Falong Lu

Publications of Falong Lu

• Crystal structure of the plant epigenetic protein arginine methyltransferase 10.

  Authors: Yuan Cheng, Monica Frazier, Falong Lu, Xiaofeng Cao, Matthew R Redinbo

  Journal of molecular biology. 11/2011; 414(1):106-22.

  Protein arginine methyltransferase 10 (PRMT10) is a type I arginine methyltransferase that is essential for regulating flowering time in Arabidopsis thaliana. We present a 2.6 Å resolution crystalProtein arginine methyltransferase 10 (PRMT10) is a type I arginine methyltransferase that is essential for regulating flowering time in Arabidopsis thaliana. We present a 2.6 Å resolution crystal structure of A. thaliana PRMT 10 (AtPRMT10) in complex with a reaction product, S-adenosylhomocysteine. The structure reveals a dimerization arm that is 12-20 residues longer than PRMT structures elucidated previously; as a result, the essential AtPRMT10 dimer exhibits a large central cavity and a distinctly accessible active site. We employ molecular dynamics to examine how dimerization facilitates AtPRMT10 motions necessary for activity, and we show that these motions are conserved in other PRMT enzymes. Finally, functional data reveal that the 10 N-terminal residues of AtPRMT10 influence substrate specificity, and that enzyme activity is dependent on substrate protein sequences distal from the methylation site. Taken together, these data provide insights into the molecular mechanism of AtPRMT10, as well as other members of the PRMT family of enzymes. They highlight differences between AtPRMT10 and other PRMTs but also indicate that motions are a conserved element of PRMT function.

• Arabidopsis REF6 is a histone H3 lysine 27 demethylase.

  Authors: Falong Lu, Xia Cui, Shuaibin Zhang, Thomas Jenuwein, Xiaofeng Cao

  Nature genetics. 01/2011; 43(7):715-9.

  Polycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation. There is evidence that H3K27me3 is actively removed inPolycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation. There is evidence that H3K27me3 is actively removed in plants, but it is not known how this occurs. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), also known as Jumonji domain-containing protein 12 (JMJ12), specifically demethylates H3K27me3 and H3K27me2, whereas its metazoan counterparts, the KDM4 proteins, are H3K9 and H3K36 demethylases. Plants overexpressing REF6 resembled mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicated that REF6 acts downstream of H3K27me3 methyltransferases. Mutations in REF6 caused ectopic and increased H3K27me3 level and decreased mRNA expression of hundreds of genes involved in regulating developmental patterning and responses to various stimuli. Our work shows that plants and metazoans use conserved mechanisms to regulate H3K27me3 dynamics but use distinct subfamilies of enzymes.

• Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.

  Authors: Soichi Inagaki, Asuka Miura-Kamio, Yasukazu Nakamura, Falong Lu, Xia Cui, Xiaofeng Cao, Hiroshi Kimura, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 10/2010; 29(20):3496-506.

  In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical forIn diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.

• Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing.

  Authors: Xian Deng, Lianfeng Gu, Chunyan Liu, Tiancong Lu, Falong Lu, Zhike Lu, Peng Cui, Yanxi Pei, Baichen Wang, Songnian Hu, Xiaofeng Cao

  Proceedings of the National Academy of Sciences of the United States of America. 10/2010; 107(44):19114-9.

  Protein arginine methylation, one of the most abundant and important posttranslational modifications, is involved in a multitude of biological processes in eukaryotes, such as transcriptionalProtein arginine methylation, one of the most abundant and important posttranslational modifications, is involved in a multitude of biological processes in eukaryotes, such as transcriptional regulation and RNA processing. Symmetric arginine dimethylation is required for snRNP biogenesis and is assumed to be essential for pre-mRNA splicing; however, except for in vitro evidence, whether it affects splicing in vivo remains elusive. Mutation in an Arabidopsis symmetric arginine dimethyltransferase, AtPRMT5, causes pleiotropic developmental defects, including late flowering, but the underlying molecular mechanism is largely unknown. Here we show that AtPRMT5 methylates a wide spectrum of substrates, including some RNA binding or processing factors and U snRNP AtSmD1, D3, and AtLSm4 proteins, which are involved in RNA metabolism. RNA-seq analyses reveal that AtPRMT5 deficiency causes splicing defects in hundreds of genes involved in multiple biological processes. The splicing defects are identified in transcripts of several RNA processing factors involved in regulating flowering time. In particular, splicing defects at the flowering regulator flowering locus KH domain (FLK) in atprmt5 mutants reduce its functional transcript and protein levels, resulting in the up-regulation of a flowering repressor flowering locus C (FLC) and consequently late flowering. Taken together, our findings uncover an essential role for arginine methylation in proper pre-mRNA splicing that impacts diverse developmental processes.

• JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis.

  Authors: Falong Lu, Xia Cui, Shuaibin Zhang, Chunyan Liu, Xiaofeng Cao

  Cell research. 02/2010; 20(3):387-90.

• Histone methylation in higher plants.

  Authors: Chunyan Liu, Falong Lu, Xia Cui, Xiaofeng Cao

  Annual review of plant biology. 01/2010; 61:395-420.

  Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. TheHistone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.

• Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice.

  Authors: Falong Lu, Guanglin Li, Xia Cui, Chunyan Liu, Xiu-Jie Wang, Xiaofeng Cao

  Journal of integrative plant biology. 08/2008; 50(7):886-96.

  Histone methylation homeostasis is achieved by controlling the balance between methylation and demethylation to maintain chromatin function and developmental regulation. In animals, a conservedHistone 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.

• Regulation of flowering time by the protein arginine methyltransferase AtPRMT10.

  Authors: Lifang Niu, Falong Lu, Yanxi Pei, Chunyan Liu, Xiaofeng Cao

  EMBO reports. 01/2008; 8(12):1190-5.

  In plants, histone H3 lysine methyltransferases are important in gene silencing and developmental regulation; however, the roles of histone H4 methylation in plant development remain unclear. RecentIn plants, histone H3 lysine methyltransferases are important in gene silencing and developmental regulation; however, the roles of histone H4 methylation in plant development remain unclear. Recent studies found a type II histone arginine methyltransferase, AtPRTM5, which is involved in promoting growth and flowering. Here, we purified a dimerized plant-specific histone H4 methyltransferase, plant histone arginine methyltransferase 10 (PHRMT10), from cauliflower. Arabidopsis thaliana protein arginine methyltransferase 10 (AtPRMT10)--the Arabidopsis homologue of PHRMT10--was shown to be a type I PRMT, which preferentially asymmetrically methylated histone H4R3 in vitro. Genetic disruption of AtPRMT10 resulted in late flowering by upregulating FLOWERING LOCUS C (FLC) transcript levels. In addition, we show that AtPRMT10 functions genetically separate from AtPRMT5, but that each acts to fine-tune expression of FLC. This work adds an extra layer of complexity to flowering-time regulation and also sheds light on the importance of asymmetric arginine methylation in plant development.

• Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis.

  Authors: Yanxi Pei, Lifang Niu, Falong Lu, Chunyan Liu, Jixian Zhai, Xiangfeng Kong, Xiaofeng Cao

  Plant physiology. 09/2007; 144(4):1913-23.

  Human PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) encodes a type II protein arginine (Arg) methyltransferase and its homologs in animals and yeast (Saccharomyces cerevisiae and SchizosaccharomycesHuman PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) encodes a type II protein arginine (Arg) methyltransferase and its homologs in animals and yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe) are known to regulate RNA processing, signal transduction, and gene expression. However, PRMT5 homologs in higher plants have not yet been reported and the biological roles of these proteins in plant development remain elusive. Here, using conventional biochemical approaches, we purified a plant histone Arg methyltransferase from cauliflower (Brassica oleracea) that was nearly identical to AtPRMT5, an Arabidopsis (Arabidopsis thaliana) homolog of human PRMT5. AtPRMT5 methylated histone H4, H2A, and myelin basic protein in vitro. Western blot using symmetric dimethyl histone H4 Arg 3-specific antibody and thin-layer chromatography analysis demonstrated that AtPRMT5 is a type II enzyme. Mutations in AtPRMT5 caused pleiotropic developmental defects, including growth retardation, dark green and curled leaves, and FlOWERING LOCUS C (FLC)-dependent delayed flowering. Therefore, the type II protein Arg methyltransferase AtPRMT5 is involved in promotion of vegetative growth and FLC-dependent flowering time regulation in Arabidopsis.