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GAMETOPHYTIC FACTOR 1,Involved in Pre-mRNA Splicing,Is Essential for Megagametogenesis and Embryogenesis in Arabidopsis

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Journal of Integrative Plant biology 2009年第3期51卷 261-271页

作者： Man Liu Li Yuan Nai-You Liu Dong-Qiao Shi Jie Liu Wei-Cai Yang Key Laboratory of molecular and Developmental biology National Center for Plant Gene Research Institute of Genetics and Developmental Biology the Chinese Academy of Sciences Beijing 100101 China Graduate University the Chinese Academy of Sciences Beijing 100049 China

RNA biogenesis is essential and vital for accurate expression of genes. It is obvious that cells cannot continue normal metabolism when RNA splicing is interfered with. sgt13018 is such a mutant, with partial loss of function of GAMETOPHYTIC FACTOR 1 （GFA1）; a gene likely involved in RNA biogenesis in Arabidopsis. The mutant is featured in the phenotype of diminished female gametophyte development at stage FG5 and is associated with the arrest of early embryo development in Arabidopsis. Bioinformatics data showed that homologs of gene GFA1 in yeast and human encode putative U5 snRNPspecific proteins required for pre-mRNA splicing. Furthermore, the result of yeast two-hybrid assay indicated that GFA1 physically interacted with AtBrr2 and AtPrp8, the putative U5 snRNP components, of Arabidopsis. This investigation suggests that GFA1 is involved in mRNA biogenesis through interaction with AtBrr2 and AtPrp8 and functions in megagametogenesis and embryogenesis in plant.

关键词： embryogenesis female gametophyte pre-mRNA splicing U5 snRNA complex.

Effects of splice sites on the intron retention in histamine H_3 receptors from rats and mice

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Journal of genetics and Genomics 2009年第8期36卷 475-482页

作者： Wenyong Ding Lin Lin Feng Ren Hanfa Zou Ziyuan Duan Jianwu Dai Department of Biochemistry and molecular biology Dalian Medical University Dalian 116044 China Key Laboratory of molecular Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100080 China National Chromatographic research and Analysis Center Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

In the alternative splicing, intron retention, of histamine H3 receptors in rats and mice, the short transcript isoforms that are excised alternatively spliced introns are easily detected in a very low level in rats and are undetectable in mice using the regular PCR protocol. The retained introns have common 5＇ splice site and different 3＇ splice sites. The detailed mechanism for the special alternative splicing remains largely unclear. In this study, we developed a minigene splicing system to recapitulate natural alternative splicing of the receptors and investigated the effects of 5＇ and 3＇ splice sites on intron retention in HeLa cells. Mutating weak 5＇ and 3＇ splice sites of the alternatively spliced introns toward the canonical consensus sequences promoted the splicing of the corresponding introns in rat and mouse minigenes. The effect of splice site strength was context-dependent and much more sigiaificant for the 3＇ splice site of the longer alternative intron than for the 3＇ splice site of the shorter alternative intron and the common 5＇ splice sites; it was also more significant in the rat minigene than in the mouse minigene. Mutating the 3＇ splice site of the longer alternative intron resulted in almost complete splicing of the intron and made the corresponding isoform to become the nearly exclusive transcript in the rat minigene.

关键词： histamine H3 receptor (H3R) altemative splicing intron retention splice site minigene

SLOW WALKER3,Encoding a Putative DEAD-box RNA Helicase,is Essential for Female Gametogenesis in Arabidopsis

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Journal of Integrative Plant biology 2010年第9期52卷 817-828页

作者： Man Liu Dong-Qiao Shi Li Yuan Jie Liu Wei-Cai Yang Key Laboratoryof molecular and Developmental biology National Centre for Plant Gene Research Institute of Genetics and Developmental Biology the Chinese Academy of Sciences Beijing 100101 China Graduate University of the Chinese Academy of Sciences Beijing 100039 China

