Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pol...Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pollen are not expressed in the sporophyte. How pollen-specific genes are down-regulated in the sporophyte has yet to be established. In this study, we have performed a bioinformatics analysis of publicly available genome-wide epigenetics data of sev- eral sporophytic tissues. By combining this analysis with DNase ! footprinting data, we assessed means by which the repression of pollen-specific genes in the Arabidopsis sporophyte is conferred. Our findings show that, in seedlings, the majority of pollen-specific genes are associated with histone-3 marked by mono- or trimethylation of Lys-27 （H3K27me1/ H3K27me3）, both of which are repressive markers for gene expression in the sporophyte. Analysis of DNase footprint profiles of pollen-specific genes in the sporophyte displayed closed chromatin proximal to the start codon. We describe a model of two-staged gene regulation in which a lack of nucleosome-free regions in promoters and histone modifications in open reading frames repress pollen-specific genes in the sporophyte.展开更多
Taraxacum kok-saghyz Rodin(TKS)is a promising alternative crop source for producing high-quality natural rubber(NR)and has become an ideal model plant for studying NR biosynthesis,regulation mechanisms,and production....Taraxacum kok-saghyz Rodin(TKS)is a promising alternative crop source for producing high-quality natural rubber(NR)and has become an ideal model plant for studying NR biosynthesis,regulation mechanisms,and production.So far,only a very limited number of functional genes related to NR biosynthesis have been identified in TKS.To achieve a systematic identification of its novel functional genes,we developed a mutant system denoted sense/antisense RNA expression(SARE)and have generated more than 8,000 transgenic TKS plants.A series of mutants with altered phenotypes,particularly changes in NR contents,were identified.To evaluate the efficiency of this library,we chose one mutant,c112,which exhibits a significant increase in NR content,for in-depth characterization.The c112 mutant arose from the sense insertion of a dormancy-associated gene1(DRM1)/auxin repressed protein(ARP)gene,which we named high natural rubber content1(HRC1).In the c112 mutant,the concentrations of NR precursors isopentenyl pyrophosphate and dimethylallyl diphosphate decreased,while geranylgeranyl diphosphate increased,suggesting that HRC1 regulates metabolic flux in NR biosynthesis.In summary,the developed TKS SARE mutant library provides valuable genetic resources for identifying key functional genes to accelerate the domestication of TKS from wild species to economic crops through molecular breeding.展开更多
Polycomb group （PcG） and trithorax group （trxG） proteins have been shown to act antagonistically to epigenetically regulate gene expression in eukaryotes. The trxG proteins counteract PcG-mediated floral repressio...Polycomb group （PcG） and trithorax group （trxG） proteins have been shown to act antagonistically to epigenetically regulate gene expression in eukaryotes. The trxG proteins counteract PcG-mediated floral repression in Arabidopsis, but their roles in other developmental processes are poorly understood. We investigated the interactions between the trxG genes, ARABIDOPSIS HOMOLOG OF TRITHORAX1 （ATX1） and ULTRAPETALA1 （ULT1）, and the PcG gene EMBRYONIC FLOWER 1 （EMF1） during early development. Unexpectedly, we found that mutations in the trxG genes failed to rescue the early-flowering phenotype of emfl mutants. Instead, emfl atxl ultl seedlings showed a novel swollen root phenotype and massive deregulation of gene expression. Greater ectopic expression of seed master regulatory genes in emfl atxl ultl triple than in emfl single mutants indicates that PcG and trxG factors together repress seed gene expression after germination. Furthermore, we found that the widespread gene derepression is asso- ciated with reduced levels of H3K27me3, an epigenetic repressive mark of gene expression, and with globally altered chromatin organization. EMF1, ATXl, and ULT1 are able to bind the chromatin of seed genes and ULT1 can physically interact with ATX1 and EMF1, suggesting that the trxG and EMF1 proteins directly associate at target gene loci for EMFl-mediated gene silencing. Thus, while ATXl, ULT1, and EMF1 interact antagonistically to regulate flowering, they work together to maintain chromatin integrity and prevent precocious seed gene expression after germination.展开更多
From mammals to plants, the Polycomb Group （PcG） machinery plays a crucial role in maintaining the repres- sion of genes that are not required in a specific differentiation status. However, the mechanism by which Pe...From mammals to plants, the Polycomb Group （PcG） machinery plays a crucial role in maintaining the repres- sion of genes that are not required in a specific differentiation status. However, the mechanism by which PeG machinery mediates gene repression is still largely unknown in plants. Compared to animals, few PcG proteins have been identi- fied in plants, not only because just some of these proteins are clearly conserved to their animal counterparts, but also because some PcG functions are carried out by plant-specific proteins, most of them as yet uncharacterized. For a long time, the apparent lack of Polycomb Repressive Complex （PRC）I components in plants was interpreted according to the idea that plants, as sessile organisms, do not need a long-term repression, as they must be able to respond rapidly to environmental signals; however, some PRC1 components have been recently identified, indicating that this may not be the case. Furthermore, new data regarding the recruitment of PcG complexes and maintenance of PcG repression in plants have revealed important differences to what has been reported so far. This review highlights recent progress in plant PcG function, focusing on the role of the putative PRC1 components.展开更多
