The first pandemic wave of coronavirus disease 2019(COVID-19)induced a considerable increase in several antivirals and antibiotics in surface water.The common symptoms of COVID-19 are viral and bacterial infections,wh...The first pandemic wave of coronavirus disease 2019(COVID-19)induced a considerable increase in several antivirals and antibiotics in surface water.The common symptoms of COVID-19 are viral and bacterial infections,while comorbidities(e.g.,hypertension and diabetes)and mental shock(e.g.,insomnia and anxiety)are nonnegligible.Nevertheless,little is known about the long-term impacts of comorbidities and mental shock on organic micropollutants(OMPs)in surface waters.Herein,we monitored 114 OMPs in surface water and wastewater treatment plants(WWTPs)in Wuhan,China,between 2019 and 2021.The pandemic-induced OMP pollution in surface water was confirmed by significant increases in 26 OMP concentrations.Significant increases in four antihypertensives and one diabetic drug suggest that the treatment of comorbidities may induce OMP pollution.Notably,cotinine(a metabolite of nicotine)increased 155 times to 187 ngL1,which might be associated with increased smoking.Additionally,the increases in zolpidem and sulpiride might be the result of worsened insomnia and depression.Hence,it is reasonable to note that mental-health protecting drugs/behavior also contributed to OMP pollution.Among the observed OMPs,telmisartan,lopinavir,and ritonavir were associated with significantly higher ecological risks because of their limited WWTP-removal rate and high ecotoxicity.This study provides new insights into the effects of comorbidities and mental shock on OMPs in surface water during a pandemic and highlights the need to monitor the fate of related pharmaceuticals in the aquatic environment and to improve their removal efficiencies in WWTPs。展开更多
Histone lysine methylation plays an essential role in regulating chromatin functions such as transcription and heterochromatin formation. Histone H3 lysine 4 （H3K4） methylation is linked to active transcription [1, ...Histone lysine methylation plays an essential role in regulating chromatin functions such as transcription and heterochromatin formation. Histone H3 lysine 4 （H3K4） methylation is linked to active transcription [1, 2]. Recent findings in mammals have demonstrated that histone methylation is reversible by a family of Jumonji C （JmjC） domain-containing proteins. KDM5/ JARID1 family proteins have been shown to be able to demethylate H3K4mel,2,3 in mammals [3]. Previously, we identified six proteins in Arabidopsis showing high sequence similarity to KDM5/JARIDI family proteins [4]. Here we demonstrate that one such protein, JMJ14, is an active histone H3K4 demethylase and is involved in flowering time regulation.展开更多
Venous sinus stent implantation is an emerging endovascular treatment technique effectively applied in diseases such as cerebral venous sinus thrombosis.However,arterial stents are commonly used in clinical practice f...Venous sinus stent implantation is an emerging endovascular treatment technique effectively applied in diseases such as cerebral venous sinus thrombosis.However,arterial stents are commonly used in clinical practice for venous sinus stent implantation,which is off-label and carries high risks and poor prognosis,highlighting the necessity of developing venous sinus-specific stents.This narrative review discusses the current situation and problems of venous sinus stent implantation and looks forward to the design focus and future development prospects of venous sinus-specific stents.展开更多
Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkali...Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years ago.Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.展开更多
Stay-green(SG)in wheat is a beneficial trait that increases yield and stress tolerance.However,conventional phenotyping techniques limited the understanding of its genetic basis.Spectral indices(SIs)as non-destructive...Stay-green(SG)in wheat is a beneficial trait that increases yield and stress tolerance.However,conventional phenotyping techniques limited the understanding of its genetic basis.Spectral indices(SIs)as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy.Here,we applied Sls to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons.Four Sis(normalized difference vegetation index,green normalized difference vegetation index,normalized difference red edge index,and optimized soil-adjusted vegetation index)were normalized to develop relative stay-green scores(RSGS)as the SG indicators.An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci(QTL)harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes.Among them,15 QTL overlapped or were adjacent to known SG-related QTL/genes,while the remaining QTL were novel.Notably,a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100,TracesCS6B03G0356400,and TracesCS2B03G1299500 are increasing following the Green Revolution,further validating the feasibility of the pipeline.This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.展开更多
