WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previo...WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.展开更多
【目的】探究山茶Related to ABI3 and VP1(CjRAV1)基因在开花调控中的功能及其分子机制,为四季山茶的分子育种提供理论依据。【方法】采用生物信息学分析、基因表达模式分析、转基因技术和DAP-seq等多种实验手段,系统研究CjRAV1的功能...【目的】探究山茶Related to ABI3 and VP1(CjRAV1)基因在开花调控中的功能及其分子机制,为四季山茶的分子育种提供理论依据。【方法】采用生物信息学分析、基因表达模式分析、转基因技术和DAP-seq等多种实验手段,系统研究CjRAV1的功能及其调控机制。生物信息学分析鉴定CjRAV1的基因结构、保守结构域及其系统进化关系。利用RT-qPCR技术分析CjRAV1在外源激素诱导下、不同组织以及花苞不同发育时期的表达模式。构建CjRAV1过表达转基因拟南芥植株,观察其表型变化,尤其是开花时间的改变。最后,采用DAP-seq技术筛选CjRAV1下游潜在的DNA结合位点及其调控基因,揭示CjRAV1的分子调控网络。【结果】生物信息学分析表明,CjRAV1的开放阅读框长度为1101 bp,共编码366个氨基酸,具有AP2和B3保守结构域。系统进化分析显示,山茶CjRAV1蛋白与茶树CsRAV蛋白的亲缘关系最近,表明两者可能具有相似的功能。亚细胞定位分析证实,CjRAV1转录因子定位于细胞核,提示其可能在转录调控中发挥直接作用。表达模式分析显示,CjRAV1在山茶叶中表达量最高;在花苞成熟过程中,CjRAV1的表达量总体呈现逐步下降的趋势。CjRAV1的过表达转基因拟南芥表现出晚花的表型。通过DAP-seq筛选出潜在的下游调控基因CjERF。【结论】CjRAV1过表达导致转基因拟南芥植株表现出晚花的表型,且这一功能可能与潜在的调控基因CjERF协作完成。展开更多
Waterlogging stress is one of the greatest environmental threats to kiwifruit growth and development.ERF-VII proteins have been demonstrated to play pivotal roles in regulating plant tolerance to waterlogging.Neverthe...Waterlogging stress is one of the greatest environmental threats to kiwifruit growth and development.ERF-VII proteins have been demonstrated to play pivotal roles in regulating plant tolerance to waterlogging.Nevertheless,the genome-wide role of ERF-VII in kiwifruit waterlogging stress tolerance remains unclear.Here,we report the function and regulatory network of an ERF-VII transcription factor located to the nucleus,Av ERF73,in kiwifruit waterlogging tolerance.Overexpression of Av ERF73 in Arabidopsis thaliana and A.chinensis cv.Hongyang enhanced waterlogging tolerance in transgenic plants.Furthermore,we performed transcriptome analysis(RNA-seq)and DNA affinity purification sequencing(DAP-seq)to explore the regulatory mechanism of Av ERF73.RNA-seq coupled with DAP-seq showed that Av ERF73 might directly activate Ac NAC022 involved in the“cellular response to hypoxia”process and Ac HMGS1 involved in the mevalonate pathway to respond to waterlogging,which were also confirmed by a dual-luciferase reporter assay.Based on our results,we propose a putative working model for controlling waterlogging tolerance by Av ERF73 in kiwifruit.展开更多
Loss of the awn in some cereals including sorghum is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage.The genetic basis for the loss of awn in sorghum during d...Loss of the awn in some cereals including sorghum is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage.The genetic basis for the loss of awn in sorghum during domestication or improvement remains unknown.Here,we identified a transcription factor gene awn1 encoding an ALOG domain,which is responsible for awn loss during sorghum domestication or improvement.awn1 arose from a gene duplication from chromosome 10 that translocated to chromosome 3,recruiting a new promoter from the neighbouring intergenic region filled with"noncoding DNA",and recreating the first exon and intron.The awn1 acquires high expr`ession after duplication and represses the elongation of awns in domesticated sorghum.Comparative mapping revealed a high collinearity at awn1 paralog locus on chromosome 10 across cereals and awn growth and development was successfully reactivated on the rice spikelet by inactivating rice awn1 orthologue.Further RNA-seq and DAP-seq revealed that as a transcription repressor,AWN1 directly bound to the motif in the regulatory regions from three MADS genes related to flower development and two genes DL and LKS2 for the development of awn,downregulated the expressions of these genes,and then repressed the elongation of awn.The preexistence of regulatory elements in the neighbouring intergenic region of awn1 before domestication signified that noncoding DNA may serve as a treasure trove for evolution during adaptation to a changing world.Our results supported that gene duplication can promptly drive the evolution of gene regulatory network.展开更多
Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin resp...Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/ Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions o1IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.展开更多
基金funded by the Start-up Foundation for High Talents of Qingdao Agricultural University(No.665/1120012)the Natural Science Foundation of Shandong Province,China(ZR2019QC017)+4 种基金the National Key Research and Development Program,China(2022YFD2300101-1)the Key Research and Development Program of Shandong Province,China(2021LZGC003 and 2021LZGC026-03)Peanut Seed Industry Project in Shandong Province,China(2022LZGC007)the Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta,China(2022SZX18)the Graduate Student Innovation Program of Qingdao Agricultural University(QNYCX23001).
