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Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance

Journal of Integrative Plant Biology 2021年第4期63卷 691-706页

作者： Wenjie Zeng Huan Huang Xueqiang Lin Chen Zhu Ken-ichi Kosami Chaofeng Huang Huiming Zhang Cheng-Guo Duan Jian-Kang Zhu daisuke miki Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences the Chinese Academy of SciencesShanghai 210602China University of the Chinese Academy of Sciences Shanghai 201602China Fruit Tree Research Center Ehime Research Institute of AgricultureForestry and FisheriesEhime 7910112Japan Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIndiana 47907USA

DNA methylation is an epigenetic mark important for genome stability and gene *** Arabidopsis thaliana,the 5-methylcytosine DNA glycosylase/demethylase DEMETER(DME)controls active DNA demethylation during the reproductive stage;however,the lethality of loss-of-function dme mutations has made it difficult to assess DME function in vegetative ***,we edited DME using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9 and created three weak dme mutants that produced a few viable *** also performed central cell-specific complementation in a strong dme mutant and combined this line with mutations in the other three Arabidopsis demethylase genes to generate the dme ros1 dml2 dml3(drdd)quadruple mutant.A DNA methylome analysis showed that DME is required for DNA demethylation at hundreds of genomic regions in vegetative tissues.A transcriptome analysis of the drdd mutant revealed that DME and the other three demethylases are important for plant responses to biotic and abiotic stresses in vegetative *** the limited role of DME in regulating DNA methylation in vegetative tissues,the dme mutants showed increased susceptibility to bacterial and fungal *** study highlights the important functions of DME in vegetative tissues and provides valuable genetic tools for future investigations of DNA demethylation in plants.

关键词： active DNA demethylation Arabidopsis disease resistance DME DNA methylation

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Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

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Journal of Integrative Plant Biology 2021年第4期63卷 707-722页

作者： Yi-Zhe Zhang Juncheng Lin Zhizhong Ren Chun-Xiang Chen daisuke miki Si-Si Xie Jian Zhang Ya-Nan Chang Jing Jiang Jun Yan Qingshun Q.Li Jian-Kang Zhu Cheng-Guo Duan Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences Chinese Academy of SciencesShanghai 201602China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and EcologyXiamen UniversityXiamen 361102China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China School of Life Sciences East China Normal UniversityShanghai 200241China Graduate College of Biomedical Sciences Western University of Health SciencesPomona 91766USA Department of Horticulture and Landscape Architecture Purdue UniversityWest Lafayette 47907USA

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic *** studies have shown that a protein complex,the ASI1-AIPP1-EDM2(AAE)complex,participates in polyadenylation regulation of several intronic heterochromatin-containing ***,the genome-wide functions of AAE are still ***,we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic ***(poly(A)sequencing reveals that AAE complex has a substantial influence on poly(A)site usage of heterochromatin-containing genes,includingnotonlyintronicheterochromatincontaining genes but also the genes showing overlap with ***,AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes,such as the disease resistance gene *** provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing *** addition to conferring RNA processing regulation at genic heterochromatin-containing genes,AAE also targets some transposable elements(TEs)outside of genes(including TEs sandwiched by genes and island TEs)for epigenetic *** results reveal new functions of AAE in RNA processing and epigenetic silencing,and thus representimportantadvancesinepigenetic regulation.

关键词： alternative polyadenylation alternative splicing epigenetic regulation heterochromatin transcription

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A putative SWI2/SNF2-like chromatin remodelling protein is important for active DNA demethylation in Arabidopsis.

A putative SWI2/SNF2-like chromatin remodelling protein is i...

