Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent years.The use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer u...Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent years.The use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental pollution.Organic fertilizer is a promising way to improve soil quality and sustain high yields.However,most studies focus on the effect of animal-based organic fertilizers.The effects of different ratios of plantbased organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been reported.Therefore,a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield,nitrogen use efficiency(NUE),and anthocyanin content of two colored rice varieties in a tropical region in China.The experimental treatments included no nitrogen fertilization(T1),100% inorganic nitrogen fertilizer(T2),30%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T3),60%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T4),and 100% plantbased organic fertilizer(T5).The total nitrogen provided to all the treatments except T1 was the same at 120 kg ha-1.Our results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with T2.On average,grain yields were increased by 9 and 8%,while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years,respectively,as compared with T2.Further study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physiochemical properties,and thus increased the rice grain yield,in the subsequent seasons.The highest grain yield of the subsequent rice crop was observed under the T5 treatment.Our results suggested that the application of plantbased organic fertilizers can sustain the production of colored rice with high anthocyanin content in tropical regions,which is beneficial in reconciling the relationship between rice production and environmental protection.展开更多
The emergence of single-cell genomic and transcriptomic sequencing accelerates the development of single-cell epigenomic technologies,providing an unprecedented opportunity for decoding cell fate decisions largely enc...The emergence of single-cell genomic and transcriptomic sequencing accelerates the development of single-cell epigenomic technologies,providing an unprecedented opportunity for decoding cell fate decisions largely encoded in the epigenome.Recent advances in single-cell multimodality epigenomic technologies facilitate directly interrogating the reg-ulatory relationship between multi-layer molecular information in the same cell.In this review,we discuss recent progress in development of single-cell multimodality epigenomic technologies and applications in elucidating cellular diversifications in development and diseases,with a focus on protein-DNA interactomics and regulatory links between epigenome and tran-scriptome.Further,we provide perspective on the future direction of single-cell multiomics tool development as well as challenges facing ahead.展开更多
The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions.However,the molecular machinery underlying these hierarchically organized three-dim...The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions.However,the molecular machinery underlying these hierarchically organized three-dimensional(3D)chromatin architecture and dynamics remains poorly understood.Here by combining imaging and sequencing,we studied the role of lamin B1 in chromatin architecture and dynamics.We found that lamin B1 depletion leads to detachment of lamina-associated domains(LADs)from the nuclear periphery accompanied with global chromatin redistribution and decompaction.Consequently,the interchromosomal as well as inter-compartment interactions are increased,but the structure of topologically associating domains(TADs)is not affected.Using live-cell genomic loci tracking,we further proved that depletion of lamin B1 leads to increased chromatin dynamics,owing to chromatin decompaction and redistribution toward nucleoplasm.Taken together,our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance,chromatin compaction,genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics,supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.展开更多
To form fully functional four-chambered structure,mammalian heart development undergoes a transient finger-shaped trabeculae,crucial for efficient contraction and exchange for gas and nutrient.Although its development...To form fully functional four-chambered structure,mammalian heart development undergoes a transient finger-shaped trabeculae,crucial for efficient contraction and exchange for gas and nutrient.Although its developmental origin and direct relevance to congenital heart disease has been studied extensively,the time-resolved cellular mechanism underlying hypotrabeculation remains elusive.Here,we employed in toto live imaging and reconstructed the holistic cell lineages and cellular behavior landscape of control and hypotrabeculed hearts of mouse embryos from E9.5 for up to 24 h.Compared to control,hypotrabeculation in ErbB2 mutants arose mainly through dual mechanisms:both reduced proliferation of trabecular cardiomyocytes from early cell fate segregation and markedly impaired oriented cell division and migration.Further examination of mosaic mutant hearts confirmed alterations in cellular behaviors in a cell autonomous manner.Thus,our work offers a framework for continuous live imaging and digital cell lineage analysis to better understand subtle pathological alterations in congenital heart disease.展开更多
基金supported by the National Natural Science Foundation of China(32060430 and 31971840)the Research Initiation Fund of Hainan University,China(KYQD(ZR)19104)。
文摘Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent years.The use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental pollution.Organic fertilizer is a promising way to improve soil quality and sustain high yields.However,most studies focus on the effect of animal-based organic fertilizers.The effects of different ratios of plantbased organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been reported.Therefore,a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield,nitrogen use efficiency(NUE),and anthocyanin content of two colored rice varieties in a tropical region in China.The experimental treatments included no nitrogen fertilization(T1),100% inorganic nitrogen fertilizer(T2),30%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T3),60%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T4),and 100% plantbased organic fertilizer(T5).The total nitrogen provided to all the treatments except T1 was the same at 120 kg ha-1.Our results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with T2.On average,grain yields were increased by 9 and 8%,while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years,respectively,as compared with T2.Further study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physiochemical properties,and thus increased the rice grain yield,in the subsequent seasons.The highest grain yield of the subsequent rice crop was observed under the T5 treatment.Our results suggested that the application of plantbased organic fertilizers can sustain the production of colored rice with high anthocyanin content in tropical regions,which is beneficial in reconciling the relationship between rice production and environmental protection.