The evolutionary conserved Polycomb Group(PcG)repressive system comprises two central protein complexes,PcG repressive complex 1(PRC1)and PRC2.These complexes,through the incorporation of histone modifications on chro...The evolutionary conserved Polycomb Group(PcG)repressive system comprises two central protein complexes,PcG repressive complex 1(PRC1)and PRC2.These complexes,through the incorporation of histone modifications on chromatin,have an essential role in the normal development of eukaryotes.In recent years,a significant effort has been made to characterize these complexes in the different kingdoms,and despite there being remarkable functional and mechanistic conservation,some key molecular principles have diverged.In this review,we discuss current views on the function of plant PcG complexes.We compare the composition of PcG complexes between animals and plants,highlight the role of recently identified plant PcG accessory proteins,and discuss newly revealed roles of known PcG partners.We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes.Finally,we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and,thus,shaping chromatin 3D architecture.展开更多
Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocyte...Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocytes is essential for precise gene repression and the acquisition of developmental competence[1–5].The ac4C modification is the third most abundant chemical modification in transcriptome[6,7].NAT10,the only known writer of ac4C,has been shown to participate in physiological and disease settings[6,8–11].However,NAT10-targeted transcripts in oocytes as well as their functions in supporting folliculogenesis are poorly understood.展开更多
In recent years,the ancient yin-yang theory has been gradually adopted by modern researchers,especially European and American scholars,and it has also been applied to modern scientific research on sleep,viruses,metabo...In recent years,the ancient yin-yang theory has been gradually adopted by modern researchers,especially European and American scholars,and it has also been applied to modern scientific research on sleep,viruses,metabolism,cancer,genes,autoimmune diseases,and so on.It is very promising and fruitful results have been reported.However,the understanding of the connotations of yin-yang theory is not sufficient and thorough enough in these studies.If we understand and apply yin-yang theory more comprehensively,it may provide us with additional potential mechanisms and research directions worthy of study.On the basis of promoting a comprehensive understanding of all three connotations of yin-yang theory,this review attempts to illustrate this theory,summarize its applications in modern scientific research,and reveal the potential research direction of modern medicine.展开更多
EMBRYONIC FLOWER （EMF） genes are required to maintain vegetative development via repression of flower homeotic genes in Arabidopsis. Removal of EMF gene function caused plants to flower upon germination, producing a...EMBRYONIC FLOWER （EMF） genes are required to maintain vegetative development via repression of flower homeotic genes in Arabidopsis. Removal of EMF gene function caused plants to flower upon germination, producing abnormal and sterile flowers. The pleiotropic effect of ernfl mutation suggests its requirement for gene programs involved in diverse developmental processes. Transgenic plants harboring EMF1 promoter：：glucuronidase （GUS） reporter gene were generated to investigate the temporal and spatial expression pattern of EMF1. These plants displayed differential GUS activity in vegetative and flower tissues, consistent with the role of EMF1 in regulating multiple gene programs. EMFI：：GUS expression pattern in emf mutants suggests organ-specific auto-regulation. Sense- and antisense （as） EMF1 cDNA were expressed under the control of stage- and tissue-specific promoters in transgenic plants. Characterization of these transgenic plants showed that EMF1 activity is required in meristematic as well as differentiating tissues to rescue emf mutant phenotype. Temporal removal or reduction of EMF1 activity in the embryo or shoot apex of wild-type seedlings was sufficient to cause early flowering and terminal flower formation in adult plants. Such reproductive cell memory is reflected in the flower MADS-box gene activity expressed prior to flowering in these early flowering plants. However, temporal removal of EMF1 activity in flower meristem did not affect flower development. Our results are consistent with EMF1＇s primary role in repressing flowering in order to allow for vegetative growth.展开更多
文摘Tissue formation, the identity of cells, and the functions they fulfill, are results of gene regulation. The male gametophyte of plants, pollen, is outstanding in this respect as several hundred genes expressed in pollen are not expressed in the sporophyte. How pollen-specific genes are down-regulated in the sporophyte has yet to be established. In this study, we have performed a bioinformatics analysis of publicly available genome-wide epigenetics data of sev- eral sporophytic tissues. By combining this analysis with DNase ! footprinting data, we assessed means by which the repression of pollen-specific genes in the Arabidopsis sporophyte is conferred. Our findings show that, in seedlings, the majority of pollen-specific genes are associated with histone-3 marked by mono- or trimethylation of Lys-27 （H3K27me1/ H3K27me3）, both of which are repressive markers for gene expression in the sporophyte. Analysis of DNase footprint profiles of pollen-specific genes in the sporophyte displayed closed chromatin proximal to the start codon. We describe a model of two-staged gene regulation in which a lack of nucleosome-free regions in promoters and histone modifications in open reading frames repress pollen-specific genes in the sporophyte.
