In this paper, an iterative method is constructed to find the least-squares solutions of generalized Sylvester equation , where is real matrices group, and satisfies different linear constraint. By this iterative meth...In this paper, an iterative method is constructed to find the least-squares solutions of generalized Sylvester equation , where is real matrices group, and satisfies different linear constraint. By this iterative method, for any initial matrix group within a special constrained matrix set, a least squares solution group with satisfying different linear constraint can be obtained within finite iteration steps in the absence of round off errors, and the unique least norm least-squares solution can be obtained by choosing a special kind of initial matrix group. In addition, a minimization property of this iterative method is characterized. Finally, numerical experiments are reported to show the efficiency of the proposed method.展开更多
The truncated singular value decomposition has been widely used in many areas of science including engineering,and statistics,etc.In this paper,the original truncated complex singular value decomposition problem is fo...The truncated singular value decomposition has been widely used in many areas of science including engineering,and statistics,etc.In this paper,the original truncated complex singular value decomposition problem is formulated as a Riemannian optimiza-tion problem on a product of two complex Stiefel manifolds,a practical algorithm based on the generic Riemannian trust-region method of Absil et al.is presented to solve the underlying problem,which enjoys the global convergence and local superlinear conver-gence rate.Numerical experiments are provided to illustrate the efficiency of the proposed method.Comparisons with some classical Riemannian gradient-type methods,the existing Riemannian version of limited-memory BFGS algorithms in the MATLAB toolbox Manopt and the Riemannian manifold optimization library ROPTLIB,and some latest infeasible methods for solving manifold optimization problems,are also provided to show the merits of the proposed approach.展开更多
RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMO...RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.展开更多
DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation a...DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.展开更多
文摘In this paper, an iterative method is constructed to find the least-squares solutions of generalized Sylvester equation , where is real matrices group, and satisfies different linear constraint. By this iterative method, for any initial matrix group within a special constrained matrix set, a least squares solution group with satisfying different linear constraint can be obtained within finite iteration steps in the absence of round off errors, and the unique least norm least-squares solution can be obtained by choosing a special kind of initial matrix group. In addition, a minimization property of this iterative method is characterized. Finally, numerical experiments are reported to show the efficiency of the proposed method.
基金supported by the National Natural Science Foundation of China(Grant Nos.12261026,11961012,12201149)by the Natural Science Foundation of Guangxi Province(Grant Nos.2016GXNSFAA380074,2023GXNSFAA026067)+4 种基金by the Innovation Project of GUET Graduate Education(Grant No.2022YXW01)by the GUET Graduate Innovation Project(Grant No.2022YCXS142)by the Guangxi Key Laboratory of Automatic Detecting Technology and Instruments(Grant Nos.YQ23103,YQ21103,YQ22106)by the Special Fund for Science and Technological Bases and Talents of Guangxi(Grant No.2021AC06001)by the Guizhou Science and Technology Program of Projects(Grant No.ZK2021G339)。
文摘The truncated singular value decomposition has been widely used in many areas of science including engineering,and statistics,etc.In this paper,the original truncated complex singular value decomposition problem is formulated as a Riemannian optimiza-tion problem on a product of two complex Stiefel manifolds,a practical algorithm based on the generic Riemannian trust-region method of Absil et al.is presented to solve the underlying problem,which enjoys the global convergence and local superlinear conver-gence rate.Numerical experiments are provided to illustrate the efficiency of the proposed method.Comparisons with some classical Riemannian gradient-type methods,the existing Riemannian version of limited-memory BFGS algorithms in the MATLAB toolbox Manopt and the Riemannian manifold optimization library ROPTLIB,and some latest infeasible methods for solving manifold optimization problems,are also provided to show the merits of the proposed approach.
基金supported by National Natural Science Foundation of China(31770782)the Ministry of Science and Technology of China(2016YFA0503200)+1 种基金the Shenzhen Science and Technology Program(JCYJ20200109110403829 and KQTD20190929173906742)Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006)to J.D.
文摘RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.
基金the Chinese Academy of Sciences and the National Natural Science Foundation of China(31970580)to M.L.the National Key R&D Program(2016YFA0503200)+1 种基金Shenzhen Science and Technology Program(JCYJ20200109110403829 and KQTD20190929173906742)Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006)to J.D.
文摘DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.
