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Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

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Oil Crop Science 2024年第2期9卷 69-80页

作者： Farjana Afroz Susmi Tasmina Islam Simi Md Nahid Hasan Md Abdur Rahim department of genetics and Plant Breeding Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health *** RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical *** also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress ***,the SRS gene family was not reported in sesame *** this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in *** identified total six SiSRS genes on seven different linkage groups in the *** genome by comparing with the other species,including the model plant Arabidopsis *** SiSRS genes showed variation in their structure like2–5 exons and 1–4 *** other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'***,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of ***,***,and some other plant *** cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1011561)showed the highest 13 and 16 elements for light-and phytohormone-responses whereas,SiSRS1(SIN_1015187)showed the highest 15 elements for *** ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1009100).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions *** SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variabl

关键词： SiSRS gene family SHI Transcription factor Characterization Sesamum indicum

Internal m^(6)A and m^(7)G RNA modifications in hematopoietic system and acute myeloid leukemia

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Chinese Medical Journal 2024年第9期137卷 1033-1043页

作者： Xiaoxu Zhang Yanni Ma Jia Yu Rui Su Xiaoshuang Wang State Key Laboratory of Common Mechanism Research for Major diseases State Key Laboratory for ComplexSevereand Rare DiseasesInstitute of Basic Medical SciencesChinese Academy of Medical Sciences/Peking Union Medical CollegeBeijing 100005China department of Systems biology Beckman Research Institute of City of HopeMonroviaCA 91016USA The Institute of Blood Transfusion Chinese Academy of Medical Sciences/Peking Union Medical CollegeChengduSichuan 610052China Key Laboratory of RNA and Hematopoietic Regulation Chinese Academy of Medical SciencesBeijing 100005China department of Biochemistry and molecular biology Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing 100005China

Epitranscriptomics focuses on the RNA-modification-mediated post-transcriptional regulation of gene *** past decade has witnessed tremendous progress in our understanding of the landscapes and biological functions of RNA modifications,as prompted by the emergence of potent analytical *** hematopoietic system provides a lifelong supply of blood cells,and gene expression is tightly controlled during the differentiation of hematopoietic stem cells(HSCs).The dysregulation of gene expression during hematopoiesis may lead to severe disorders,including acute myeloid leukemia(AML).Emerging evidence supports the involvement of the mRNA modification system in normal hematopoiesis and AML pathogenesis,which has led to the development of small-molecule inhibitors that target N6-methyladenosine(m^(6)A)modification machinery as ***,we summarize the latest findings and our most up-to-date information on the roles of m^(6)A and N7-methylguanine in both physiological and pathological conditions in the hematopoietic ***,we will discuss the therapeutic potential and limitations of cancer treatments targeting m^(6)A.

关键词： N6-methyladenosine N7-methylguanine Hematopoiesis Acute myeloid leukemia Therapeutic target RNA modifications

Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses

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molecular Plant 2024年第3期17卷 438-459页

作者： Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu Chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Nanjing Agricultural University NanjingJiangsu 210095China Key Laboratory of Crop biology College of Life SciencesShandong Agricultural UniversityTaianShandong 271018China department of Life Science Tcuni Inc.ChengduSichuan 610000China John Innes Centre Norwich Research ParkNorwich NR47UHUK Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyCASBeijing 100101China

The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding *** this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering *** constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and *** integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown *** investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and *** particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet ***,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic ***,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.***.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.

关键词： wheat spike development epigenome TRN TaMYB30-A1 breeding selection

Association of TRMT2B gene variants with juvenile amyotrophic lateral sclerosis

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Frontiers of Medicine 2024年第1期18卷 68-80页

