Grain protein content(GPC)is an indicator of cereal nutritional quality.Identification of genes involved in the regulation of GPC provides targets for molecular breeding for crop protein quality.We characterized a mai...Grain protein content(GPC)is an indicator of cereal nutritional quality.Identification of genes involved in the regulation of GPC provides targets for molecular breeding for crop protein quality.We characterized a maize gene encoding the putative amino acid transporter ZmAAP6,a gene expressed mainly in immature seeds,especially in the basal endosperm transfer layer.Total protein and zein contents were decreased in ZmAAP6 null mutants and increased in ZmAAP6 overexpression(OE)lines,consistent with their changed in the size of protein bodies.Metabolic and transcriptomic analysis supported the regulatory role of ZmAAP6 in amino acid transportation.These results suggest that ZmAAP6 functions as a positive regulator of GPC in maize,shedding new light on the genetic basis of GPC regulation.展开更多
The membrane trafficking of cation-independent mannose 6-phosphate receptor（CI-M6PR） between the transGolgi network（TGN） and endosomal compartments is not only critical for maintaining lysosomal function but also ...The membrane trafficking of cation-independent mannose 6-phosphate receptor（CI-M6PR） between the transGolgi network（TGN） and endosomal compartments is not only critical for maintaining lysosomal function but also a well-known event for understanding molecular and cellular mechanisms in retrograde endosome-to-TGN trafficking.Although it has been well established in literature that the C-terminus of bovine CI-M6PR determines its retrograde trafficking,it remains unclear whether the luminal domain of the protein plays a role on these sorting events.In this study,we found that partial deletion of luminal domain of human CI-M6PR mistargeted the mutant protein to nonTGN compartments.Moreover,replacing the luminal domain of both bovine and human CI-M6PR with that from irrelevant membrane proteins such as CD8 or Tac also altered the TGN targeting of the chimeric proteins.On the other hand,only short sequence from HA fused with the transmembrane domain and C-terminus of the receptor,HA-hCIM6PR-tail,resulted in its preferential targeting to TGN as for the full length receptor,strongly suggesting that sorting of the receptor may be influenced by luminal sequence.Furthermore,using this luminal truncated form of HA-hCIM6 PR as a model cargo,we found that the trafficking of the chimeric protein was regulated by the retromer complex through interacting with SNX5.In conclusion,our study strongly suggested that the disrupted luminal domain from hCI-M6PR or other irrelevant membrane proteins interfere with the process of membrane trafficking and TGN targeting of CI-M6PR.展开更多
The LGS1(Large grain size 1)gene,also known as GS2/GL2/Os GRF4,is involved in regulating grain size and quality in rice,but the mechanism governing grain size has not been elucidated.We performed transcriptomic,proteo...The LGS1(Large grain size 1)gene,also known as GS2/GL2/Os GRF4,is involved in regulating grain size and quality in rice,but the mechanism governing grain size has not been elucidated.We performed transcriptomic,proteomic,and phosphoproteomic analyses of young rice panicles in Samba(a wild-type cultivar with extra-small grain)and NIL-LGS1(a nearly isogenic line of LGS1 with large grain in the Samba genetic background)at three developmental stages(4–6)to identify internal dynamic functional networks determining grain size that are mediated by LGS1.Differentially expressed proteins formed seven highly functionally correlated clusters.The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice.In stage 5,16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated,and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks.Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development.Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level,and this analysis also suggested a regulatory mechanism,regulation of protein translation levels,in the biological process that extends from transcript to protein to the development of grain.Functional analysis suggested that biological processes including MAPK signaling,calcium signaling,cell proliferation,cell wall,energy metabolism,hormone pathway,and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length.Thus,LGS1-mediated regulation of grain size is affected by dynamic transcriptional,posttranscriptional,translational and posttranslational changes.展开更多