recanalization.Yet,due to ischemia-reperfusion injury,over half of these patients still experience poor prognoses.Thus,neuroprotective treatment is imperative to alleviate the ischemic brain injury,and a proof-of-conc...recanalization.Yet,due to ischemia-reperfusion injury,over half of these patients still experience poor prognoses.Thus,neuroprotective treatment is imperative to alleviate the ischemic brain injury,and a proof-of-concept study was conducted on“biodegradable neuroprotective stent”.This concept is premised on the hypothesis that locally released Mg^(2+)/H_(2) from Mg metal within the bloodstream could offer synergistic neuroprotection against reperfusion injury in distant cerebral ischemic tissues.Initially,the study evaluated pure Mg’s neuroactive potential using oxygen-glucose deprivation/reoxygenation(OGD/R)injured neuron cells.Subsequently,a pure Mg wire was implanted into the common carotid artery of the transient middle cerebral artery occlusion(MCAO)rat model to simulate human brain ischemia/reperfusion injury.In vitro analyses revealed that pure Mg extract aided mouse hippocampal neuronal cell(HT-22)in defending against OGD/R injury.Additionally,the protective effects of the Mg wire on behavioral abnormalities,neural injury,blood-brain barrier disruption,and cerebral blood flow reduction in MCAO rats were verified.Conclusively,Mg-based biodegradable neuroprotective implants could serve as an effective local Mg^(2+)/H_(2) delivery system for treating distant cerebral ischemic diseases.展开更多
The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically i...The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system.We systematically compared different induction strategies and achieved high efficiency in target gene activation.We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration.Further experiments showed that induced activation of these morphogenic genes can accelerate regenera-tion and improve regeneration efficiency in both eudicot and monocot plants,including alfalfa,woodland strawberry,and sheepgrass.Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.展开更多
The life sciences field has experienced profound impacts from genome editing,a technology that enables precise genetic sequence modifications in living cells.Developments in genome editing have significantly propelled...The life sciences field has experienced profound impacts from genome editing,a technology that enables precise genetic sequence modifications in living cells.Developments in genome editing have significantly propelled advances in biomedicine and agricultural breeding.With the introduction of CRISPR as a genome editing tool in 2012[1],rapid progress has paved the way for emerging technologies such as base editing and prime editing[2,3].These sophisticated editing methods facilitate more accurate genome modifications and promise to profoundly impact the future of precision medicine,crop improvement,and even the de novo design of organisms.展开更多
Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conserved Jumonji C （JmjC） doma...Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conserved Jumonji C （JmjC） domain was found in a large group of histone demethylases. However, it is still unclear whether plants also contain the JmjC domain- containing active histone demethylases. Here we performed genome-wide screen and phylogenetic analysis of JmjC domain-containing proteins in the dicot plant, Arabidopsis, and monocot plant rice, and found 21 and 20 JmjC domain-containing, respectively. We also examined the expression of JmjC domain-containing proteins and compared them to human JmjC counterparts for potential enzymatic activity. The spatial expression patterns of the Arabidopsis JmjC domain-containing genes revealed that they are all actively transcribed genes. These active plant JmjC domain-containing genes could possibly function in epigenetic regulation to antagonize the activity of the large number of putative SET domain-containing histone methyltransferase activity to dynamically regulate histone methylation homeostasis.展开更多
In plants,microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored.However,the mechanisms regulating the accumulation of miRNAs remain poorly under.stood.Here,we report...In plants,microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored.However,the mechanisms regulating the accumulation of miRNAs remain poorly under.stood.Here,we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA,rice (Oryza sativa) miR528.At the transcriptional level,miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves;at the post-transcriptional level,aging also modulated miR528 levels by enhancing pri-miR528 alter.native splicing.We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE2 (OsRFI2).Moreover,natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties,which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528.Taken together,our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.展开更多