RNA helicases are adenosine tri-phosphatases that unwind the secondary structures of RNAs and are required in almost any aspect of RNA metabolism. They are highly conserved from prokaryotic to eukaryotic organisms. However, their precise roles in plant physiology and development remain to be clarified. Here we report that the mutation in the gene SLOW WALKER3 （SWA3） results in the slow and retarded progression of mitosis during megagametogenesis in Arabidopsis. SWA3 is a putative RNA helicase of the DEAD-box subfamily. Mutant megagametophyte development is arrested at fouror eight-nucleate stages, furthermore, one of the synergids in about half of the mutant embryo sacs displays abnormal polarity, with its nucleus locating at the chalazal end, instead of the micropylar end in the wild-type. Transmission of the mutation through female gametophytes is severely reduced in swa3. However, a small portion of mutant embryo sacs are able to develop into mature and functional female gametophytes when pollination was postponed. The SWA3 in Arabidopsis is a homolog of Dbp8 in yeast. Dbp8 interacts with Efs2 and is essential for biogenesis of 18S rRNA in yeast. Our data suggest that SWA3 may form a complex with AtEfs2 and take roles in ribosomal biogenesis as RNA helicase during megagametogenesis in Arabidopsis.

关键词： RNA Mutation Females Yeasts Mutants Arabidopsis

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation

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Journal of molecular Cell biology 2015年第4期7卷 366-382页

作者： Nickolai A.Tchurikov Daria M.Fedoseeva Dmitri V.Sosin Anastasia V.Snezhkina Nataliya V.Melnikova Anna V.Kudryavtseva Yuri V.Kravatsky Olga V.Kretova Department of Epigenetic Mechanisms of Gene Expression Regulation Engelhardt Institute of Molecular BiologyMoscow 119334Russia group of Postgenomic Studies Engelhardt Institute of Molecular BiologyMoscow 119334Russia Laboratory of DNA-Protein Interactions Engelhardt Institute of Molecular BiologyMoscow 119334Russia

DNA double-strand breaks(DSBs)are involved in many cellular mechanisms,including replication,transcription,and genome *** recent observation that hot spots of DSBs in human chromosomes delimit DNA domains that possess coordinately expressed genes suggests a strong relationship between the organization of transcription patterns and hot spots of *** this study,we performed mapping of hot spots of DSBs in a human 43-kb ribosomal DNA(rDNA)repeated *** observed that rDNA units corresponded to the most fragile sites in human chromosomes and that these units possessed at least nine specific regions containing clusters of extremely frequently occurring DSBs,which were located exclusively in non-coding intergenic spacer(IGS)*** hot spots of DSBs corresponded to only a specific subset of DNase-hypersensitive sites,and coincided with CTCF,PARP1,and HNRNPA2B1 binding sites,and H3K4me3 *** rDNA-4C data indicate that the regions of IGS containing the hot spots of DSBs often form contacts with specific regions in different chromosomes,including the pericentromeric regions,as well as regions that are characterized by H3K27ac and H3K4me3 marks,CTCF binding sites,ChIA-PET and RIP signals,and high levels of *** data suggest a strong link between chromosome breakage and several different mechanisms of epigenetic regulation of gene expression.

关键词： double-strand breaks fragile sites rDNA IGS PARP1 HNRNPA2B1 4C

Why does caloric restriction increase life and healthspan? The ‘clean cupboards’ hypothesis

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National Science Review 2020年第7期7卷 1153-1156页

作者： John R.Speakman State Key Laboratory of molecular Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Institute of Biological and EnvironmentalSciences University of Aberdeen CAS Center of Excellence in Animal Evolution and genetics Kunming Institute of Zoology Chinese Academy of Sciences

The disposable soma hypothesis explanation of the effects of caloric restriction(CR) on lifespan fails to explain why CR generates negative impacts alongside the positive effects and does not work in all species. I pr...