作者： Yanling Liu Xi He Yanchun Yuan Bin Li Zhen Liu Wanzhen Li Kaixuan Li Shuo Tan Quan Zhu Zhengyan Tang Feng Han Ziqiang Wu Lu Shen Hong Jiang Beisha Tang Jian Qiu Zhengmao Hu Junling Wang department of Neurology Xiangya HospitalCentral South UniversityJiangxiNational Regional Center for Neurological DiseasesNanchang330038China Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease Department of UrologyXiangya HospitalCentral South UniversityChangsha410078China department of Orthopedics The First Affiliated HospitalZhejiang University School of MedicineHangzhou310002China department of Neurology Xiangya HospitalCentral South UniversityChangsha410078China National Clinical Research Center for Geriatric diseases Xiangya HospitalCentral South UniversityChangsha410008China Key Laboratory of Hunan Province in Neurodegenerative Disorders Central South UniversityChangsha410008China Center for Medical genetics School of Life SciencesCentral South UniversityChangsha410008China Engineering Research Center of Hunan Province in Cognitive Impairment Disorders Central South UniversityChangsha410078China Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic diseases Changsha410078China Hunan Key Laboratory of molecular Precision Medicine Xiangya HospitalCentral South UniversityChangsha410078China

Amyotrophic lateral sclerosis(ALS)is a fatal neurodegenerative disease characterized by progressive degeneration of motor neurons,and it demonstrates high clinical heterogeneity and complex genetic architecture.A variation within TRMT2B(c.1356G>T;p.K452N)was identified to be associated with ALS in a family comprising two patients with juvenile ALS(JALS).Two missense variations and one splicing variation were identified in 10 patients with ALS in a cohort with 910 patients with ALS,and three more variants were identified in a public ALS database including 3317 patients with ALS.A decreased number of mitochondria,swollen mitochondria,lower expression of ND1,decreased mitochondrial complex I activities,lower mitochondrial aerobic respiration,and a high level of ROS were observed functionally in patient-originated lymphoblastoid cell lines and TRMT2B interfering HEK293 ***,TRMT2B variations overexpression cells also displayed decreased *** conclusion,a novel JALS-associated gene called TRMT2B was identified,thus broadening the clinical and genetic spectrum of ALS.

关键词： TRMT2B amyotrophic lateral sclerosis mitochondrial complex I tRNA methylation reactive oxygen species

Stay in touch with the endoplasmic reticulum

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Science China(Life Sciences) 2024年第2期67卷 230-257页

作者： Sha Sun Gan Zhao Mingkang Jia Qing Jiang Shulin Li Haibin Wang Wenjing Li Yunyun Wang Xin Bian Yan G.Zhao Xun Huang Ge Yang Huaqing Cai Jose C.Pastor-Pareja Liang Ge Chuanmao Zhang Junjie Hu National Laboratory of Biomacromolecules Institute of BiophysicsUniversity of Chinese Academy of SciencesChinese Academy of SciencesBeijing 100101China The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation College of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Membrane biology Tsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China Laboratory of Computational biology&Machine Intelligence School of Artificial IntelligenceUniversity of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Medicinal Chemical biology College of Life SciencesNankai UniversityTianjin 300071China Brain Research Center Department of BiologySchool of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China State Key Laboratory of molecular Developmental biology Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Institute of Neurosciences Consejo Superior de Investigaciones Científicas-Universidad Miguel HernándezSan Juan de Alicante 03550Spain

The endoplasmic reticulum(ER),which is composed of a continuous network of tubules and sheets,forms the most widely distributed membrane system in eukaryotic *** a result,it engages a variety of organelles by establishing membrane contact sites(MCSs).These contacts regulate organelle positioning and remodeling,including fusion and fission,facilitate precise lipid exchange,and couple vital signaling ***,we systematically review recent advances and converging themes on ER-involved organellar *** molecular basis,cellular influence,and potential physiological functions for ER/nuclear envelope contacts with mitochondria,Golgi,endosomes,lysosomes,lipid droplets,autophagosomes,and plasma membrane are summarized.

关键词： endoplasmic reticulum nuclear envelope mitochondria Golgi apparatus endosome lysosome lipid droplets autophagosome plasma membrane membrane contact site

Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

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molecular Plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun Yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China department of Computational molecular biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops ***,its genetic origin remains controversial,and its domestication history remains *** this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of *** diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to *** tetraploid progenitor of sweetpotato was most likely *** 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast *** most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome *** addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome *** analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of *** study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

High-throughput screening of novel TFEB agonists in protecting against acetaminopheninduced liver injury in mice

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Acta Pharmaceutica Sinica B 2024年第1期14卷 190-206页