N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulat...N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulating alternative polyadenylation(APA)in plants.APA is controlled by a large protein-RNA complex with many components,including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30(CPSF30).In Arabidopsis,CPSF30 has two isoforms and the longer isoform(CPSF30-L)contains a YT512-B Homology(YTH)domain,which is unique to plants.In this study,we showed that CPSF30-L YTH domain binds to m^(6)A in v itro.In the cpsf30-2 mutant,the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m^(6)A peaks,indicating that these gene transcripts carrying m^(6)A tend to be regulated by APA.Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2,but m^(6)A-binding-defective mutants of CPSF30-L could not.Taken together,our results demonstrated that m^(6)A modification regulates APA in Arabidops is and revealed that the m^(6)A reader CPSF30-L affects nitrate signaling by controlling APA,shedding new light on the roles of the m^(6)A modification during RNA 3-end processing in nitrate metabolism.展开更多
Many microRNAs (miRNAs) are critical regulators of plant antiviral defense.However,little is known about how these miRNAs respond to virus invasion at the transcriptional level.We previously show that defense against ...Many microRNAs (miRNAs) are critical regulators of plant antiviral defense.However,little is known about how these miRNAs respond to virus invasion at the transcriptional level.We previously show that defense against Rice stripe virus (RSV) invasion entailed a reduction of miR528 accumulation in rice,alleviating miR528-mediated degradation of L-Ascorbate Oxidase (AO) mRNA and bolstering the antiviral activity of AO.Here we show that the miR528-A0 defense module is regulated by the transcription factor SPL9.SPL9 displayed high-affinity binding to specific motifs within the promoter region of miR528 and activated the expression of miR528 gene in vivo.Loss-of-function mutations in SPL9 caused a significant reduction in miR528 accumulation but a substantial increase of AO mRNA,resulting in enhanced plant resistance to RSV.Conversely,transgenic overexpression of SPL9 stimulated the expression of miR528 gene,hence lowering the level of AO mRNA and compromising rice defense against RSV.Importantly,gain in RSV susceptibility did not occur when SPL9 was overexpressed in mir528 loss-of-function mutants,or in transgenic rice expressing a miR528-resistant AO.Taken together,the finding of SPL9-mediated transcriptional activation of miR528 expression adds a new regulatory layer to the miR528-A0 antiviral defense pathway.展开更多
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environme...Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer(two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications(PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato.Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation(RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects.We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.展开更多
Summary It was noted that circadian components function in plant adaptation to diurnal temperature cycles and freezing tolerance. Our genome-wide transcriptome analysis revealed that evening-phased COR27 and COR28 mai...Summary It was noted that circadian components function in plant adaptation to diurnal temperature cycles and freezing tolerance. Our genome-wide transcriptome analysis revealed that evening-phased COR27 and COR28 mainly repress the transcription of clockassociated evening genes PRRS, ELF4 and cold-responsive genes. Chromatin immunoprecipitation indicated that CCAI is recruited to the site containing EE elements of COR27 and COR28 promoters in a temperaturedependent way. Further genetic analysis shows COR28 is essential for the circadian function of PRR9 and PRRT. Together, our results support a role of COR27 and COR28 as nighttime repressors integrating circadian clock and plant cold stress responses.展开更多
Transposable elements(TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to u...Transposable elements(TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.展开更多
Evidence is emerging that t RNA-derived fragments(t RFs)are regulatory molecules.Studies of t RFs in plants have been based on conventional small RNA sequencing,and focused on profiling of t RF-5 and t RF-3 species.A ...Evidence is emerging that t RNA-derived fragments(t RFs)are regulatory molecules.Studies of t RFs in plants have been based on conventional small RNA sequencing,and focused on profiling of t RF-5 and t RF-3 species.A more comprehensive and quantitative analysis of the entire t RF population is highly necessary.Here,we employ t RNA-seq and YAMAT-seq,and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants.We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed,accounting for only 1%of total t RNA abundance,while~12%of t RNA genes contribute to~80%of t RNA abundance.Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern.By characterizing the composition of a highly heterogeneous t RF population,we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions.The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products.Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.展开更多