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2013全国植物生物学大会

作者： YANG Donglei daisuke miki ZHANG Guiping LI Jingwen ZENG Liang TANG Kai YANG Lan ZHU Jiankang Department of Horticulture and Landscape Purdue UniversityWest LafayetteIN 47906USA

Active DNA demethylation is an important epigenetic process that is essential for growth and development in animals and *** Arabidopsis,active DNA demethylation involves a series of enzymes that function in a base excision repair ***,the relationship between active DNA demethylation and the chromatin environment remains unclear. Here,we report that the SALK T-DNA library was used to screen for hypermethylation mutants with chop-PCR markers and two mutant alleles of CHR40,a CLSY1 homolog,were identified. Whole genome bisulfite sequencing identified over thousands of hypermethylated DMRs(differentially methylated regions) and only hundreds of hypomethylated DMRs in the chr40 mutant. Interestingly,most the hypermethylated DMRs overlap with those identified in the rosl dml2 dml3 demethylase triple mutant,suggesting that CHR40 and the demethylases function in the same demethylation ***,genetic analyses demonstrated that the DNA methylation established by RdDM pathway is epistatic to CHR40 mediated DNA demethylation. Together,we propose that CHR40 is an important factor for active DNA demethylation.

关键词： DNA methylation DNA demethylation chromatin remodeling SWI2/SNF2

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A pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis

A pre-mRNA-splicing factor is required for RNA-directed DNA ...

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2013全国植物生物学大会

作者： HUANG Chaofeng miki daisuke TANG Kai ZHOU Haoran ZHENG Zhimin CHEN Wei MA Zeyang YANG Lan ZHANG Heng LIU Renyi HE Xinjian ZHU Jiankang Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology Chinese Academy of Sciences State Key Laboratory of Crop Genetics and Germplasm Enhancement College of Resources and Environmental ScienceNanjing Agricultural University Department of Horticulture and Landscape Architecture Purdue UniversityIN 47907USA National Institute of Biological Sciences Department of Botany&Plant Sciences University of California RiversideCA 92521USA

Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements(TEs).In Arabidopsis,the establishment of DNA methylation is through the RNA-directed DNA methylation(RdDM) *** identify components of the RdDM machinery,we carried out a forward genetic screen on a T-DNA-mutagenized population in the rosl background,based on reactivation of the RD29A promoter-driven luciferase reporter ***,we report the identification and characterization of RDM16,a new factor in the RdDM *** of RDM16 reduced the DNA methylation levels and partially released the silencing of a reporter gene as well as some endogenous genomic loci in the DNA demethylase rosl-1 mutant *** rdm16 mutant had morphological defects and was hypersensitive to salt stress and abscisic acid (ABA).Map-based cloning and complementation test led to the identification of RDM16, which encodes a pre-mRNA-splicing factor 3,a component of the U4/U6 ***-seq analysis showed that 308 intron retention events occurred in rdm16,confirming that RDM16 is involved in pre-mRNA splicing in ***-seq and mRNA expression analysis also revealed that the RDM16 mutation did not affect the pre-mRNA splicing of known RdDM genes, suggesting that RDM16 might be directly involved in *** RNA expression analysis on loci showing RDM16-dependent DNA methylation suggested that unlike the previously reported putative splicing factor mutants,rdm16 did not affect small RNA levels;instead,the rdm16 mutation caused a decrease in the levels of Pol V *** assays revealed that RDM16 was enriched at some Pol V target *** results suggest that RDM16 regulates DNA methylation through influencing Pol V transcript ***,our genome-wide DNA methylation analysis indicated that RDM16 regulates the overall methylation of TEs and gene-surrounding regions,and preferentially targets PolⅣ-dependent DNA methylation loc

关键词： DNA methylation DNA demethylation ROS1 RNA splicing small RNA

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Clinical and computed tomography findings of appendiceal diverticulitis vs acute appendicitis

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World Journal of Gastroenterology 2015年第13期21卷 3921-3927页

作者： daisuke Ito Kenji miki Shimizu Seiichiro Shojiro Hata Kaoru Kobayashi Masanori Teruya Michio Kaminishi Department of Gastro- intestinal Surgery Showa General HospitalTokyo 187--8510Japan Department of Pathology Showa General HospitalTokyo 187-8510Japan