基金supported by grants from the National Key Research and Development Program of China(2023YFA0914801)the National Natural Science Foundation of China(32000312)+1 种基金the Young Elite Scientists Sponsorship Program by CAST(2023QNRC001)the Strategic Priority Research Program of Chinese Academy of Sciences(XDA24030504 and XDC06010103)。
文摘Taraxacum kok-saghyz Rodin(TKS)is a promising alternative crop source for producing high-quality natural rubber(NR)and has become an ideal model plant for studying NR biosynthesis,regulation mechanisms,and production.So far,only a very limited number of functional genes related to NR biosynthesis have been identified in TKS.To achieve a systematic identification of its novel functional genes,we developed a mutant system denoted sense/antisense RNA expression(SARE)and have generated more than 8,000 transgenic TKS plants.A series of mutants with altered phenotypes,particularly changes in NR contents,were identified.To evaluate the efficiency of this library,we chose one mutant,c112,which exhibits a significant increase in NR content,for in-depth characterization.The c112 mutant arose from the sense insertion of a dormancy-associated gene1(DRM1)/auxin repressed protein(ARP)gene,which we named high natural rubber content1(HRC1).In the c112 mutant,the concentrations of NR precursors isopentenyl pyrophosphate and dimethylallyl diphosphate decreased,while geranylgeranyl diphosphate increased,suggesting that HRC1 regulates metabolic flux in NR biosynthesis.In summary,the developed TKS SARE mutant library provides valuable genetic resources for identifying key functional genes to accelerate the domestication of TKS from wild species to economic crops through molecular breeding.
基金This work was supported by Beijing Natural Science Foundation （grant 5182028 to L.P.）, the Agricultural Science and Technology Innovation Program, CAAS, China （to L.P.）, the National Science Foundation, USA （NSF grant lOS 0956409 to Z.R.So）, and the National Science Council, Taiwan, China （grant NSC 98-2311-B-001-001-MY3 to L.O.C.）.
文摘Polycomb group （PcG） and trithorax group （trxG） proteins have been shown to act antagonistically to epigenetically regulate gene expression in eukaryotes. The trxG proteins counteract PcG-mediated floral repression in Arabidopsis, but their roles in other developmental processes are poorly understood. We investigated the interactions between the trxG genes, ARABIDOPSIS HOMOLOG OF TRITHORAX1 （ATX1） and ULTRAPETALA1 （ULT1）, and the PcG gene EMBRYONIC FLOWER 1 （EMF1） during early development. Unexpectedly, we found that mutations in the trxG genes failed to rescue the early-flowering phenotype of emfl mutants. Instead, emfl atxl ultl seedlings showed a novel swollen root phenotype and massive deregulation of gene expression. Greater ectopic expression of seed master regulatory genes in emfl atxl ultl triple than in emfl single mutants indicates that PcG and trxG factors together repress seed gene expression after germination. Furthermore, we found that the widespread gene derepression is asso- ciated with reduced levels of H3K27me3, an epigenetic repressive mark of gene expression, and with globally altered chromatin organization. EMF1, ATXl, and ULT1 are able to bind the chromatin of seed genes and ULT1 can physically interact with ATX1 and EMF1, suggesting that the trxG and EMF1 proteins directly associate at target gene loci for EMFl-mediated gene silencing. Thus, while ATXl, ULT1, and EMF1 interact antagonistically to regulate flowering, they work together to maintain chromatin integrity and prevent precocious seed gene expression after germination.