Post-translational methylation at arginine residues is one of the most important covalent modifications of proteins, involved in a myriad of essential cellular processes in eukaryotes, such as transcriptional regulati...Post-translational methylation at arginine residues is one of the most important covalent modifications of proteins, involved in a myriad of essential cellular processes in eukaryotes, such as transcriptional regulation, RNA processing, signal transduction, and DNA repair. Methylation at arginine residues is catalyzed by a family of enzymes called protein arginine methyltransferases （PRMTs）. PRMTs have been extensively studied in various taxa and there is a growing tendency to unveil their functional importance in plants. Recent studies in plants revealed that this evolutionarily conserved family of enzymes regulates essential traits including vegetative growth, flowering time, circadian cycle, and response to high medium salinity and ABA. In this review, we highlight recent advances in the field of post- translational arginine methylation with special emphasis on the roles and future prospects of this modification in plants.展开更多
The central dogma states that genes encoded in the DNA should be first transcribed into messenger RNA(mRNA)and then translated into functional proteins(Crick,1970).This dogma has been written in numerous textbooks and...The central dogma states that genes encoded in the DNA should be first transcribed into messenger RNA(mRNA)and then translated into functional proteins(Crick,1970).This dogma has been written in numerous textbooks and learned by myriad students.However,along with the completion of the human genome project in June 2000,an astonishing fact was revealed:only 1.5%of the human genome encodes for proteins(Lander et al.,2001;Venter et al.,2001).This fact raised three fundamental questions:(i)why does the human genome have so few protein-coding genes?(ii)how to explain the apparent differences between humans and other species using the limited coding genes?(iii)what are the roles of the noncoding regions in our genome?展开更多
基金supported by the National Natural Science Foundation of China(52221004,52091542,and 51820105011)the Scientific Research Project of China Three Gorges Corporation(201903139)the Research Fund of Vanke School of Public Health(2021JC009),Tsinghua University.
文摘The first pandemic wave of coronavirus disease 2019(COVID-19)induced a considerable increase in several antivirals and antibiotics in surface water.The common symptoms of COVID-19 are viral and bacterial infections,while comorbidities(e.g.,hypertension and diabetes)and mental shock(e.g.,insomnia and anxiety)are nonnegligible.Nevertheless,little is known about the long-term impacts of comorbidities and mental shock on organic micropollutants(OMPs)in surface waters.Herein,we monitored 114 OMPs in surface water and wastewater treatment plants(WWTPs)in Wuhan,China,between 2019 and 2021.The pandemic-induced OMP pollution in surface water was confirmed by significant increases in 26 OMP concentrations.Significant increases in four antihypertensives and one diabetic drug suggest that the treatment of comorbidities may induce OMP pollution.Notably,cotinine(a metabolite of nicotine)increased 155 times to 187 ngL1,which might be associated with increased smoking.Additionally,the increases in zolpidem and sulpiride might be the result of worsened insomnia and depression.Hence,it is reasonable to note that mental-health protecting drugs/behavior also contributed to OMP pollution.Among the observed OMPs,telmisartan,lopinavir,and ritonavir were associated with significantly higher ecological risks because of their limited WWTP-removal rate and high ecotoxicity.This study provides new insights into the effects of comorbidities and mental shock on OMPs in surface water during a pandemic and highlights the need to monitor the fate of related pharmaceuticals in the aquatic environment and to improve their removal efficiencies in WWTPs。
基金We thank Dr T Jenuwein for providing us the H3K27me3 antibody and Qingbao Zhu for technical support. We thank the Arabidopsis Biological Resources Center at Ohio State for providing SALK T-DNA-insertion lines. This work was supported by grants from the National Basic Research Program of China （2009CB941500 and 2005CB522400 to XC） and the National Natural Science Foundation of China （30771209 to CL, and 30930048 and 30921061 to XC）.