AIM: To study the clinical features and computed tomography(CT) findings of appendiceal diverticulitis vs acute ***: We retrospectively reviewed the records of 451 patients who had undergone appendectomy inour in stitution from January 2007 to September 2012. Patient demographics, clinical features, pathological findings, and surgical outcomes were analyzed. We also compared preoperative CT images of 25 patients with appendiceal diverticulitis with those of 25 patients with acute ***: Among 451 patients, 44(9.7%) were diagnosed to have appendiceal diverticulitis and 398(86.9%) to have acute appendicitis. Patients with appendiceal diverticulitis were older(59 vs 37 years, P < 0.001) and had a longer duration of the illness(4.0 d vs 1.0 d, P < 0.001). Perforation rates in patients with appendiceal diverticulitis were higher(68% vs 27%, P < 0.001). The appendix could be visualized in only 13 patients(52%) among the appendiceal diverticulitis cases, but in all acute appendicitis cases. CT findings suggestive of appendiceal diverticulitis included the absence of fluid collection in the appendix(84% vs 12%, P < 0.001), absence of appendicolith(92% vs 52%, P = 0.005), and formation of abscess(68% vs 16%, P < 0.001). Appendiceal diverticula were identified in 6 patients(24%).CONCLUSION: Among patients who had undergone appendectomy, 9.7% had appendiceal diverticulitis. Patients with appendiceal diverticulitis had different clinical features and CT findings from patients with acute appendicitis.

关键词： Appendiceal diverticulitis Acute appendicitis Comp

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Cortical transcriptome analysis after spinal cord injury reveals the regenerative mechanism of central nervous system in CRMP2 knock-in mice

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Neural Regeneration Research 2021年第7期16卷 1258-1265页

作者： Ayaka Sugeno Wenhui Piao miki Yamazaki Kiyofumi Takahashi Koji Arikawa Hiroko Matsunaga Masahito Hosokawa daisuke Tominaga Yoshio Goshima Haruko Takeyama Toshio Ohshima Laboratory for Molecular Brain Science Department of Life Science and Medical BioscienceGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Biomolecular Engineering Laboratory Department of Life Science and Medical BioscienceGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Computational Bio Big-Data Open Innovation Laboratory(CBBD-OIL) National Institute of Advanced Industrial Science and Technology(AIST)TokyoJapan Research Organization for Nano and Life Innovation Waseda UniversityTokyoJapan Institute for Advanced Research of Biosystem Dynamics Waseda Research Institute for Science and EngineeringGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology(AIST)TsukubaJapan Department of Molecular Pharmacology and Neurobiology Graduate School of MedicineYokohama City UniversityYokohamaJapan

Recent studies have shown that mutation at Ser522 causes inhibition of collapsin response mediator protein 2(CRMP2) phosphorylation and induces axon elongation and partial recovery of the lost sensorimotor function after spinal cord injury(SCI).We aimed to reveal the intracellular mechanism in axotomized neurons in the CRMP2 knock-in(CRMP2KI) mouse model by performing transcriptome analysis in mouse sensorimotor cortex using micro-dissection punching *** to that, we analyzed the structural pathophysiology in axotomized or neighboring neurons after SCI and found that somatic atrophy and dendritic spine reduction in sensorimotor cortex were suppressed in CRMP2KI *** analysis of the transcriptome has aided in the identification of four hemoglobin genes Hba-a1, Hba-a2, Hbb-bs, and Hbb-bt that are significantly upregulated in wild-type mice with concomitant upregulation of genes involved in the oxidative phosphorylation and ribosomal pathways after ***, we observed substantial upregulation in channel activity genes and downregulation of genes regulating vesicles, synaptic function, glial cell differentiation in CRMP2KI ***, the transcriptome profile of CRMP2KI mice has been discussed wherein energy metabolism and neuronal pathways were found to be differentially *** results showed that CRMP2KI mice displayed improved SCI pathophysiology not only via microtubule stabilization in neurons, but also possibly via the whole metabolic system in the central nervous system, response changes in glial cells, and *** together, we reveal new insights on SCI pathophysiology and the regenerative mechanism of central nervous system by the inhibition of CRMP2 phosphorylation at *** these experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee at Waseda University, Japan(2017-A027 approved on March 21, 2017;2018-A003 approved on March 25, 2018;2019-A026 approved on March