The bromodomain-containing protein 9(BRD9)is a core subunit of mammalian SWI/SNF chromatin remodeling complex termed ncBAF.BRD9 has emerged as a potential target for anticancer drugs,particularly in the treatment of a...The bromodomain-containing protein 9(BRD9)is a core subunit of mammalian SWI/SNF chromatin remodeling complex termed ncBAF.BRD9 has emerged as a potential target for anticancer drugs,particularly in the treatment of acute myeloid leukemia(AML).Herein,we reported 10m(Y22073)and 10t as new BRD9 selective bromodomain inhibitors.Crystallographic studies revealed that the key active imidazolyl group discovered from structure-activity relationship(SAR)can induce Phe163 flipping and significantly enhance the cellular potency of the compounds,making 10m the first BRD9 selective inhibitor with significant cellular activity against AML cells.We also validated the critical role of imidazolyl groups by modifying existing BRD9 inhibitors.The representative compounds 10m and 10t demonstrated potent binding affinity,outstanding selectivity toward BRD9 bromodomain,and significantly inhibited the proliferation of AML cell lines.10m also showed good metabolic stability,solubility and pharmacokinetic properties.Additionally,oral administration of compounds 10m and 10t exhibited potent anti-tumor efficacy in the MV4-11 xenograft mouse model.The potent,selective,and orally available BRD9 bromodomain inhibitors may address the challenges of weak cellular activity and limited phenotypic efficacy faced by BRD9 inhibitors,and serve as new lead compounds for the development of anticancer agents for the treatment of AML.展开更多
The Saccharum complex is known for having one of the most intricate genomes among plants,primarily originating from autopolyploidization.Erianthus rockii(E.rockii),an allotetraploid species within the Sac-charum compl...The Saccharum complex is known for having one of the most intricate genomes among plants,primarily originating from autopolyploidization.Erianthus rockii(E.rockii),an allotetraploid species within the Sac-charum complex,serves as a key phylogenetic reference for studying polyploidization in Saccharum.Here,we present the gap-closed genome of E.rockii and investigate the origin and evolution of the Saccharum complex.The Saccharum complex species are thought to have originated from chromosome fusion and polyploidization events that trace back to a diploid common ancestor,approximately 5.1 million years ago.Comparative genomics analyses reveal the driving forces behind the rapid mobility of centromeres,as well as the fates of multiple centromeres after chromosome fusion events.Differences in transposable elements and DNA methylation,structural variations,reorganizations in three-dimensional chromatin ar-chitecture,and expression biases offer insights into the concerted diploidization process and the interplay between the A and B sub-genomes of E.rockii.Population genetics and spatiotemporal distribution data suggest that Saccharum lineages originated in the pan-Himalayan regions from a diploid last common ancestor.Dynamic processes such as chromosome reduction,autopolyploidization,and allopolyploidization,likely driven by climate change,contributed to the spread and emergence of the Saccharum lineage.Our findings highlight the evolution of polyploid genomes and provide a fundamental genetic resource for the breeding and genetic improvement of sugarcane.展开更多
Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the And...Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the Andropogoneae remains unresolved.Here,we generated a high-quality genome assembly of coix comprising～1.73 Gb with 44485 predicted protein-coding genes.We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome,despite its drastic genome expansion(～2.3-fold)due mainly to the activity of transposable elements.Phylogenetic analysis revealed that coix diverged with sorghum～10.41 million years ago,which was～1.49 million years later than the divergence between sorghum and maize.Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars,and suggested that coix experienced a strong genetic bottleneck,resulting in the loss of about half of the genetic diversity during domestication,even though many traits have remained undomesticated.Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage,but also an important resource that will greatly benefit molecular breeding of this important crop.展开更多
JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a ...JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl millet.We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO.Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA methylation.The three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A subgenome.We investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic efficiency.NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield.Taken together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses.展开更多