文摘Histone lysine methylation plays an essential role in regulating chromatin functions such as transcription and heterochromatin formation. Histone H3 lysine 4 （H3K4） methylation is linked to active transcription [1, 2]. Recent findings in mammals have demonstrated that histone methylation is reversible by a family of Jumonji C （JmjC） domain-containing proteins. KDM5/ JARID1 family proteins have been shown to be able to demethylate H3K4mel,2,3 in mammals [3]. Previously, we identified six proteins in Arabidopsis showing high sequence similarity to KDM5/JARIDI family proteins [4]. Here we demonstrate that one such protein, JMJ14, is an active histone H3K4 demethylase and is involved in flowering time regulation.
基金funded by National Natural Science Foundation of China(82027802,82102220)Research Funding on Translational Medicine from Beijing Municipal Science and Technology Commission(Z221100007422023)+5 种基金Beijing Hospitals Authority Clinical Medicine Development of Special Funding Support(YGLX202325)Non-profit Central Research Institute Fund of Chinese Academy of Medical(2023-JKCS-09)Beijing Association for Science and Technology Youth Talent Support Program(BYESS2022081)Beijing Municipal Natural Science Foundation(7244510)Science and Technology Innovation Service Capacity Building Project of Beijing Municipal Education Commission(11000023T000002157177)Outstanding Young Talents Program of Capital Medical University(B2305).
文摘Venous sinus stent implantation is an emerging endovascular treatment technique effectively applied in diseases such as cerebral venous sinus thrombosis.However,arterial stents are commonly used in clinical practice for venous sinus stent implantation,which is off-label and carries high risks and poor prognosis,highlighting the necessity of developing venous sinus-specific stents.This narrative review discusses the current situation and problems of venous sinus stent implantation and looks forward to the design focus and future development prospects of venous sinus-specific stents.
基金This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA28030000)the National Key Research and Development Program of China(2022YFD1500503,2022YFF1003401)+2 种基金Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta(2022SZX14)the earmarked fund for CARS-Green Manure(CARS-22)the Youth Innovation Promotion Association of CAS(Y2022039).
文摘Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years ago.Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.
基金supported by the National Key R&D Program of China(no.2022YFE0116200)the Key R&D Program of Qinghai Province(2022-NK-125)the Key R&D Program of Yangling Seed Industry Innovation Center(grant no.Ylzy-xm-01).
文摘Stay-green(SG)in wheat is a beneficial trait that increases yield and stress tolerance.However,conventional phenotyping techniques limited the understanding of its genetic basis.Spectral indices(SIs)as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy.Here,we applied Sls to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons.Four Sis(normalized difference vegetation index,green normalized difference vegetation index,normalized difference red edge index,and optimized soil-adjusted vegetation index)were normalized to develop relative stay-green scores(RSGS)as the SG indicators.An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci(QTL)harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes.Among them,15 QTL overlapped or were adjacent to known SG-related QTL/genes,while the remaining QTL were novel.Notably,a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100,TracesCS6B03G0356400,and TracesCS2B03G1299500 are increasing following the Green Revolution,further validating the feasibility of the pipeline.This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.
基金funded by National Natural Science Foundation of China(82027802,82102220)Research Funding on Translational Medicine from Beijing Municipal Science and Technology Commission(Z221100007422023)+4 种基金Beijing Hospitals Authority Clinical Medicine Development of Special Funding Support(YGLX202325)Non-profit Central Research Institute Fund of Chinese Academy of Medical(2023-JKCS-09)Beijing Association for Science and Technology Youth Talent Support Program(BYESS2022081)Science and Technology Innovation Service Capacity Building Project of Beijing Municipal Education Commission(11000023T000002157177)Outstanding Young Talents Program of Capital Medical University(B2305),Beijing Municipal Natural Science Foundation(7244510),Beijing Nova Program(20230484286).