关键词： CNS regeneration cortex CRMP2 hemoglobin metabolic pathway spinal cord injury spine transcriptome

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Successful embolization of an intrahepatic portosystemic shunt using balloon-occluded retrograde transvenous obliteration:A case report

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World Journal of Clinical Cases 2022年第6期10卷 2023-2029页

作者： Hidemasa Saito Satoru Murata Fumie Sugihara Tatsuo Ueda daisuke Yasui Izumi miki Hiromitsu Hayashi Shin-Ichiro Kumita Department of Radiology Nippon Medical SchoolTokyo 113-8602Japan Center for Interventional Radiology Teikyo University Chiba Medical CenterChiba 299-0011Japan

BACKGROUND A congenital intrahepatic portosystemic shunt(IPSVS)is a rare vascular abnormality that is characterized by an anomalous intrahepatic venous tract that connects the intrahepatic portal vein with the hepatic venous *** encephalopathy is an indication for IPSVS embolization,which is technically challenging because rapid blood flow through shunts can induce the migration of embolization material to systemic *** case report discusses the efficacy of percutaneous balloon-occluded retrograde transvenous obliteration for treating patients with *** SUMMARY A 75-year-old woman presented with a six-month history of repeated hepatic encephalopathy due to an IPSVS without liver *** successfully embolized the IPSVS using percutaneous balloon-occluded retrograde transvenous obliteration with interlocking detachable *** the procedure,the patient exhibited no symptoms of hepatic encephalopathy for 14 *** Balloon-occluded retrograde transvenous obliteration with detachable coils can be effective for the endovascular treatment of an IPSVS.

关键词： Hepatic veins Portal vein Hepatic encephalopathy Endovascular procedures Embolization Therapeutic Case report

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拟南芥中多重基因沉默途径共同参与等位遗传现象

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科学新闻 2016年第1期 115-115页

作者：郑志民 Hasi Yu daisuke miki Dan Jin Qingzhu Zhang ZhonghaiRen Zhizhong Gong 张蘅 Jian-Kang Zhu 中国科学院上海生命科学研究院沈阳善达中国科学院上海植物逆境生物学研究中心基因组学平台研究组

文章简介"等位遗传"和"转座子跳跃"是非孟德尔遗传现象的两个典型代表。等位遗传是指等位基因位于各自染色体上,通过染色体的反式修饰等相互作用,一个等位基因在转录水平上被另一个等位基因所沉默,且这种能力是可遗传的。其作为一个现... 详细信息

文章简介"等位遗传"和"转座子跳跃"是非孟德尔遗传现象的两个典型代表。等位遗传是指等位基因位于各自染色体上,通过染色体的反式修饰等相互作用,一个等位基因在转录水平上被另一个等位基因所沉默,且这种能力是可遗传的。其作为一个现象广泛存在于真菌、植物和动物中,但是对于其分子机制还有众多问题亟待解决,尤其是等位遗传的形成、维持及传递机制等方面依然存在着众多疑惑。借助正向遗传学的筛选方法,本研究发现在DNA去甲基化关键蛋白ROS1的突变体中,一个外源的重复串联

关键词：遗传现象基因沉默甲基化烷基化等位基因

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Evaluation of the relationship between hepatocellular carcinoma location and transarterial chemoembolization efficacy

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World Journal of Gastroenterology 2017年第35期23卷 6437-6447页

作者： Izumi miki Satoru Murata Fumio Uchiyama daisuke Yasui Tatsuo Ueda Fumie Sugihara Hidemasa Saito Hidenori Yamaguchi Ryusuke Murakami Chiaki Kawamoto Eiji Uchida Shin-ichiro Kumita Department of Radiology Center of Advanced MedicineNippon Medical School Department of Radiology Ebina-Sogo Hospital Department of Radiology Tamanagayama HospitalNippon Medical School Division of Gastroenterology and Hepatology Department of Internal MedicineNippon Medical School Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery Nippon Medical School