文摘From mammals to plants, the Polycomb Group （PcG） machinery plays a crucial role in maintaining the repres- sion of genes that are not required in a specific differentiation status. However, the mechanism by which PeG machinery mediates gene repression is still largely unknown in plants. Compared to animals, few PcG proteins have been identi- fied in plants, not only because just some of these proteins are clearly conserved to their animal counterparts, but also because some PcG functions are carried out by plant-specific proteins, most of them as yet uncharacterized. For a long time, the apparent lack of Polycomb Repressive Complex （PRC）I components in plants was interpreted according to the idea that plants, as sessile organisms, do not need a long-term repression, as they must be able to respond rapidly to environmental signals; however, some PRC1 components have been recently identified, indicating that this may not be the case. Furthermore, new data regarding the recruitment of PcG complexes and maintenance of PcG repression in plants have revealed important differences to what has been reported so far. This review highlights recent progress in plant PcG function, focusing on the role of the putative PRC1 components.
基金This work was supported by a PID2019-106664GB-I00 grant from the Spanish Ministry of Science and Innovation.
文摘The evolutionary conserved Polycomb Group(PcG)repressive system comprises two central protein complexes,PcG repressive complex 1(PRC1)and PRC2.These complexes,through the incorporation of histone modifications on chromatin,have an essential role in the normal development of eukaryotes.In recent years,a significant effort has been made to characterize these complexes in the different kingdoms,and despite there being remarkable functional and mechanistic conservation,some key molecular principles have diverged.In this review,we discuss current views on the function of plant PcG complexes.We compare the composition of PcG complexes between animals and plants,highlight the role of recently identified plant PcG accessory proteins,and discuss newly revealed roles of known PcG partners.We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes.Finally,we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and,thus,shaping chromatin 3D architecture.
基金supported by the National Key Research and Development Program of China(2021YFC2700100)the Natural Science Foundation of Zhejiang Province(LD22C060001)+2 种基金the National Natural Science Foundation of China(31930031)the fellowship of China National Postdoctoral Program for Innovative Talents(BX20230031)Beijing Natural Science Foundation(7244435).
文摘Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocytes is essential for precise gene repression and the acquisition of developmental competence[1–5].The ac4C modification is the third most abundant chemical modification in transcriptome[6,7].NAT10,the only known writer of ac4C,has been shown to participate in physiological and disease settings[6,8–11].However,NAT10-targeted transcripts in oocytes as well as their functions in supporting folliculogenesis are poorly understood.
基金Supported by the National Key R&D Program of China(No.2020YFC2003100,No.2020YFC2003103)。
文摘In recent years,the ancient yin-yang theory has been gradually adopted by modern researchers,especially European and American scholars,and it has also been applied to modern scientific research on sleep,viruses,metabolism,cancer,genes,autoimmune diseases,and so on.It is very promising and fruitful results have been reported.However,the understanding of the connotations of yin-yang theory is not sufficient and thorough enough in these studies.If we understand and apply yin-yang theory more comprehensively,it may provide us with additional potential mechanisms and research directions worthy of study.On the basis of promoting a comprehensive understanding of all three connotations of yin-yang theory,this review attempts to illustrate this theory,summarize its applications in modern scientific research,and reveal the potential research direction of modern medicine.
文摘EMBRYONIC FLOWER （EMF） genes are required to maintain vegetative development via repression of flower homeotic genes in Arabidopsis. Removal of EMF gene function caused plants to flower upon germination, producing abnormal and sterile flowers. The pleiotropic effect of ernfl mutation suggests its requirement for gene programs involved in diverse developmental processes. Transgenic plants harboring EMF1 promoter：：glucuronidase （GUS） reporter gene were generated to investigate the temporal and spatial expression pattern of EMF1. These plants displayed differential GUS activity in vegetative and flower tissues, consistent with the role of EMF1 in regulating multiple gene programs. EMFI：：GUS expression pattern in emf mutants suggests organ-specific auto-regulation. Sense- and antisense （as） EMF1 cDNA were expressed under the control of stage- and tissue-specific promoters in transgenic plants. Characterization of these transgenic plants showed that EMF1 activity is required in meristematic as well as differentiating tissues to rescue emf mutant phenotype. Temporal removal or reduction of EMF1 activity in the embryo or shoot apex of wild-type seedlings was sufficient to cause early flowering and terminal flower formation in adult plants. Such reproductive cell memory is reflected in the flower MADS-box gene activity expressed prior to flowering in these early flowering plants. However, temporal removal of EMF1 activity in flower meristem did not affect flower development. Our results are consistent with EMF1＇s primary role in repressing flowering in order to allow for vegetative growth.