文摘recanalization.Yet,due to ischemia-reperfusion injury,over half of these patients still experience poor prognoses.Thus,neuroprotective treatment is imperative to alleviate the ischemic brain injury,and a proof-of-concept study was conducted on“biodegradable neuroprotective stent”.This concept is premised on the hypothesis that locally released Mg^(2+)/H_(2) from Mg metal within the bloodstream could offer synergistic neuroprotection against reperfusion injury in distant cerebral ischemic tissues.Initially,the study evaluated pure Mg’s neuroactive potential using oxygen-glucose deprivation/reoxygenation(OGD/R)injured neuron cells.Subsequently,a pure Mg wire was implanted into the common carotid artery of the transient middle cerebral artery occlusion(MCAO)rat model to simulate human brain ischemia/reperfusion injury.In vitro analyses revealed that pure Mg extract aided mouse hippocampal neuronal cell(HT-22)in defending against OGD/R injury.Additionally,the protective effects of the Mg wire on behavioral abnormalities,neural injury,blood-brain barrier disruption,and cerebral blood flow reduction in MCAO rats were verified.Conclusively,Mg-based biodegradable neuroprotective implants could serve as an effective local Mg^(2+)/H_(2) delivery system for treating distant cerebral ischemic diseases.
基金supported by the National Key R&D Program of China (2022YFD1500503 to X.S.)the Key Projects in Science and Technology of Inner Mongolia (2021ZD0031 to X.C.and S.Z.)+6 种基金the National Key Research and Development Program (2022YFF1002802 to X.D.)the Youth Innovation Promotion Association,CAS (Y2022039 to X.D.)the Youth Innovation Promotion Association,CAS (2022096 to S.Z.)the National Science Foundation of China (NSFC32272692 to J.Z.)Project ZR2022QC054 of the Shandong Provincial Natural Science Foundation (to Y.T.)funding from the State Key Laboratory of Protein and Plant Gene Research (to Q.L.).
文摘The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system.We systematically compared different induction strategies and achieved high efficiency in target gene activation.We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration.Further experiments showed that induced activation of these morphogenic genes can accelerate regenera-tion and improve regeneration efficiency in both eudicot and monocot plants,including alfalfa,woodland strawberry,and sheepgrass.Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.
文摘The life sciences field has experienced profound impacts from genome editing,a technology that enables precise genetic sequence modifications in living cells.Developments in genome editing have significantly propelled advances in biomedicine and agricultural breeding.With the introduction of CRISPR as a genome editing tool in 2012[1],rapid progress has paved the way for emerging technologies such as base editing and prime editing[2,3].These sophisticated editing methods facilitate more accurate genome modifications and promise to profoundly impact the future of precision medicine,crop improvement,and even the de novo design of organisms.
基金the Hi-Tech Research and Development (863) Program of China (2006AA10A101)the State Key Basic Research and Development Plan of China (2005CB522400)+1 种基金the National Natural Science Foundation of China (30771209 to C.Liu and 30621001 to X.Cao)the Chinese Academy of Sciences (CXTD-S2005-2) to X.Cao
文摘Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conserved Jumonji C （JmjC） domain was found in a large group of histone demethylases. However, it is still unclear whether plants also contain the JmjC domain- containing active histone demethylases. Here we performed genome-wide screen and phylogenetic analysis of JmjC domain-containing proteins in the dicot plant, Arabidopsis, and monocot plant rice, and found 21 and 20 JmjC domain-containing, respectively. We also examined the expression of JmjC domain-containing proteins and compared them to human JmjC counterparts for potential enzymatic activity. The spatial expression patterns of the Arabidopsis JmjC domain-containing genes revealed that they are all actively transcribed genes. These active plant JmjC domain-containing genes could possibly function in epigenetic regulation to antagonize the activity of the large number of putative SET domain-containing histone methyltransferase activity to dynamically regulate histone methylation homeostasis.