作者： Xiaojuan Chao Mengwei Niu Shaogui Wang Xiaowen Ma Xiao Yang Hua Sun Xujia Hu Hua Wang Li Zhang Ruili Huang Menghang Xia Andrea Ballabio Hartmut Jaeschke Hong-Min Ni Wen-Xing Ding department of Pharmacology Toxicology and TherapeuticsUniversity of Kansas Medical CenterKansas CityKS 66160USA NMPA Key Laboratory for Research and Evaluation of Drug Metabolism&Guangdong Provincial Key Laboratory of New Drug Screening School of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou 510515China department of Oncology the First Affiliated Hospital of Anhui Medical UniversityAnhui Medical UniversityHefei 230032China National Center for Advancing Translational Sciences National Institutes of HealthBethesdaMD 20892USA Telethon Institute of genetics and Medicine TIGEMPozzuoliNaples 80131Italy Medical genetics Department of Translational MedicineFederico II UniversityNaples 80131Italy department of molecular and Human genetics Baylor College of MedicineHoustonTX 77030USA department of Internal Medicine Division of GastroenterologyHepatology&MotilityUniversity of Kansas Medical CenterKansas CityKS 66160USA

Macroautophagy(referred to as autophagy hereafter)is a major intracellular lysosomal degradation pathway that is responsible for the degradation of misfolded/damaged proteins and *** studies showed that autophagy protects against acetaminophen(APAP)-induced injury(AILI)via selective removal of damaged mitochondria and APAP protein *** lysosome is a critical organelle sitting at the end stage of autophagy for autophagic degradation via fusion with *** the present study,we showed that transcription factor EB(TFEB),a master transcription factor for lysosomal biogenesis,was impaired by APAP resulting in decreased lysosomal biogenesis in mouse *** loss-of and gain-of function of hepatic TFEB exacerbated or protected against AILI,***,overexpression of TFEB increased clearance of APAP protein adducts and mitochondria biogenesis as well as SQSTM1/p62-dependent non-canonical nuclear factor erythroid 2-related factor 2(NRF2)activation to protect against *** also performed an unbiased cell-based imaging high-throughput chemical screening on TFEB and identified a group of TFEB *** these agonists,salinomycin,an anticoccidial and antibacterial agent,activated TFEB and protected against AILI in *** conclusion,genetic and pharmacological activating TFEB may be a promising approach for protecting against AILI.

关键词： Autophagy DILI Drug screening Hepatotoxicity Lysosome Mitochondria Mitophagy NRF2

PCR-HRM for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

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American Journal of molecular biology 2024年第3期14卷 166-185页

作者： Aboubacar Sylla Solange Kakou-Ngazoa Tata Gniré Safiatou Coulibaly Yakoura Karidja Ouattara Mireille Sylvie Kouamé-Sina Zeinab Ouattara David Ngolo Coulibaly Brice Kouakou Bla Mireille Dosso molecular biology Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Laboratory of biology and Health UFR Biosciences University Flix Houphout Boigny Abidjan Cte dIvoire Genetic and Cancer Laboratory Molecular Genetics Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Epidemic Virus department Pasteur Institute Cte dIvoire Abidjan Cte dIvoire

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRM could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEM-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRM. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRM analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRM findings of the variations. These mutations led to the detection of L452R or L452M and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRM is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

关键词： Genomic Surveillance SARS-CoV-2 PCR-HRM Variants Côte d’Ivoire

New insights into astrocyte diversity from the lens of transcriptional regulation and their implications for neurodegenerative disease treatments

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Neural Regeneration Research 2024年第11期19卷 2335-2336页

作者： Ibrahim Olabayode Saliu Guoyan Zhao department of genetics Washington University School of MedicineSt.LouisMOUSA department of Neurology Department of Pathology and ImmunologyWashington University School of MedicineSt.LouisMOUSA

Astrocytes are a major glial cell type in the central nervous system,and they provide trophic and metabolic support to *** addition to these roles,they play crucial roles in modulating synaptic functions,development,and pruning(Brandebura et al.,2023).Astrocytes become reactive(activated)by undergoing morphological,molecular,and functional alterations in response to neuropathology such as in injuries and neurodegenerative diseases(NDs)(Escartin et al.,2021).

关键词： degenerative injuries