The fetal liver(FL)is the key erythropoietic organ during fetal development,but knowledge on human FL erythropoiesis is very limited.In this study,we sorted primary erythroblasts from FL cells and performed RNA sequen...The fetal liver(FL)is the key erythropoietic organ during fetal development,but knowledge on human FL erythropoiesis is very limited.In this study,we sorted primary erythroblasts from FL cells and performed RNA sequencing(RNA-seq)analyses.We found that temporal gene expression patterns reflected changes in function during primary human FL terminal erythropoiesis.Notably,the expression of genes enriched in proteolysis and autophagy was up-regulated in orthochromatic erythroblasts(OrthoEs),suggesting the involvement of these pathways in enucleation.We also performed RNA-seq of in vitro cultured erythroblasts derived from FL CD34+cells.Comparison of transcriptomes between the primary and cultured erythroblasts revealed significant differences,indicating impacts of the culture system on gene expression.Notably,the expression of lipid metabolism-related genes was increased in cultured erythroblasts.We further immortalized erythroid cell lines from FL and cord blood(CB)CD34+cells(FL-iEry and CB-iEry,respectively).FL-iEry and CB-iEry were immortalized at the proerythroblast stage and can be induced to differentiate into OrthoEs,but their enucleation ability was very low.Comparison of the transcriptomes between OrthoEs with and without enucleation capability revealed the down-regulation of pathways involved in chromatin organization and mitophagy in OrthoEs without enucleation capacity,indicating that defects in chromatin organization and mitophagy contribute to the inability of OrthoEs to enucleate.Additionally,the expression of HBE1,HBZ,and HBG2 was up-regulated in FL-iEry compared with CB-iEry,and such up-regulation was accompanied by down-regulated expression of BCL11A and up-regulated expression of LIN28B and IGF2BP1.Our study provides new insights into human FL erythropoiesis and rich resources for future studies.展开更多
基金supported by the 2022 Research Program of Sanya Yazhou Bay Science and Technology City(SYND-2022-10 to Wei Huang and SYND-2022-03 to Weiwei Jin)。
文摘Grain protein content(GPC)is an indicator of cereal nutritional quality.Identification of genes involved in the regulation of GPC provides targets for molecular breeding for crop protein quality.We characterized a maize gene encoding the putative amino acid transporter ZmAAP6,a gene expressed mainly in immature seeds,especially in the basal endosperm transfer layer.Total protein and zein contents were decreased in ZmAAP6 null mutants and increased in ZmAAP6 overexpression(OE)lines,consistent with their changed in the size of protein bodies.Metabolic and transcriptomic analysis supported the regulatory role of ZmAAP6 in amino acid transportation.These results suggest that ZmAAP6 functions as a positive regulator of GPC in maize,shedding new light on the genetic basis of GPC regulation.
基金supported by the National Nature Science Foundation of China to Y.Liu(Grant No.31371436 and No.8157051134)Y.Huang(Grant No.81500678)the laboratory start-up grant from Nanjing Medical University to Y.Liu
文摘The membrane trafficking of cation-independent mannose 6-phosphate receptor（CI-M6PR） between the transGolgi network（TGN） and endosomal compartments is not only critical for maintaining lysosomal function but also a well-known event for understanding molecular and cellular mechanisms in retrograde endosome-to-TGN trafficking.Although it has been well established in literature that the C-terminus of bovine CI-M6PR determines its retrograde trafficking,it remains unclear whether the luminal domain of the protein plays a role on these sorting events.In this study,we found that partial deletion of luminal domain of human CI-M6PR mistargeted the mutant protein to nonTGN compartments.Moreover,replacing the luminal domain of both bovine and human CI-M6PR with that from irrelevant membrane proteins such as CD8 or Tac also altered the TGN targeting of the chimeric proteins.On the other hand,only short sequence from HA fused with the transmembrane domain and C-terminus of the receptor,HA-hCIM6PR-tail,resulted in its preferential targeting to TGN as for the full length receptor,strongly suggesting that sorting of the receptor may be influenced by luminal sequence.Furthermore,using this luminal truncated form of HA-hCIM6 PR as a model cargo,we found that the trafficking of the chimeric protein was regulated by the retromer complex through interacting with SNX5.In conclusion,our study strongly suggested that the disrupted luminal domain from hCI-M6PR or other irrelevant membrane proteins interfere with the process of membrane trafficking and TGN targeting of CI-M6PR.