AIM To evaluate the relationship between the location of hepatocellular carcinoma(HCC) and the efficacy of transarterial chemoembolization(TACE).METHODS We evaluated 115 patients(127 nodules), excluding recurrent nodules, treated with TACE between January 2011 and June 2014. TACE efficacy was evaluated according to m RECIST. The HCC location coefficient was calculated as the distance from the central portal portion to the HCC center(mm)/liver diameter(mm) on multiplanar reconstruction images rendered(MPR) to visualize bifurcation of the right and left branches of the portal vein and HCC center. The HCC location coefficient was compared between complete response(CR) and non-CR groups in Child-Pugh grade A and B *** The median location coefficient of HCC among all nodules, the right lobe, and the medial segment was significantly higher in the CR group than in the non-CR group in the Child-Pugh grade A patients(0.82 vs 0.62, P 0.05). On the other hand, in the Child-Pugh grade B patients, the HCC median location coefficient in each lobe and segment was not significantly different between in the CR and in the non-CR *** Improved TACE efficacy may be obtained for HCC in the peripheral zone of the right lobe and the medial segment in Child-Pugh grade A patients.

关键词： Hepatocellular carcinoma location Transarterial chemoembolization efficacy Child-Pugh Modified response evaluation criteria in solid tumors Central zone Peripheral zone

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Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics

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Quantitative Biology 2020年第3期8卷 228-237页

作者： Naoki Matsuda Ken-ichi Hironaka Masashi Fujii Takumi Wada Katsuyuki Kunida Haruki Inoue miki Eto daisuke Hoshino Yasuro Furuichi Yasuko Manabe Nobuharu LFujii Hiroyuki Noji Hiromi Imamura Shinya Kuroda Department of Biological Sciences Graduate School of ScienceUniversity of TokyoTokyo 113-0033Japan Molecular Genetics Research Laboratory Graduate School of ScienceUniversity of TokyoTokyo 113-0033Japan Department of Mathematical and Life Sciences Graduate School of Integrated Sciences for LifeHiroshima UniversityHiroshima 739-8526Japan Laboratory of Computati onal Biology Graduate School of Biological SciencesNara Institute of Science and Tech no logyNara 630-0192Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier SciencesUniversity of TokyoTokyo 113-0033Japan Department of Engineering Science Graduate School of Informatics and EngineeringUniversity of Electro-CommunicationsTokyo 182-8585Japan Department of Health Promotion Sciences Graduate School of Human Health SciencesTokyo Metropolitan UniversityTokyo 192-0397Japan Department of Applied Chemistry Graduate School of EngineeringUniversity of TokyoTokyo 113-8656Japan Department of Functional Biology Graduate School of BiostudiesKyoto UniversityKyoto 606-8501Japan CREST Japan Science and Technology CorporationTokyo 113-0033Japan

Backgrounds ATP is the major energy source for myotube contraction,and is quickly produced to compensate ATP consumption and to maintain sufficient ATP *** is consumed mainly in cytoplasm and produced in mitochondria during myotube *** understand the mechanism of ATP homeostasis during myotube contraction,it is essential to monitor mitochondrial ATP at single-cell level,and examine how ATP is produced and consumed in ***:We established C2C12 cell line stably expressing fluorescent probe of mitochondrial ATP,and induced differentiation into myotubes・We gave electric pulse stimulation to the differentiated myotubes,and measured mitochondrial *** constructed mathematical model of mitochondrial ATP at single-cell level,and analyzed kinetic parameters of ATP production and ***:We performed hierarchical clustering analysis of time course of mitochondrial ATP,which resulted in two *** 1 showed strong transient increase,whereas cluster 2 showed weak transient *** modeling at single-cell level revealed that the ATP production rate of cluster 1 was larger than that of cluster 2,and that both regulatory pathways of ATP production and consumption of cluster 1 were faster than those of cluster *** 1 showed larger mitochondrial mass than cluster 2,suggesting that cluster 1 shows the similar property of slow muscle fibers,and cluster 2 shows the similar property of fast muscle *** Cluster 1 showed the stronger mitochondrial ATP increase by larger ATP production rate,but not smaller *** 1 might reflect the larger oxidative capacity of slow muscle fiber.

关键词： mitocondrial ATP production ATP consumption single-cell analysis mathematical modeling

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