基金supported by the National Key Research and Development Program of China(2021YFA1100101 and 2017YFA0103402)the National Natural Science Foundation of China(32025015 and 31771607)the Peking-Tsinghua Center for Life Sciences.
文摘The emergence of single-cell genomic and transcriptomic sequencing accelerates the development of single-cell epigenomic technologies,providing an unprecedented opportunity for decoding cell fate decisions largely encoded in the epigenome.Recent advances in single-cell multimodality epigenomic technologies facilitate directly interrogating the reg-ulatory relationship between multi-layer molecular information in the same cell.In this review,we discuss recent progress in development of single-cell multimodality epigenomic technologies and applications in elucidating cellular diversifications in development and diseases,with a focus on protein-DNA interactomics and regulatory links between epigenome and tran-scriptome.Further,we provide perspective on the future direction of single-cell multiomics tool development as well as challenges facing ahead.
基金This work is supported by grants from National Key R&D Program of China,No.2017YFA0505302the National Science Foundation of China 21573013,21825401 for Y.S.+1 种基金Chinese National Key Projects of Research and Development,No.2016YFA0100103,Peking-Tsinghua Center for Life SciencesNational Natural Science Foundation of China Key Research Grant 31871266 for C.L。
文摘The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions.However,the molecular machinery underlying these hierarchically organized three-dimensional(3D)chromatin architecture and dynamics remains poorly understood.Here by combining imaging and sequencing,we studied the role of lamin B1 in chromatin architecture and dynamics.We found that lamin B1 depletion leads to detachment of lamina-associated domains(LADs)from the nuclear periphery accompanied with global chromatin redistribution and decompaction.Consequently,the interchromosomal as well as inter-compartment interactions are increased,but the structure of topologically associating domains(TADs)is not affected.Using live-cell genomic loci tracking,we further proved that depletion of lamin B1 leads to increased chromatin dynamics,owing to chromatin decompaction and redistribution toward nucleoplasm.Taken together,our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance,chromatin compaction,genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics,supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.
基金the National Basic Research Program of China(Grants No.2019YFA0801802 and 2017YFA0103402)the National Natural Science Foundation of China(Grants No.32025015 and 31771607)the Peking-Tsinghua Center for Life Sciences,and the 1000 Youth Talents Program of China.We thank the Confocal LSM 710 Core at National Center for Protein Sciences at Peking University for technical help.
文摘To form fully functional four-chambered structure,mammalian heart development undergoes a transient finger-shaped trabeculae,crucial for efficient contraction and exchange for gas and nutrient.Although its developmental origin and direct relevance to congenital heart disease has been studied extensively,the time-resolved cellular mechanism underlying hypotrabeculation remains elusive.Here,we employed in toto live imaging and reconstructed the holistic cell lineages and cellular behavior landscape of control and hypotrabeculed hearts of mouse embryos from E9.5 for up to 24 h.Compared to control,hypotrabeculation in ErbB2 mutants arose mainly through dual mechanisms:both reduced proliferation of trabecular cardiomyocytes from early cell fate segregation and markedly impaired oriented cell division and migration.Further examination of mosaic mutant hearts confirmed alterations in cellular behaviors in a cell autonomous manner.Thus,our work offers a framework for continuous live imaging and digital cell lineage analysis to better understand subtle pathological alterations in congenital heart disease.