基金supported by the National Natural Science Foundation of China (grants 91540203 and 31788103 to X.C.,31771872 to X.S.)The National Key Research and Development Program of China (2016YFD0100904)+3 种基金the Genetically Modified Breeding Major Projects (grant no.2016ZX08009001 -005 to X.S.)the Key Research Program of Frontier Sciences Chinese Academy of Sciences (QYZDY-SSWSMC022 to X.C.)Strategic Priority Research Program of Chinese Academy of Sciences (XDB27030201 to X.C.)the State Key Laboratory of Plant Genomics.
文摘In plants,microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored.However,the mechanisms regulating the accumulation of miRNAs remain poorly under.stood.Here,we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA,rice (Oryza sativa) miR528.At the transcriptional level,miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves;at the post-transcriptional level,aging also modulated miR528 levels by enhancing pri-miR528 alter.native splicing.We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE2 (OsRFI2).Moreover,natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties,which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528.Taken together,our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.
基金This work was supported by grants from the National Natural Science Foundation of China(31788103 to X.C.,31670247 to Y.W.,31870755 to S.L.,31801063 to Y.H.,31701096 to J.S.,31900435 to B.W.)the Chinese Academy of Sciences(Strategic Priority Research Program XDB27030201 and QYZDY-SSW-SMC022 to X.C.)+3 种基金the Guangdong Innovation Research Team Fund(2016ZT06S172 to S.L.)the Shenzhen Sci-Tech Fund(No.KYTDPT20181011104005 to S.L)the China Postdoctoral Science Foundation(2016M600143 to Y.H.)the Guangdong Science and Technology Department(2020B1212060018 and 2020B1212030004 to B.W.).
文摘N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulating alternative polyadenylation(APA)in plants.APA is controlled by a large protein-RNA complex with many components,including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30(CPSF30).In Arabidopsis,CPSF30 has two isoforms and the longer isoform(CPSF30-L)contains a YT512-B Homology(YTH)domain,which is unique to plants.In this study,we showed that CPSF30-L YTH domain binds to m^(6)A in v itro.In the cpsf30-2 mutant,the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m^(6)A peaks,indicating that these gene transcripts carrying m^(6)A tend to be regulated by APA.Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2,but m^(6)A-binding-defective mutants of CPSF30-L could not.Taken together,our results demonstrated that m^(6)A modification regulates APA in Arabidops is and revealed that the m^(6)A reader CPSF30-L affects nitrate signaling by controlling APA,shedding new light on the roles of the m^(6)A modification during RNA 3-end processing in nitrate metabolism.
基金supported by grants from the Natural Science Foundation of China (31530062,31420103904 and 31722045)Transgenic Research Program (2016ZX08010-001,2016ZX08009003-001)Y.L.,and GARS- 01-06 to 乙H.X.,and Y.L.:ZY was supported by the National Postdoctoral Program for Innovative Talents (BX201700004).
文摘Many microRNAs (miRNAs) are critical regulators of plant antiviral defense.However,little is known about how these miRNAs respond to virus invasion at the transcriptional level.We previously show that defense against Rice stripe virus (RSV) invasion entailed a reduction of miR528 accumulation in rice,alleviating miR528-mediated degradation of L-Ascorbate Oxidase (AO) mRNA and bolstering the antiviral activity of AO.Here we show that the miR528-A0 defense module is regulated by the transcription factor SPL9.SPL9 displayed high-affinity binding to specific motifs within the promoter region of miR528 and activated the expression of miR528 gene in vivo.Loss-of-function mutations in SPL9 caused a significant reduction in miR528 accumulation but a substantial increase of AO mRNA,resulting in enhanced plant resistance to RSV.Conversely,transgenic overexpression of SPL9 stimulated the expression of miR528 gene,hence lowering the level of AO mRNA and compromising rice defense against RSV.Importantly,gain in RSV susceptibility did not occur when SPL9 was overexpressed in mir528 loss-of-function mutants,or in transgenic rice expressing a miR528-resistant AO.Taken together,the finding of SPL9-mediated transcriptional activation of miR528 expression adds a new regulatory layer to the miR528-A0 antiviral defense pathway.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27040203)the National Natural Science Foundation of China (No.31770155)
文摘Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer(two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications(PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato.Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation(RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects.We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
基金supported by grants from the National Science Foundation of China (31170265)the Program for New Century Excellent Talents in University of the Ministry of Education of China (NCET-13-0771)the Hebei Science Fund for Distinguished Young Scholars (GCC2014063) to X.X
文摘Summary It was noted that circadian components function in plant adaptation to diurnal temperature cycles and freezing tolerance. Our genome-wide transcriptome analysis revealed that evening-phased COR27 and COR28 mainly repress the transcription of clockassociated evening genes PRRS, ELF4 and cold-responsive genes. Chromatin immunoprecipitation indicated that CCAI is recruited to the site containing EE elements of COR27 and COR28 promoters in a temperaturedependent way. Further genetic analysis shows COR28 is essential for the circadian function of PRR9 and PRRT. Together, our results support a role of COR27 and COR28 as nighttime repressors integrating circadian clock and plant cold stress responses.
