Solid-state zinc-ion capacitors are emerging as promising candidates for large-scale energy storage owing to improved safety,mechanical and thermal stability and easy-to-direct stacking.Hydrogel electrolytes are appea...Solid-state zinc-ion capacitors are emerging as promising candidates for large-scale energy storage owing to improved safety,mechanical and thermal stability and easy-to-direct stacking.Hydrogel electrolytes are appealing solid-state electrolytes because of eco-friendliness,high conductivity and intrinsic flexibility.However,the electrolyte/electrode interfacial contact and anti-freezing properties of current hydrogel electrolytes are still challenging for practical applications of zinc-ion capacitors.Here,we report a class of hydrogel electrolytes that couple high interfacial adhesion and anti-freezing performance.The synergy of tough hydrogel matrix and chemical anchorage enables a well-adhered interface between hydrogel electrolyte and electrode.Meanwhile,the cooperative solvation of ZnCl2 and LiCl hybrid salts renders the hydrogel electrolyte high ionic conductivity and mechanical elasticity simultaneously at low temperatures.More significantly,the Zn||carbon nanotubes hybrid capacitor based on this hydrogel electrolyte exhibits low-temperature capacitive performance,delivering high-energy density of 39 Wh kg^(-1)at-60°C with capacity retention of 98.7%over 10,000 cycles.With the benefits of the well-adhered electrolyte/electrode interface and the anti-freezing hydrogel electrolyte,the Zn/Li hybrid capacitor is able to accommodate dynamic deformations and function well under 1000 tension cycles even at-60°C.This work provides a powerful strategy for enabling stable operation of low-temperature zinc-ion capacitors.展开更多
Under the pressure of sustained growth in energy consumption in China,the implementation of a carbon pricing mechanism is an effective economic policy measure for promoting emission reduction,as well as a hotspot of r...Under the pressure of sustained growth in energy consumption in China,the implementation of a carbon pricing mechanism is an effective economic policy measure for promoting emission reduction,as well as a hotspot of research among scholars and policy makers.In this paper,the effects of carbon prices on Beijing's economy are analyzed using input-output tables.The carbon price costs are levied in accordance with the products'embodied carbon emission.By calculation,given the carbon price rate of 10 RMB/t-CO_2,the total carbon costs of Beijing account for approximately 0.22-0.40%of its gross revenue the same year.Among all industries,construction bears the largest carbon cost Among export sectors,the coal mining and washing industry has much higher export carbon price intensity than other industries.Apart from traditional energy-intensive industries,tertiary industry,which accounts for more than 70%of Beijing's economy,also bears a major carbon cost because of its large economic size.However,from 2007 to 2010,adjustment of the investment structure has reduced the emission intensity in investment sectors,contributing to the reduction of overall emissions and carbon price intensity.展开更多
Dear Editor,Common wheat(Triticum aestivum,2n=6×=42,AABBDD)is the staple crop worldwide.Elucidating the gene regulatory network provides essential information for mechanism studies and targeted manipulation of ge...Dear Editor,Common wheat(Triticum aestivum,2n=6×=42,AABBDD)is the staple crop worldwide.Elucidating the gene regulatory network provides essential information for mechanism studies and targeted manipulation of gene activity for breeding.However,it is a challenging task given the extremely large(16 Gb)and complicated allohexaploid genome of common wheat.Integrating multi-omics data is a compelling approach to construct the hierarchical regulatory network.展开更多
Triticeae species encompass many important crops including wheat,barley,and rye,which are essential for ensuring human survival and world food security.Expansions of genes involved in stress responses are common in Tr...Triticeae species encompass many important crops including wheat,barley,and rye,which are essential for ensuring human survival and world food security.Expansions of genes involved in stress responses are common in Triticeae genomes,which contributed to the high adaptability of Triticeae species.Secondary metabolites are key weapons for plants to deal with changing environments.However,metabolic enzymes generally underwent diversifying selection depending on the environments.展开更多
Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with ...Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.展开更多
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy fo...The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.展开更多