基金the National Key Research and Development Program of China(2017YFD0100103)the Seed Industry Innovation and Industrialization Project of Fujian Province(fjzycxny2017004,zycxny2021004)+1 种基金the Program on Technology of Fujian Province(2020NZ08016,2020N0049)the Open Program of State Key Laboratory of Rice Biology of China(170101)。
文摘The LGS1(Large grain size 1)gene,also known as GS2/GL2/Os GRF4,is involved in regulating grain size and quality in rice,but the mechanism governing grain size has not been elucidated.We performed transcriptomic,proteomic,and phosphoproteomic analyses of young rice panicles in Samba(a wild-type cultivar with extra-small grain)and NIL-LGS1(a nearly isogenic line of LGS1 with large grain in the Samba genetic background)at three developmental stages(4–6)to identify internal dynamic functional networks determining grain size that are mediated by LGS1.Differentially expressed proteins formed seven highly functionally correlated clusters.The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice.In stage 5,16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated,and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks.Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development.Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level,and this analysis also suggested a regulatory mechanism,regulation of protein translation levels,in the biological process that extends from transcript to protein to the development of grain.Functional analysis suggested that biological processes including MAPK signaling,calcium signaling,cell proliferation,cell wall,energy metabolism,hormone pathway,and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length.Thus,LGS1-mediated regulation of grain size is affected by dynamic transcriptional,posttranscriptional,translational and posttranslational changes.
基金supported in part by grants from the National Key R&D Program of China(Nos.2022YFE0210600 and 2019YFE0123700)the National Natural Science Foundation of China(Nos.22307116 and 82173745)+4 种基金the Guangdong Basic and Applied Basic Research Foundation(No.2024A1515012186,China)the Science and Technology Program of Guangzhou(No.2025A04J4520,China)Guangdong Province Grant for Belt and Road Joint Laboratory(No.2022B1212050004,China)the Youth Innovation Promotion Association CAS(No.2023372,China)the Basic Research Project of Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences(Nos.GIBHBRP24-03 and GIBHBRP24-04,China).
文摘The bromodomain-containing protein 9(BRD9)is a core subunit of mammalian SWI/SNF chromatin remodeling complex termed ncBAF.BRD9 has emerged as a potential target for anticancer drugs,particularly in the treatment of acute myeloid leukemia(AML).Herein,we reported 10m(Y22073)and 10t as new BRD9 selective bromodomain inhibitors.Crystallographic studies revealed that the key active imidazolyl group discovered from structure-activity relationship(SAR)can induce Phe163 flipping and significantly enhance the cellular potency of the compounds,making 10m the first BRD9 selective inhibitor with significant cellular activity against AML cells.We also validated the critical role of imidazolyl groups by modifying existing BRD9 inhibitors.The representative compounds 10m and 10t demonstrated potent binding affinity,outstanding selectivity toward BRD9 bromodomain,and significantly inhibited the proliferation of AML cell lines.10m also showed good metabolic stability,solubility and pharmacokinetic properties.Additionally,oral administration of compounds 10m and 10t exhibited potent anti-tumor efficacy in the MV4-11 xenograft mouse model.The potent,selective,and orally available BRD9 bromodomain inhibitors may address the challenges of weak cellular activity and limited phenotypic efficacy faced by BRD9 inhibitors,and serve as new lead compounds for the development of anticancer agents for the treatment of AML.
基金supported by the National Key Research and Development Program(2024YFF1000800)the National Natural Science Foundation of China(32272196 and U24A20387)+4 种基金the Guangxi Science and Technology Major Project(AA24206023,AB24153006 and AA24206006)the Guangxi Bagui Scholars Talent Support Program(GXR-6BG2424009)the Sugarcane Research Foundation of Guangxi University(grant no.2022GZB007)the Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation(GZC20230580)the National Key Research and Development Program(2021YFF1000104 and 2021YFF1000101).
