved various regulatory mechanisms that adjust gene expression levels to enhance their salt adaptability. Here, the seedling height, root length, plant fresh weight, total root surface area, and total root volume of <em>Tritipyrum</em> ‘Y1805’ increased significantly under salt-stress and recovery conditions. The plant water content showed limited changes under salt stress. The cytokinin, amino acid, soluble protein, and pyruvate contents, as well as the peroxidase activity, increased under salt stress and decreased quickly after recovery. The MDA content and electrical conductivity increased after 5 h of salt stress, but they returned rapidly to the control level afterwards. ‘Y1805’ had strong salt tolerance and could adapt quickly to salt-stress conditions. An assay of transposase-accessible chromatin with sequencing (ATAC-seq) indicated that most peaks were located in the distal intergenic regions under salt-stress and control conditions. We found 85 motifs in the 1776 location-specific peaks and 478 motifs in altered signal peaks under salt stress. The transcription factors binding to these motifs belonged mainly to the MYB family, followed by the AP2/EREBP, bZIP, bHLH, and WRKY families. The main Gene Ontology terms organic acid catabolic process, carboxylic acid catabolic process, cellular hormone metabolic process, cytokinin metabolic process, and cellular amino acid catabolic process were significantly enriched based on the associated differentially expressed genes between ATAC-seq and transcriptomics. Based on the transcriptional regulatory network and gene expression level, the <em>Tritipyrum</em> ‘Y1805’ <em>HSF6–1</em> gene was selected and cloned. Leaves of the wild-type plants appeared seriously wilted under salt stress, but most leaves of the <em>TtHSF6–1</em> transgenic line remained upright. The seedling height, root length, plant fresh weight, and plant dry weight of the <em>TtHSF6–1</em> transgenic line increased significantly compared with those of the WT plant under salt-stress and recovery conditions. The MDA content and electrical conductivity values of the <em>TtHSF6–1</em> transgenic line were significantly less than those of the WT plants under salt-stress conditions. Thus, <em>TtHSF6–1</em> contributed to salt tolerance. These results provided valuable genes for wheat improvement and offer fundamental insights into the transcriptional regulatory mechanisms of salt tolerance in <em>Tritipyrum</em>.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"228 ","pages":"Article 106014"},"PeriodicalIF":4.5000,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"ATAC sequencing and transcriptomics reveal the impact of chromatin accessibility on gene expression in Tritipyrum under salt-stress conditions\",\"authors\":\"Huaizhi Tian , Yuanhang Mu , Shasha Yang , Jv Zhang , Xiaolian Yang , Qingqin Zhang , Guangdong Geng , Suqin Zhang\",\"doi\":\"10.1016/j.envexpbot.2024.106014\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Plants have evolved various regulatory mechanisms that adjust gene expression levels to enhance their salt adaptability. Here, the seedling height, root length, plant fresh weight, total root surface area, and total root volume of <em>Tritipyrum</em> ‘Y1805’ increased significantly under salt-stress and recovery conditions. The plant water content showed limited changes under salt stress. The cytokinin, amino acid, soluble protein, and pyruvate contents, as well as the peroxidase activity, increased under salt stress and decreased quickly after recovery. The MDA content and electrical conductivity increased after 5 h of salt stress, but they returned rapidly to the control level afterwards. ‘Y1805’ had strong salt tolerance and could adapt quickly to salt-stress conditions. An assay of transposase-accessible chromatin with sequencing (ATAC-seq) indicated that most peaks were located in the distal intergenic regions under salt-stress and control conditions. We found 85 motifs in the 1776 location-specific peaks and 478 motifs in altered signal peaks under salt stress. The transcription factors binding to these motifs belonged mainly to the MYB family, followed by the AP2/EREBP, bZIP, bHLH, and WRKY families. The main Gene Ontology terms organic acid catabolic process, carboxylic acid catabolic process, cellular hormone metabolic process, cytokinin metabolic process, and cellular amino acid catabolic process were significantly enriched based on the associated differentially expressed genes between ATAC-seq and transcriptomics. Based on the transcriptional regulatory network and gene expression level, the <em>Tritipyrum</em> ‘Y1805’ <em>HSF6–1</em> gene was selected and cloned. Leaves of the wild-type plants appeared seriously wilted under salt stress, but most leaves of the <em>TtHSF6–1</em> transgenic line remained upright. The seedling height, root length, plant fresh weight, and plant dry weight of the <em>TtHSF6–1</em> transgenic line increased significantly compared with those of the WT plant under salt-stress and recovery conditions. The MDA content and electrical conductivity values of the <em>TtHSF6–1</em> transgenic line were significantly less than those of the WT plants under salt-stress conditions. Thus, <em>TtHSF6–1</em> contributed to salt tolerance. These results provided valuable genes for wheat improvement and offer fundamental insights into the transcriptional regulatory mechanisms of salt tolerance in <em>Tritipyrum</em>.