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Drosophila Homolog of FMRP Maintains Genome Integrity by Interacting with Piwi

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Journal of genetics and Genomics 2016年第1期43卷 11-24页

作者： Fangfang Jiang Falong Lu Peixue Li Wei Liu Lu Zhao Qifu Wang Xiaofeng Cao Lei Zhang Yong Q.Zhang State Key Laboratory for molecular and Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences State Key Laboratory of Plant Genomics and National Center for Plant Gene research Institute of Genetics and Developmental Biology Chinese Academy of Sciences State Key Laboratory of molecular biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Science and Technology Center Fenyang College Shanxi Medical University Department of Medical Laboratory Science Fenyang College Shanxi Medical University

Fragile X syndrome （FraX）, the most common form of inherited mental retardation, is caused by the absence of the evolutionally conserved fragile X mental retardation protein （FMRP）. While neuronal functions of FMRP have been intensively studied for the last two decades, its role in non-neuronal cells remains poorly understood. Piwi, a key component of the Piwi-interacting RNA （piRNA） pathway, plays an essential role in germline development. In the present study, we report that similar to piwi, dfmrl, the Drosophila homolog of human FMR1, is required for transposon suppression in the germlines. Genetic analyses showed that dfmrl and piwi act synergistically in heterochromatic silencing, and in inhibiting the differentiation of primordial germline cells and transposon expression. Northern analyses showed that roo piRNA expression levels are reduced in dfmrl mutant ovaries, suggesting a role of dfmrl in piRNA biogenesis. Biochemical analysis demonstrated a physical interaction between dFMRP and Piwi via their N-termini. Taken together, we propose that dFMRP cooperates with Piwi in maintaining genome integrity by regulating heterochromatic silencing in somatic cells and suppressing transposon activity via the piRNA pathway in germlines.

关键词： Fragile X syndrome FMRP piwi piRNA Germline

Comprehensive screening for reg1α gene rules out association with tropical calcific pancreatitis

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World Journal of Gastroenterology 2007年第44期13卷 5938-5943页

作者： Swapna Mahurkar Seema Bhaskar D Nageshwar Reddy G Venkat Rao Giriraj Ratan Chandak Genome research group Centre for Cellular and Molecular Biology Uppal Road Hyderabad 500 007 India Asian Institute of Gastroenterology Punjagutta Hyderabad 500 082 India

AIM: To investigate the allelic and haplotypic association of reg1α gene with tropical calcific pancreatitis (TCP). Since TCP is known to have a variable genetic basis, we investigated the interaction between mutations in the susceptibility genes, SPINK1 and CTSB with reg1α polymorphisms. METHODS: We analyzed the polymorphisms in the reg1α gene by sequencing the gene including its promoter region in 195 TCP patients and 150 ethnically matched controls, compared their allele and haplotype frequencies, and their association with the pathogenesis and pancreaticolithiasis in TCP and fibro-calculous pancreatic diabetes. RESULTS: We found 8 reported and 2 novel polymo-rphisms including an insertion-deletion polymorphism in the promoter region of reg1α. None of the 5' UTR variants altered any known transcription factor binding sites, neither did any show a statistically significant association with TCP. No association with any reg1α variants was observed on dichotomization of patients based on their N34S SPINK1 or L26V CTSB status. CONCLUSION: Polymorphisms in reg1α gene, including the regulatory variants singly or in combination with the known mutations in SPINK1 and/or CTSB genes, are not associated with tropical calcific pancreatitis.

关键词： Tropical calcific pancreatitis Lithostathine Stone formation Polymorphism Haplotype

CYP1A1,CYP2E1 and EPHX1 polymorphisms in sporadic colorectal neoplasms

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World Journal of Gastroenterology 2016年第45期22卷 9974-9983页

作者： Glaucia Maria M Fernandes Anelise Russo Marcela Alcantara Proenca Nathalia Fernanda Gazola Gabriela Helena Rodrigues Patrícia Matos Biselli-Chicote Ana Elizabete Silva Joao Gomes Netinho érika Cristina Pavarino Eny Maria Goloni-Bertollo genetics and molecular biology research Unit-UPGEM Department of Molecular Biology Sao José do Rio Preto Medical School FAMERP Departament of biology UNESP-Sao Paulo State University Departament of Surgery and Coloproctology Service Sao José do Rio Preto Medical School FAMERP