Polycomb group proteins are important repressors of numerous genes in higher eukaryotes. However, the mechanism by which Polycomb group proteins are recruited to specific genes is poorly understood. In Arabidopsis, LI...Polycomb group proteins are important repressors of numerous genes in higher eukaryotes. However, the mechanism by which Polycomb group proteins are recruited to specific genes is poorly understood. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1(LHP1), also known as TERMINAL FLOWER 2, was originally proposed as a subunit of polycomb repressive complex 1(PRC1) that could bind the tri-methylated lysine 27 of histone H3(H3K27me3) established by the PRC2. In this work, we show that LHP1 mainly functions with PRC2 to establish H3K27me3, but not with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2 A. Our results show that complexes of the transcription factors ASYMMETRIC LEAVES 1(AS1) and AS2 could help to establish the H3K27me3 modification at the chromatin regions of Class-I KNOTTED1-like homeobox(KNOX) genes BREVIPEDICELLUS andKNAT2 via direct interactions with LHP1. Additionally, our transcriptome analysis indicated that there are probably more common target genes of AS1 and LHP1 besides Class-I KNOX genes during leaf development in Arabidopsis.展开更多
De novo root regeneration(DNRR) has wide applications in agriculture such as those related to cutting technology. Detached Arabidopsis thaliana leaf explants can regenerate adventitious roots without added hormones. T...De novo root regeneration(DNRR) has wide applications in agriculture such as those related to cutting technology. Detached Arabidopsis thaliana leaf explants can regenerate adventitious roots without added hormones. The regenerative ability is highly dependent on the developmental status of the leaf. An immature leaf has a higher regenerative ability, while a mature leaf is difficult to regenerate. Using RNASeq analysis, we showed that the expression levels of many genes, including those in the auxin network,changed during leaf maturation. Particularly, the expression levels of many YUCCA(YUC) genes in the auxin biosynthesis pathway are responsive to leaf maturation. Overexpression of YUC1 in the yuc-1 D dominant mutant rescued the rooting defects caused by leaf maturation. In addition, YUC4 expression levels were also affected by circadian rhythms. The regenerative ability was reduced in both immature and mature mutant leaf explants from the new wuschel-related homeobox 11-3(wox11-3) and wox12-3 mutant alleles created by the CRISPR/Cas9 method. Overall, the transcriptome and genetic data, together with the auxin concentration analysis, indicate that the ability to upregulate auxin levels upon detachment may be reduced during leaf maturation. Thus, multiple developmental and environmental signals may converge to control auxin accumulation, which affects the efficiency of the WOX11/12-mediated DNRR from leaf explants.展开更多
Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called nodules.Studies have shown that abiotic and biotic stresses alter the profile of gene exp...Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called nodules.Studies have shown that abiotic and biotic stresses alter the profile of gene expression and transcript mobility in plants.However,little is known about the systemic transport of RNA between roots and shoots in response to rhizobial infection on a genome-wide scale during the formation of legume-rhizobia symbiosis.In our study,we found that two soybean(Glycine max)cultivars,Peking and Williams,show a high frequency of single nucleotide polymorphisms;this allowed us to characterize the origin and mobility of transcripts in hetero-grafts of these two cultivars.We identified 4,552 genes that produce mobile RNAs in soybean,and found that rhizobial infection triggers mass transport of m RNAs between shoots and roots at the early stage of nodulation.The majority of these mRNAs are of relatively low abundance and their transport occurs in a selective manner in soybean plants.Notably,the mRNAs that moved from shoots to roots at the early stage of nodulation were enriched in many nodule-related responsive processes.Moreover,the transcripts of many known symbiosis-related genes that are induced by rhizobial infection can move between shoots and roots.Our findings provide a deeper understanding of endogenous RNA transport in legume-rhizobia symbiotic processes.展开更多
