A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis

Hou, Xianhui; Li, Linchuan; Peng, Zhiyu; Wei, Baoye; Tang, Saijun; MaoYu, Ding; Liu, Jingjing; Zhang, Fangxian; Zhao, Yunde; Gu, Hongya; Liu, Qu

doi:10.1111/j.1365-313x.2010.04277.x

Cited by 73 publications

(58 citation statements)

References 26 publications

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“…Low-resolution mapping by bulked segregant analysis places m90 and s215 on the long arm of chromosome 1 between simple sequence length polymorphism (SSLP) markers 1-AC002986-9779 and 1-AC011713-9987 (2.5-cM), a region that covered 184 putative genes annotated in TAIR10 (Fig. S2A) (23). To identify the point mutations, we sequenced the genomic DNA of the F3 progeny of m90 by Illumina Genome Analyzer IIx.…”

Section: Point Mutations In Prp8 Are Responsible For Suppressors Of Amentioning

confidence: 99%

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Deng

Wang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Protein arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is involved in a multitude of biological processes in eukaryotes. Symmetric arginine dimethylation mediated by PRMT5 modulates constitutive and alternative pre-mRNA splicing of diverse genes to regulate normal growth and development in multiple species; however, the underlying molecular mechanism remains largely unknown. A genetic screen for suppressors of an Arabidopsis symmetric arginine dimethyltransferase mutant, atprmt5, identified two gain-of-function alleles of pre-mRNA processing factor 8 gene (prp8-8 and prp8-9), the highly conserved core component of the U5 small nuclear ribonucleoprotein (snRNP) and the spliceosome. These two atprmt5 prp8 double mutants showed suppression of the developmental and splicing alterations of atprmt5 mutants. In atprmt5 mutants, the NineTeen complex failed to be assembled into the U5 snRNP to form an activated spliceosome; this phenotype was restored in the atprmt5 prp8-8 double mutants. We also found that loss of symmetric arginine dimethylation of Sm proteins prevents recruitment of the NineTeen complex and initiation of spliceosome activation. Together, our findings demonstrate that symmetric arginine dimethylation has important functions in spliceosome assembly and activation, and uncover a key molecular mechanism for arginine methylation in pre-mRNA splicing that impacts diverse developmental processes.arginine methylation | protein arginine methyltransferase | AtPRMT5 | pre-mRNA splicing | Prp19C/NTC P rotein arginine methyltransferase 5 (PRMT5), a highly conserved type II protein arginine methyltransferase, transfers methyl groups to arginine residues, generating monomethylarginine and symmetric ω-N G , N′ G -dimethylarginine (SDMA) (1-3). In mammals, PRMT5 methylates and interacts with diverse proteins, including histones and other proteins, and has long been implicated in the modulation of a variety of processes, such as transcriptional regulation, RNA metabolism (4), apoptosis (5), signal transduction (6), and germ cell development (7). Both loss-of-function and overexpression of PRMT5 are fatal in mammals (8). AtPRMT5, the Arabidopsis homolog of PRMT5, regulates multiple aspects of plant growth and development, such as flowering time, growth rate, leaf morphology, sensitivity to stress conditions, and circadian rhythm, by modulating transcription, constitutive and alternative precursor mRNA (pre-mRNA) splicing of diverse genes (9-13). AtPRMT5 also mediates the symmetric arginine dimethylation of uridine-rich small nuclear ribonucleoproteins (U snRNPs) AtSmD1, D3, and AtLSm4 proteins, thus linking arginine methylation and splicing (10,11,13). However, the exact mechanism remains elusive.Pre-mRNA splicing occurs in the nucleus, removing introns and ligating exons (14). In eukaryotes, most introns are spliced in a series of reactions catalyzed by the spliceosome, which consists of five subcomplexes of U snRNPs and several non-snRNP factors. Each U snRNP contains distinct splicing...

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Section: Point Mutations In Prp8 Are Responsible For Suppressors Of Amentioning

confidence: 99%

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Deng

Wang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Simple sequence length polymorphism (SSLP) markers were used to define the mutant gene to chromosome 2 [65]–[67]. The markers used in fine mapping are listed in the Table S1 on line, including In/Del and CAPS.…”

Section: Methodsmentioning

confidence: 99%

Arabidopsis DELLA Protein Degradation Is Controlled by a Type-One Protein Phosphatase, TOPP4

et al. 2014

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Gibberellins (GAs) are a class of important phytohormones regulating a variety of physiological processes during normal plant growth and development. One of the major events during GA-mediated growth is the degradation of DELLA proteins, key negative regulators of GA signaling pathway. The stability of DELLA proteins is thought to be controlled by protein phosphorylation and dephosphorylation. Up to date, no phosphatase involved in this process has been identified. We have identified a dwarfed dominant-negative Arabidopsis mutant, named topp4-1. Reduced expression of TOPP4 using an artificial microRNA strategy also resulted in a dwarfed phenotype. Genetic and biochemical analyses indicated that TOPP4 regulates GA signal transduction mainly via promoting DELLA protein degradation. The severely dwarfed topp4-1 phenotypes were partially rescued by the DELLA deficient mutants rga-t2 and gai-t6, suggesting that the DELLA proteins RGA and GAI are required for the biological function of TOPP4. Both RGA and GAI were greatly accumulated in topp4-1 but significantly decreased in 35S-TOPP4 transgenic plants compared to wild-type plants. Further analyses demonstrated that TOPP4 is able to directly bind and dephosphorylate RGA and GAI, confirming that the TOPP4-controlled phosphorylation status of DELLAs is associated with their stability. These studies provide direct evidence for a crucial role of protein dephosphorylation mediated by TOPP4 in the GA signaling pathway.

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“…26–28 Similar work has been done in other species, such as Arabidopsis and rice. 29–33 In tomato, a total of 749 966 putative InDels of 3–300 bp have been identified by comparing the genome sequences of Solanum pimpinellifolium accession LA 1589 and S. lycopersicum variety Heinz 1706, 34 and more than 80 000 putative InDels of 1–15 bp have been discovered by comparative analysis of transcriptome between wild species S. galapagense and cultivated tomato. 35 However, less work on discovery of InDels in cultivated tomato has been done.…”

Section: Introductionmentioning

confidence: 99%

In Silico Identification and Experimental Validation of Insertion-Deletion Polymorphisms in Tomato Genome

et al. 2014

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Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion–deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.

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A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis

Cited by 73 publications

References 26 publications

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5

Arabidopsis DELLA Protein Degradation Is Controlled by a Type-One Protein Phosphatase, TOPP4

In Silico Identification and Experimental Validation of Insertion-Deletion Polymorphisms in Tomato Genome

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