基金supported by the National Natural Science Foundation of China(3121010390131123007)+2 种基金the National Basic Research Program of China(2013CB835200)the State Key Laboratory of Plant Genomics(2015B0129-01)Liya Wei was supported by the China Postdoctoral Science Foundation(2015M570170)
文摘Transposable elements(TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.
基金supported by the National Natural Science Foundation of China(31871321,31788103,31770874)Tianjin Natural Science Foundation of China(16JCZDJC33400)Tianjin Rice Industrial Technology System of China(ITTRRS2018006)。
文摘Evidence is emerging that t RNA-derived fragments(t RFs)are regulatory molecules.Studies of t RFs in plants have been based on conventional small RNA sequencing,and focused on profiling of t RF-5 and t RF-3 species.A more comprehensive and quantitative analysis of the entire t RF population is highly necessary.Here,we employ t RNA-seq and YAMAT-seq,and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants.We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed,accounting for only 1%of total t RNA abundance,while~12%of t RNA genes contribute to~80%of t RNA abundance.Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern.By characterizing the composition of a highly heterogeneous t RF population,we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions.The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products.Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.
基金supported by National Basic Research Program of China(grant Nos.2011CB9154002009CB941500)+1 种基金National Natural Science Foundation of China(grant No.30621001)the Chinese Academy of Sciences(Grant No.KSCX2-YW-N-047) to X.Cao
文摘Post-translational methylation at arginine residues is one of the most important covalent modifications of proteins, involved in a myriad of essential cellular processes in eukaryotes, such as transcriptional regulation, RNA processing, signal transduction, and DNA repair. Methylation at arginine residues is catalyzed by a family of enzymes called protein arginine methyltransferases （PRMTs）. PRMTs have been extensively studied in various taxa and there is a growing tendency to unveil their functional importance in plants. Recent studies in plants revealed that this evolutionarily conserved family of enzymes regulates essential traits including vegetative growth, flowering time, circadian cycle, and response to high medium salinity and ABA. In this review, we highlight recent advances in the field of post- translational arginine methylation with special emphasis on the roles and future prospects of this modification in plants.
基金This work was supported by the National Natural Science Foundation of China(91940000).We thank Drs.Xiaorong Zhang and Jing Hu for critical reading of this manuscript.We are sorry for the excellent works supported by the Major Research Program that are not highlighted in this comment due to space limitations.
文摘The central dogma states that genes encoded in the DNA should be first transcribed into messenger RNA(mRNA)and then translated into functional proteins(Crick,1970).This dogma has been written in numerous textbooks and learned by myriad students.However,along with the completion of the human genome project in June 2000,an astonishing fact was revealed:only 1.5%of the human genome encodes for proteins(Lander et al.,2001;Venter et al.,2001).This fact raised three fundamental questions:(i)why does the human genome have so few protein-coding genes?(ii)how to explain the apparent differences between humans and other species using the limited coding genes?(iii)what are the roles of the noncoding regions in our genome?