Triticeae species,including wheat,barley,and rye,are critical for global food security.Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops.However,Triticeae includ...Triticeae species,including wheat,barley,and rye,are critical for global food security.Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops.However,Triticeae includes many wild relatives with desirable agronomic traits,and frequent introgressions occurred during Triticeae evolution and domestication.Thus,Triticeae genomes are generally large and complex,making the localization of genes or functional elements that control agronomic traits challenging.Here,we developed Triti-Map,which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae,as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits.The Triti-Map pipeline accepts bothDNA and RNAbulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions.We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process.We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.展开更多
A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to furt...A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to further mechanistic studies.Because epigenetic activity can reflect RE activity,defining chromatin states based on epigenomic features is an effective way to detect REs.Here,we present the web-based platform Chinese Spring chromatin state(CSCS),which provides CS chromatin signature information.CSCS indudes 15 recently published epigenomic data sets including open chromatin and major chromatin marks,which are further partitioned into 15 distinct chromatin states.CSCS curates detailed information about these chromatin states,with trained self-organization mapping(SOM)for segments in all chromatin states and JBrowse visualization for genomic regions or genes.Motif analysis for genomic regions or genes,GO analysis for genes and SOM analysis for new epige-nomic data sets are also integrated into CSCS.In summary,the CSCS database contains the combina-torial patterns of chromatin signatures in wheat and facilitates the detection of functi onal elements and further clarification of regulatory activities.We illustrate how CSCS enables biological insights using one example,demonstrating that CSCS is a highly useful resource for intensive data mining.CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.展开更多
Detached Arabidopsis thaliana leaves can regenerate adventitious roots,providing a platformfor studying de novo root regeneration(DNRR).However,the comprehensive transcriptional framework of DNRR remains elusive.Here,...Detached Arabidopsis thaliana leaves can regenerate adventitious roots,providing a platformfor studying de novo root regeneration(DNRR).However,the comprehensive transcriptional framework of DNRR remains elusive.Here,we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR.Time-lapse RNA sequencing(RNA-seq)of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate,ethylene,and reactive oxygen species(ROS)pathways in response towounding.Genetic analyses confirmed that ethylene andROSmay serve as wound signals to promoteDNRR.Next,time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis,wound-induced regeneration,and resource allocation in the wounded region of detached leaves during adventitious rooting.Genetic studies showed that BLADE-ON-PETIOLE1/2,which control aboveground organs,PLETHORA3/5/7,which control root organogenesis,and ETHYLENE RESPONSE FACTOR115,which controlswound-induced regeneration,are involved in DNRR.Furthermore,single-cell RNA-seq data revealed gene expression patterns in thewounded region of detached leaves during adventitious rooting.Overall,our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.展开更多
Nucleic acid therapeutics,which involve transferring exogenous genes inside target cells,are a promising clinical treatment option that can regulate gene expression at the transcriptional or post-transcriptional level...Nucleic acid therapeutics,which involve transferring exogenous genes inside target cells,are a promising clinical treatment option that can regulate gene expression at the transcriptional or post-transcriptional level.Ideally,this kind of treatment modality will not lead to an unwanted immune response.Compared with traditional treatment methods,nucleic acid therapeutics can achieve prolonged and stable curative effects.As an emerging treatment method,nucleic acid therapeutics have played an increasingly important role in clinical settings for the treatment of various conditions,including infectious diseases,cancer,immune-related diseases,and monogenetic diseases.To date,a large number of clinical trials have been conducted,and more than 30 nucleic acid drugs have been approved,highlighting the strong potential of this approach in clinical practice.Diverse carriers are used to protect nucleic acids from being degraded and to help them reach their targets accurately.However,some carriers are known to cause negative effects on the release and expression of nucleic acid drugs as well as adverse effects such as allergic reactions and accumulation in the liver.Therefore,biosafety assessment of delivery systems before their application in clinical settings is critical.In this review,we describe different delivery systems for nucleic acid drugs and discuss their biosafety in both preclinical and clinical studies,with particular focus on the carriers themselves,drug administration method,and overall treatment of the disease.展开更多