文摘The Saccharum complex is known for having one of the most intricate genomes among plants,primarily originating from autopolyploidization.Erianthus rockii(E.rockii),an allotetraploid species within the Sac-charum complex,serves as a key phylogenetic reference for studying polyploidization in Saccharum.Here,we present the gap-closed genome of E.rockii and investigate the origin and evolution of the Saccharum complex.The Saccharum complex species are thought to have originated from chromosome fusion and polyploidization events that trace back to a diploid common ancestor,approximately 5.1 million years ago.Comparative genomics analyses reveal the driving forces behind the rapid mobility of centromeres,as well as the fates of multiple centromeres after chromosome fusion events.Differences in transposable elements and DNA methylation,structural variations,reorganizations in three-dimensional chromatin ar-chitecture,and expression biases offer insights into the concerted diploidization process and the interplay between the A and B sub-genomes of E.rockii.Population genetics and spatiotemporal distribution data suggest that Saccharum lineages originated in the pan-Himalayan regions from a diploid last common ancestor.Dynamic processes such as chromosome reduction,autopolyploidization,and allopolyploidization,likely driven by climate change,contributed to the spread and emergence of the Saccharum lineage.Our findings highlight the evolution of polyploid genomes and provide a fundamental genetic resource for the breeding and genetic improvement of sugarcane.
基金supported by the National Key Research and Development Program(2016YFD0101003)of China and the National Natural Science Foundation of China(91735305,91435206,91635303-3,31701430 and 31421005).
文摘Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the Andropogoneae remains unresolved.Here,we generated a high-quality genome assembly of coix comprising～1.73 Gb with 44485 predicted protein-coding genes.We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome,despite its drastic genome expansion(～2.3-fold)due mainly to the activity of transposable elements.Phylogenetic analysis revealed that coix diverged with sorghum～10.41 million years ago,which was～1.49 million years later than the divergence between sorghum and maize.Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars,and suggested that coix experienced a strong genetic bottleneck,resulting in the loss of about half of the genetic diversity during domestication,even though many traits have remained undomesticated.Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage,but also an important resource that will greatly benefit molecular breeding of this important crop.
基金supported by grants from the Major Special Project of Fujian Province(2021NZ029009)the Natural Science foundation of Fujian Province(2019J01665).
文摘JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl millet.We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO.Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA methylation.The three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A subgenome.We investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic efficiency.NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield.Taken together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses.
基金supported by the Science and Technology Research Project of Henan(Grant No.232102311003)the National Natural Science Foundation of China(Grant No.U1804282)。
文摘The fetal liver(FL)is the key erythropoietic organ during fetal development,but knowledge on human FL erythropoiesis is very limited.In this study,we sorted primary erythroblasts from FL cells and performed RNA sequencing(RNA-seq)analyses.We found that temporal gene expression patterns reflected changes in function during primary human FL terminal erythropoiesis.Notably,the expression of genes enriched in proteolysis and autophagy was up-regulated in orthochromatic erythroblasts(OrthoEs),suggesting the involvement of these pathways in enucleation.We also performed RNA-seq of in vitro cultured erythroblasts derived from FL CD34+cells.Comparison of transcriptomes between the primary and cultured erythroblasts revealed significant differences,indicating impacts of the culture system on gene expression.Notably,the expression of lipid metabolism-related genes was increased in cultured erythroblasts.We further immortalized erythroid cell lines from FL and cord blood(CB)CD34+cells(FL-iEry and CB-iEry,respectively).FL-iEry and CB-iEry were immortalized at the proerythroblast stage and can be induced to differentiate into OrthoEs,but their enucleation ability was very low.Comparison of the transcriptomes between OrthoEs with and without enucleation capability revealed the down-regulation of pathways involved in chromatin organization and mitophagy in OrthoEs without enucleation capacity,indicating that defects in chromatin organization and mitophagy contribute to the inability of OrthoEs to enucleate.Additionally,the expression of HBE1,HBZ,and HBG2 was up-regulated in FL-iEry compared with CB-iEry,and such up-regulation was accompanied by down-regulated expression of BCL11A and up-regulated expression of LIN28B and IGF2BP1.Our study provides new insights into human FL erythropoiesis and rich resources for future studies.