AIM To investigate the contribution of polymorphisms in the CYP1A1, CYP2E1 and EPHX1 genes on sporadic colorectal cancer(SCRC) risk. METHODS Six hundred forty-one individuals(227 patients with SCRC and 400 controls) were enrolled in the study. The variables analyzed were age, gender, tobacco and alcohol consumption, and clinical and histopathological tumor parameters. The CYP1A1 *2A, CYP1A1 *2C CYP2E1 *5B and CYP2E1 *6 polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP). The EPHX1 Tyr113 His, EPHX1 His139 Arg and CYP1A1 *2C polymorphisms were detected by real-time PCR. Chisquared test and binary logistic regression were used in the statistical analysis. Haplotype analysis was conducted using the Haploview program, version *** Age over 6 2 years was a risk factor for SCRC development(OR = 7.54, 95%CI: 4.94-11.50, P < 0.01). Male individuals were less susceptible to SCRC(OR = 0.55, 95%CI: 0.35-0.85, P < 0.01). The CYP2E1*5B polymorphism was associated with SCRC in the codominant(heterozygous genotype: OR = 2.66, 95%CI: 1.64-4.32, P < 0.01), dominant(OR = 2.82, 95%CI: 1.74-4.55, P < 0.01), overdominant(OR = 2.58, 95%CI: 1.59-4.19, P < 0.01), and log-additive models(OR = 2.84, 95%CI: 1.78-4.52, P < 0.01). The CYP2E1*6 polymorphism was associated with an increased SCRC risk in codominant(heterozygous genotype: OR = 2.81, 95%CI: 1.84-4.28, P < 0.01; homozygous polymorphic : OR = 7. 3 2, 9 5 % C I : 1.85-28.96, P < 0.01), dominant(OR = 2.97, 95%CI: 1.97-4.50, P < 0.01), recessive(OR = 5.26, 95%CI: 1.35-20.50, P = 0.016), overdominant(OR = 2.64, 95%CI: 1.74-4.01, P < 0.01), and log-additive models(OR = 2.78, 95%CI: 1.91-4.06, P < 0.01). The haplotype formed by the minor alleles of the CYP2E1*5B(C) and CYP2E1*6(A) polymorphisms was associated with SCRC(P = 0.002). However, the CYP1A1 *2A, CYP1A1 *2C, EPHX1 Tyr113 His and EPHX1 His139 Arg polymorphisms were not associated with *** In conclusion, the

关键词： Single-nucleotide polymorphisms Colorectal neoplasms Cytochrome P-450 CYP2E1 Cytochrome P-450 CYP1A1 Epoxide hydrolases 1

Identification of a Ubiquitin-Binding Structure in the S-Locus F-Box Protein Controlling S-RNase-Based Self-Incompatibility

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Journal of genetics and Genomics 2012年第2期39卷 93-102页

作者： Guang Chen BinZhang Lijing Liu Qun Li Yu'e Zhang Qi Xie Yongbiao Xue State Key Laboratory of molecular Developmental biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences and National Center for Plant Gene ResearchBeijing 100101China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences and National Center for Plant Gene ResearchBeijing 100101China Graduate University of Chinese Academy of Sciences Beijing 100190China

In flowering plants, self-incompatibility （SI） serves as an important intraspecific reproductive barrier to promote outbreeding. In species from the Solanaceae, Plantaginaceae and Rosaceae, S-RNase and SLF （S-locus F-box） proteins have been shown to control the female and male specificity of SI, respectively. However, little is known about structure features of the SLF protein apart from its conserved F-box domain. Here we show that the SLF C-terminal region possesses a novel ubiquitin-binding domain （UBD） structure conserved among the SLF protein family. By using an ex vivo system of Nicotiana benthamiana, we found that the UBD mediates the SLF protein turnover by the ubiquitin-proteasome pathway. Furthermore, we detected that the SLF protein was directly involved in S-RNase degradation. Taken together, our results provide a novel insight into the SLF structure and highlight a potential role of SLF protein stability and degradation in S-RNase-based self-incompatibility.

关键词： Protein degradation SLF Ubiquitin Self-incompatibility Ubiquitin-binding structure S-RNase