The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture;the timing of this transition has important implications for agriculture.The microRNA miR156 regulates this trans...The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture;the timing of this transition has important implications for agriculture.The microRNA miR156 regulates this transition and shoot maturation in plants.In Arabidopsis thaliana,deposition of histone H3 trimethylation on lysine 27(H3K27me3,a repressive mark)at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1(PRC1)or PRC2,depending on the developmental stage.The levels of miR156 progressively decline during shoot maturation.The amount of H3K27me3 at MIR156A/C loci affects miR156 levels;however,whether this epigenetic regulation is conserved remains unclear.Here,we found that in rice(Oryza sativa),the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1(OsLHP1),with the miR156–SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)module,affects developmental phase transitions.Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E,phenocopy of miR156 overexpression,and reduced H3k27me3 levels at MIR156B/C/I/E.This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1.Genetic and transcriptome analyses of wild-type,miR156b/c-overexpression,and Oslhp1-2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile-to-adult transition.Therefore,modifying the OsLHP1–miR156–SPL pathway may enable alteration of the vegetative period and plant architecture.展开更多
基金This work was supported by the Natural Science Foundation of Jiangsu Province(BK20220213)the Fundamental Research Funds of Jiangsu Key Laboratory of Biomass Energy and Material(JSBEM-S-202210 and JSBEM-S-202102).
文摘Solid-state zinc-ion capacitors are emerging as promising candidates for large-scale energy storage owing to improved safety,mechanical and thermal stability and easy-to-direct stacking.Hydrogel electrolytes are appealing solid-state electrolytes because of eco-friendliness,high conductivity and intrinsic flexibility.However,the electrolyte/electrode interfacial contact and anti-freezing properties of current hydrogel electrolytes are still challenging for practical applications of zinc-ion capacitors.Here,we report a class of hydrogel electrolytes that couple high interfacial adhesion and anti-freezing performance.The synergy of tough hydrogel matrix and chemical anchorage enables a well-adhered interface between hydrogel electrolyte and electrode.Meanwhile,the cooperative solvation of ZnCl2 and LiCl hybrid salts renders the hydrogel electrolyte high ionic conductivity and mechanical elasticity simultaneously at low temperatures.More significantly,the Zn||carbon nanotubes hybrid capacitor based on this hydrogel electrolyte exhibits low-temperature capacitive performance,delivering high-energy density of 39 Wh kg^(-1)at-60°C with capacity retention of 98.7%over 10,000 cycles.With the benefits of the well-adhered electrolyte/electrode interface and the anti-freezing hydrogel electrolyte,the Zn/Li hybrid capacitor is able to accommodate dynamic deformations and function well under 1000 tension cycles even at-60°C.This work provides a powerful strategy for enabling stable operation of low-temperature zinc-ion capacitors.
基金The authors would like to thank Key Projects in the National Science&Technology Pillar Program during the Twelfth Five Year Plan Period[grant number 2012BAC20B03]Beijing Natural Science Foundation[grant number 9112008]for supporting this research
文摘Under the pressure of sustained growth in energy consumption in China,the implementation of a carbon pricing mechanism is an effective economic policy measure for promoting emission reduction,as well as a hotspot of research among scholars and policy makers.In this paper,the effects of carbon prices on Beijing's economy are analyzed using input-output tables.The carbon price costs are levied in accordance with the products'embodied carbon emission.By calculation,given the carbon price rate of 10 RMB/t-CO_2,the total carbon costs of Beijing account for approximately 0.22-0.40%of its gross revenue the same year.Among all industries,construction bears the largest carbon cost Among export sectors,the coal mining and washing industry has much higher export carbon price intensity than other industries.Apart from traditional energy-intensive industries,tertiary industry,which accounts for more than 70%of Beijing's economy,also bears a major carbon cost because of its large economic size.However,from 2007 to 2010,adjustment of the investment structure has reduced the emission intensity in investment sectors,contributing to the reduction of overall emissions and carbon price intensity.