</div></div>\",\"PeriodicalId\":11758,\"journal\":{\"name\":\"Environmental and Experimental Botany\",\"volume\":\"228 \",\"pages\":\"Article 106014\"},\"PeriodicalIF\":4.5000,\"publicationDate\":\"2024-10-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Environmental and Experimental Botany\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0098847224003721\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"ENVIRONMENTAL SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Environmental and Experimental Botany","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0098847224003721","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
ATAC sequencing and transcriptomics reveal the impact of chromatin accessibility on gene expression in Tritipyrum under salt-stress conditions
Plants have evolved various regulatory mechanisms that adjust gene expression levels to enhance their salt adaptability. Here, the seedling height, root length, plant fresh weight, total root surface area, and total root volume of Tritipyrum ‘Y1805’ increased significantly under salt-stress and recovery conditions. The plant water content showed limited changes under salt stress. The cytokinin, amino acid, soluble protein, and pyruvate contents, as well as the peroxidase activity, increased under salt stress and decreased quickly after recovery. The MDA content and electrical conductivity increased after 5 h of salt stress, but they returned rapidly to the control level afterwards. ‘Y1805’ had strong salt tolerance and could adapt quickly to salt-stress conditions. An assay of transposase-accessible chromatin with sequencing (ATAC-seq) indicated that most peaks were located in the distal intergenic regions under salt-stress and control conditions. We found 85 motifs in the 1776 location-specific peaks and 478 motifs in altered signal peaks under salt stress. The transcription factors binding to these motifs belonged mainly to the MYB family, followed by the AP2/EREBP, bZIP, bHLH, and WRKY families. The main Gene Ontology terms organic acid catabolic process, carboxylic acid catabolic process, cellular hormone metabolic process, cytokinin metabolic process, and cellular amino acid catabolic process were significantly enriched based on the associated differentially expressed genes between ATAC-seq and transcriptomics. Based on the transcriptional regulatory network and gene expression level, the Tritipyrum ‘Y1805’ HSF6–1 gene was selected and cloned. Leaves of the wild-type plants appeared seriously wilted under salt stress, but most leaves of the TtHSF6–1 transgenic line remained upright. The seedling height, root length, plant fresh weight, and plant dry weight of the TtHSF6–1 transgenic line increased significantly compared with those of the WT plant under salt-stress and recovery conditions. The MDA content and electrical conductivity values of the TtHSF6–1 transgenic line were significantly less than those of the WT plants under salt-stress conditions. Thus, TtHSF6–1 contributed to salt tolerance. These results provided valuable genes for wheat improvement and offer fundamental insights into the transcriptional regulatory mechanisms of salt tolerance in Tritipyrum.
期刊介绍:
Environmental and Experimental Botany (EEB) publishes research papers on the physical, chemical, biological, molecular mechanisms and processes involved in the responses of plants to their environment.
In addition to research papers, the journal includes review articles. Submission is in agreement with the Editors-in-Chief.
The Journal also publishes special issues which are built by invited guest editors and are related to the main themes of EEB.
The areas covered by the Journal include:
(1) Responses of plants to heavy metals and pollutants
(2) Plant/water interactions (salinity, drought, flooding)
(3) Responses of plants to radiations ranging from UV-B to infrared
(4) Plant/atmosphere relations (ozone, CO2 , temperature)
(5) Global change impacts on plant ecophysiology
(6) Biotic interactions involving environmental factors.