文摘WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.
文摘【目的】探究山茶Related to ABI3 and VP1(CjRAV1)基因在开花调控中的功能及其分子机制,为四季山茶的分子育种提供理论依据。【方法】采用生物信息学分析、基因表达模式分析、转基因技术和DAP-seq等多种实验手段,系统研究CjRAV1的功能及其调控机制。生物信息学分析鉴定CjRAV1的基因结构、保守结构域及其系统进化关系。利用RT-qPCR技术分析CjRAV1在外源激素诱导下、不同组织以及花苞不同发育时期的表达模式。构建CjRAV1过表达转基因拟南芥植株,观察其表型变化,尤其是开花时间的改变。最后,采用DAP-seq技术筛选CjRAV1下游潜在的DNA结合位点及其调控基因,揭示CjRAV1的分子调控网络。【结果】生物信息学分析表明,CjRAV1的开放阅读框长度为1101 bp,共编码366个氨基酸,具有AP2和B3保守结构域。系统进化分析显示,山茶CjRAV1蛋白与茶树CsRAV蛋白的亲缘关系最近,表明两者可能具有相似的功能。亚细胞定位分析证实,CjRAV1转录因子定位于细胞核,提示其可能在转录调控中发挥直接作用。表达模式分析显示,CjRAV1在山茶叶中表达量最高;在花苞成熟过程中,CjRAV1的表达量总体呈现逐步下降的趋势。CjRAV1的过表达转基因拟南芥表现出晚花的表型。通过DAP-seq筛选出潜在的下游调控基因CjERF。【结论】CjRAV1过表达导致转基因拟南芥植株表现出晚花的表型,且这一功能可能与潜在的调控基因CjERF协作完成。
基金funded by the National Key Research and Development Program(Grant No.2022YFD1600700)Major Science and Technology Projects of Henan Province(Grant No.221100110400)+3 种基金the China Agriculture Research System of MOF and MARA(Grant No.CARS-26)Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-2023-ZFRI-03)Yunnan Science and Technology Program(Grant No.202205AF150043)Sichuan Science and Technology Program(Grant No.2021YFN0060)。
文摘Waterlogging stress is one of the greatest environmental threats to kiwifruit growth and development.ERF-VII proteins have been demonstrated to play pivotal roles in regulating plant tolerance to waterlogging.Nevertheless,the genome-wide role of ERF-VII in kiwifruit waterlogging stress tolerance remains unclear.Here,we report the function and regulatory network of an ERF-VII transcription factor located to the nucleus,Av ERF73,in kiwifruit waterlogging tolerance.Overexpression of Av ERF73 in Arabidopsis thaliana and A.chinensis cv.Hongyang enhanced waterlogging tolerance in transgenic plants.Furthermore,we performed transcriptome analysis(RNA-seq)and DNA affinity purification sequencing(DAP-seq)to explore the regulatory mechanism of Av ERF73.RNA-seq coupled with DAP-seq showed that Av ERF73 might directly activate Ac NAC022 involved in the“cellular response to hypoxia”process and Ac HMGS1 involved in the mevalonate pathway to respond to waterlogging,which were also confirmed by a dual-luciferase reporter assay.Based on our results,we propose a putative working model for controlling waterlogging tolerance by Av ERF73 in kiwifruit.
基金This work was supported by the National Natural Science Foundation of China(92035302 and 31871632 to Z.L.)the National Key Research and Development Program of China(2016YFD0100303 and 2016YFD0101803 to Z.L.)the Chinese Universities Scientific Fund(2021TC065 to Z.L.).
文摘Loss of the awn in some cereals including sorghum is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage.The genetic basis for the loss of awn in sorghum during domestication or improvement remains unknown.Here,we identified a transcription factor gene awn1 encoding an ALOG domain,which is responsible for awn loss during sorghum domestication or improvement.awn1 arose from a gene duplication from chromosome 10 that translocated to chromosome 3,recruiting a new promoter from the neighbouring intergenic region filled with"noncoding DNA",and recreating the first exon and intron.The awn1 acquires high expr`ession after duplication and represses the elongation of awns in domesticated sorghum.Comparative mapping revealed a high collinearity at awn1 paralog locus on chromosome 10 across cereals and awn growth and development was successfully reactivated on the rice spikelet by inactivating rice awn1 orthologue.Further RNA-seq and DAP-seq revealed that as a transcription repressor,AWN1 directly bound to the motif in the regulatory regions from three MADS genes related to flower development and two genes DL and LKS2 for the development of awn,downregulated the expressions of these genes,and then repressed the elongation of awn.The preexistence of regulatory elements in the neighbouring intergenic region of awn1 before domestication signified that noncoding DNA may serve as a treasure trove for evolution during adaptation to a changing world.Our results supported that gene duplication can promptly drive the evolution of gene regulatory network.
文摘Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/ Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions o1IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.