基金supported by the National Science Fund for Excellent Young Scholars(32022012)National Natural Science Foundation of China(31921005)+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27010302)Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]006).
文摘Dear Editor,Common wheat(Triticum aestivum,2n=6×=42,AABBDD)is the staple crop worldwide.Elucidating the gene regulatory network provides essential information for mechanism studies and targeted manipulation of gene activity for breeding.However,it is a challenging task given the extremely large(16 Gb)and complicated allohexaploid genome of common wheat.Integrating multi-omics data is a compelling approach to construct the hierarchical regulatory network.
基金supported by the National Natural Science Foundation of China(32270628,32270629)State Key Laboratory of Crop Gene Exploration and Utilization in Southwest(SKL-KF202305)State Key Laboratory of Genetic Engineering(SKLGE-2312).
文摘Triticeae species encompass many important crops including wheat,barley,and rye,which are essential for ensuring human survival and world food security.Expansions of genes involved in stress responses are common in Triticeae genomes,which contributed to the high adaptability of Triticeae species.Secondary metabolites are key weapons for plants to deal with changing environments.However,metabolic enzymes generally underwent diversifying selection depending on the environments.
基金the Collaborative Innovation Center for Henan Grain Crops,the Ministry of Science and Technology of the People's Republic of China(2021YFF1000200)the National Natural Science Foundation of China(Major Program,31991213)+4 种基金the Central Publicinterest Scientific Institution Basal Research Fund(Y2021YJ01)the Major Public Welfare Projects of Henan Province(201300110800)the Key Research and Development Program of China(2016YFD0100102)the CAAS Agricultural Science and Technology Innovation Program(CAASZDRW202002)the seed innovation program of the Ministry of Agriculture and Rural Affairs of China,and the Henan Provincial R&D Projects of Interregional Cooperation for Local Scientific and Technological Development Guided by the Central Government(YDZX20214100004191).
文摘Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.
基金supported by funding from the National Key Research and Development Program of China(2022YFF1003402)the China Natural Science Foundation(31371622)the CAAS Innovation Program.
文摘The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.
基金supported by the National Basic Research Program of China (2012CB910500 and 2011CB944600)the National Natural Science Foundation of China (31370752)
文摘Polycomb group proteins are important repressors of numerous genes in higher eukaryotes. However, the mechanism by which Polycomb group proteins are recruited to specific genes is poorly understood. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1(LHP1), also known as TERMINAL FLOWER 2, was originally proposed as a subunit of polycomb repressive complex 1(PRC1) that could bind the tri-methylated lysine 27 of histone H3(H3K27me3) established by the PRC2. In this work, we show that LHP1 mainly functions with PRC2 to establish H3K27me3, but not with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2 A. Our results show that complexes of the transcription factors ASYMMETRIC LEAVES 1(AS1) and AS2 could help to establish the H3K27me3 modification at the chromatin regions of Class-I KNOTTED1-like homeobox(KNOX) genes BREVIPEDICELLUS andKNAT2 via direct interactions with LHP1. Additionally, our transcriptome analysis indicated that there are probably more common target genes of AS1 and LHP1 besides Class-I KNOX genes during leaf development in Arabidopsis.
基金supported by grants from the National Natural Science Foundation of China (31630007, 31770399 and 21375066)the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27030103)+1 种基金the Key Research Program of CAS (QYZDB-SSWSMC010)the National Key Laboratory of Plant Molecular Genetics
文摘De novo root regeneration(DNRR) has wide applications in agriculture such as those related to cutting technology. Detached Arabidopsis thaliana leaf explants can regenerate adventitious roots without added hormones. The regenerative ability is highly dependent on the developmental status of the leaf. An immature leaf has a higher regenerative ability, while a mature leaf is difficult to regenerate. Using RNASeq analysis, we showed that the expression levels of many genes, including those in the auxin network,changed during leaf maturation. Particularly, the expression levels of many YUCCA(YUC) genes in the auxin biosynthesis pathway are responsive to leaf maturation. Overexpression of YUC1 in the yuc-1 D dominant mutant rescued the rooting defects caused by leaf maturation. In addition, YUC4 expression levels were also affected by circadian rhythms. The regenerative ability was reduced in both immature and mature mutant leaf explants from the new wuschel-related homeobox 11-3(wox11-3) and wox12-3 mutant alleles created by the CRISPR/Cas9 method. Overall, the transcriptome and genetic data, together with the auxin concentration analysis, indicate that the ability to upregulate auxin levels upon detachment may be reduced during leaf maturation. Thus, multiple developmental and environmental signals may converge to control auxin accumulation, which affects the efficiency of the WOX11/12-mediated DNRR from leaf explants.
基金supported by the Key Research Program from the Chinese Academy of Sciences(ZDRW-ZS-2019-2)the“Strategic Priority Research Program”of the Chinese Academy of Sciences(XDA08000000)。
文摘Legumes have evolved a symbiotic relationship with rhizobial bacteria and their roots form unique nitrogen-fixing organs called nodules.Studies have shown that abiotic and biotic stresses alter the profile of gene expression and transcript mobility in plants.However,little is known about the systemic transport of RNA between roots and shoots in response to rhizobial infection on a genome-wide scale during the formation of legume-rhizobia symbiosis.In our study,we found that two soybean(Glycine max)cultivars,Peking and Williams,show a high frequency of single nucleotide polymorphisms;this allowed us to characterize the origin and mobility of transcripts in hetero-grafts of these two cultivars.We identified 4,552 genes that produce mobile RNAs in soybean,and found that rhizobial infection triggers mass transport of m RNAs between shoots and roots at the early stage of nodulation.The majority of these mRNAs are of relatively low abundance and their transport occurs in a selective manner in soybean plants.Notably,the mRNAs that moved from shoots to roots at the early stage of nodulation were enriched in many nodule-related responsive processes.Moreover,the transcripts of many known symbiosis-related genes that are induced by rhizobial infection can move between shoots and roots.Our findings provide a deeper understanding of endogenous RNA transport in legume-rhizobia symbiotic processes.
基金supported by the National Science Fund for Excellent Young Scholars(32022012).
文摘Triticeae species,including wheat,barley,and rye,are critical for global food security.Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops.However,Triticeae includes many wild relatives with desirable agronomic traits,and frequent introgressions occurred during Triticeae evolution and domestication.Thus,Triticeae genomes are generally large and complex,making the localization of genes or functional elements that control agronomic traits challenging.Here,we developed Triti-Map,which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae,as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits.The Triti-Map pipeline accepts bothDNA and RNAbulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions.We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process.We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.
基金This study was supported by the Strategic Priority Resea rch Program of the Chinese Academy of Sciences(XDB27010302).
文摘A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to further mechanistic studies.Because epigenetic activity can reflect RE activity,defining chromatin states based on epigenomic features is an effective way to detect REs.Here,we present the web-based platform Chinese Spring chromatin state(CSCS),which provides CS chromatin signature information.CSCS indudes 15 recently published epigenomic data sets including open chromatin and major chromatin marks,which are further partitioned into 15 distinct chromatin states.CSCS curates detailed information about these chromatin states,with trained self-organization mapping(SOM)for segments in all chromatin states and JBrowse visualization for genomic regions or genes.Motif analysis for genomic regions or genes,GO analysis for genes and SOM analysis for new epige-nomic data sets are also integrated into CSCS.In summary,the CSCS database contains the combina-torial patterns of chromatin signatures in wheat and facilitates the detection of functi onal elements and further clarification of regulatory activities.We illustrate how CSCS enables biological insights using one example,demonstrating that CSCS is a highly useful resource for intensive data mining.CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(grant no.XDB27030103)the National Natural Science Foundation of China(32000175/31770285/32070397)+1 种基金the Youth Innovation Promotion Association CAS(2014241)the Chinese Academy of Sciences.A portion of this research was supported by a Global Research Collaboration Grant from the Offices of Research and Global Engagement to L.Y.from the University of Georgia and National Science Foundation under Grant NO.IOS2039313 to L.Y.
文摘Detached Arabidopsis thaliana leaves can regenerate adventitious roots,providing a platformfor studying de novo root regeneration(DNRR).However,the comprehensive transcriptional framework of DNRR remains elusive.Here,we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR.Time-lapse RNA sequencing(RNA-seq)of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate,ethylene,and reactive oxygen species(ROS)pathways in response towounding.Genetic analyses confirmed that ethylene andROSmay serve as wound signals to promoteDNRR.Next,time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis,wound-induced regeneration,and resource allocation in the wounded region of detached leaves during adventitious rooting.Genetic studies showed that BLADE-ON-PETIOLE1/2,which control aboveground organs,PLETHORA3/5/7,which control root organogenesis,and ETHYLENE RESPONSE FACTOR115,which controlswound-induced regeneration,are involved in DNRR.Furthermore,single-cell RNA-seq data revealed gene expression patterns in thewounded region of detached leaves during adventitious rooting.Overall,our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.
基金support from the National Natural Science Foundation of China(Nos.22161132008 and 81822024)the Natural Science Foundation of Shanghai,China(Nos.19520714100 and 19ZR1475800)the Project of Shanghai Jiao Tong University(2019QYA03 and YG2017ZD07).
文摘Nucleic acid therapeutics,which involve transferring exogenous genes inside target cells,are a promising clinical treatment option that can regulate gene expression at the transcriptional or post-transcriptional level.Ideally,this kind of treatment modality will not lead to an unwanted immune response.Compared with traditional treatment methods,nucleic acid therapeutics can achieve prolonged and stable curative effects.As an emerging treatment method,nucleic acid therapeutics have played an increasingly important role in clinical settings for the treatment of various conditions,including infectious diseases,cancer,immune-related diseases,and monogenetic diseases.To date,a large number of clinical trials have been conducted,and more than 30 nucleic acid drugs have been approved,highlighting the strong potential of this approach in clinical practice.Diverse carriers are used to protect nucleic acids from being degraded and to help them reach their targets accurately.However,some carriers are known to cause negative effects on the release and expression of nucleic acid drugs as well as adverse effects such as allergic reactions and accumulation in the liver.Therefore,biosafety assessment of delivery systems before their application in clinical settings is critical.In this review,we describe different delivery systems for nucleic acid drugs and discuss their biosafety in both preclinical and clinical studies,with particular focus on the carriers themselves,drug administration method,and overall treatment of the disease.
基金This researchwas financially supported by the National NaturalScience Foundation of China(91735304,31771887).
文摘The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture;the timing of this transition has important implications for agriculture.The microRNA miR156 regulates this transition and shoot maturation in plants.In Arabidopsis thaliana,deposition of histone H3 trimethylation on lysine 27(H3K27me3,a repressive mark)at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1(PRC1)or PRC2,depending on the developmental stage.The levels of miR156 progressively decline during shoot maturation.The amount of H3K27me3 at MIR156A/C loci affects miR156 levels;however,whether this epigenetic regulation is conserved remains unclear.Here,we found that in rice(Oryza sativa),the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1(OsLHP1),with the miR156–SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)module,affects developmental phase transitions.Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E,phenocopy of miR156 overexpression,and reduced H3k27me3 levels at MIR156B/C/I/E.This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1.Genetic and transcriptome analyses of wild-type,miR156b/c-overexpression,and Oslhp1-2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile-to-adult transition.Therefore,modifying the OsLHP1–miR156–SPL pathway may enable alteration of the vegetative period and plant architecture.
