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Versatile and efficient mammalian genome editing with Type I-C CRISPR System of Desulfovibrio vulgaris

Science China Life Sciences 2024年

作者： Pan Li Dingcai Dong Fei Gao Yuyang Xie Honglin Huang Siwei Sun Zhao Ma Cheng He jinsheng lai Xuguang Du Sen Wu State Key Laboratory of Animal Biotech Breeding College of Biological SciencesNational Engineering Laboratory for Animal BreedingFrontiers Science Center for Molecular Design BreedingChina Agricultural University College of Veterinary Medicine China Agricultural University Sanya Institute of China Agricultural University State Key Laboratory of Maize Bio-breeding National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural University Frontiers Science Center for Molecular Design Breeding China Agricultural University Center for Crop Functional Genomics and Molecular Breeding China Agricultural University

CRISPR-Cas tools for mammalian genome editing typically rely on single Cas9 or Cas12a *** type I CRISPR systems in Class I may offer greater specificity and versatility,they are not well-developed for genome ***,we present an alternative type I-C CRISPR system from Desulfovibrio vulgaris (Dvu) for efficient and precise genome editing in mammalian cells and *** optimized the Dvu type I-C editing complex to generate precise deletions at multiple loci in various cell lines and pig primary fibroblast cells using a paired PAM-in crRNA *** edited pig cells can serve as donors for generating transgenic cloned *** Dvu type I-C editor also enabled precise large fragment replacements with homology-directed ***,we adapted the Dvu-Cascade effector for cytosine and adenine base editing,developing Dvu-CBE and Dvu-ABE *** systems efficiently induced C-to-T and A-to-G substitutions in human genes without double-strand ***-target analysis confirmed the high specificity of the Dvu type I-C *** findings demonstrate the Dvu type I-C editor′s potential for diverse mammalian genome editing applications,including deletions,fragment replacement,and base editing,with high efficiency and specificity for biomedicine and agriculture.

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Plant pan-genomics and its applications

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Molecular Plant 2023年第1期16卷 168-186页

作者： Junpeng Shi Zhixi Tian jinsheng lai Xuehui Huang State Key Laboratory of Biocontrol School of AgricultureSun Yat-sen UniversityShenzhen 518107China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China

Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among *** variable DNA sequences,along with the conserved core sequences,compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a *** rapid progress in genome sequencing technologies,pan-genome research in plants is now *** we review recent advances in plant pan-genomics,including major driving forces of structural variations that constitute the variable sequences,methodological innovations for representing the pan-genome,and major successes in constructing plant *** also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant *** new genome resources,which have remarkable advantages over numerous previously assembled less-than-perfect genomes,are expected to become new references for genetic studies and plant breeding.

关键词： plant pan-genome genome assembly structural variations graph genome T-2-T genome

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Potassium nutrition of maize:Uptake,transport,utilization,and role in stress tolerance

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The Crop Journal 2023年第4期11卷 1048-1058页

作者： Meiling Zhang Yingying Hu Wu Han Jian Chen jinsheng lai Yi Wang State Key Laboratory of Plant Environmental Resilience(SKLPER) College of Biological SciencesChina Agricultural UniversityBeijing 100193China National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Potassium(K) is an essential macronutrient for plant growth and development and influences yield and quality of agricultural ***(Zea mays) is one of the most widely distributed crops *** China,although maize consumes a large amount of K fertilizer,the K uptake/utilization efficiency(KUE)of maize cultivars is relatively *** of KUE mechanisms and development of maize cultivars with higher KUE are *** KUE is determined by K+uptake,transport,and remobilization,which depend on a variety of K+channels and *** review basic information about K+channels and transporters in maize,their functions and regulation,and the roles of K+in nitrogen transport,sugar transport,and salt *** discuss challenges and prospects for maize KUE improvement.

关键词： Maize Potassium Channel Transporter K uptake/utilization efficiency

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Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize

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Journal of Integrative Plant Biology 2022年第7期64卷 1394-1410页

作者： Yingjia Han Mingjian Hu Xuxu Ma Ge Yan Chunyu Wang Siqi Jiang jinsheng lai Mei Zhang Key Laboratory of Plant Molecular Physiology Institute of BotanyThe Chinese Academy of SciencesBeijing 100093China State Key Laboratory of Plant Physiology and Biochemistry&National Maize Improvement Center of China Department of Plant Genetics and Breeding China Agricultural UniversityBeijing 100193China University of Chinese Academy of Sciences Beijing 100049China

Anther development from stamen primordium to pollen dispersal is complex and essential to sexual *** this highly dynamic and complex developmental process is controlled genetically is not well understood,especially for genes involved in specific key developmental *** we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize(Zea mays).Global transcriptome analyses revealed distinct phases of cell division and expansion,meiosis,pollen maturation,and mature pollen,for which we detected 50,245,42,and 414 phase-specific marker genes,***-specific transcription factor genes were significantly enriched in the phase of *** phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23,indicating they might have important roles in anther *** explored a desiccationrelated protein gene,ZmDRP1,which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage,by generating knockout ***,mutants in ZmDRP1 were completely male-sterile,with abnormal Ubisch bodies and defective pollen *** work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.

关键词： anther development maize male-sterile phase-specific genes transcriptome ZmDRP1

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Stereoselective Synthesis and Immunological Evaluation of Common O-antigen of P. mirabilis OE and P. vulgaris TG103

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Chinese Journal of Chemistry 2023年第5期41卷 535-543页

作者： Xiaopei Wu jinsheng lai Kexin Yang Yunxia Xue Jinxi Liao Liming Wang Jian-song Sun Jing Hu Jian Yin Qingju Zhang National Research Centrefor Carbohydrate Synthesis Jiangxi Normal University99 Ziyang AvenueNanchangJiangxi 330022China Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministryof EducationSchoolof Biotechnology and Wuxi School of MedicineJiangnan UniversityWuxiJiangsu 214122China

Proteus species especially Proteus mirabilis and Proteus vulgaris are zoonotic pathogens which can cause public health *** to their antibiotic-resistance,developing vaccines against these pathogens is urgently ***,we ... 详细信息

关键词： Stereoselective glycosylation Proteus mirabilis OE proteus vulgaris TG 103 Common O-antigen Immunological evaluation Syntheticcarbohydrate-based vaccine Total synthesis

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DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through

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Journal of Genetics and Genomics 2016年第8期43卷 513-523页

作者： Xiaojing Yan Xiaomei Dong Lei Liu Yongqing Yang jinsheng lai Yan Guo State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural University

The strict and efficient transcription termination is required to prevent production of aberrant read- through transcripts that may cause transcriptional interference at neighboring genes. However, the exact regulatory mechanism remains poorly understood. Through a genetic screening of a LUCIFERASE （LUC） reporter system, we found that Arabidopsis nucleosome remodeler DECREASE IN DNA METHYL- ATION1 （DDM1） is a key component of this regulatory machinery and plays an important role in tran- scription termination, thus limiting transcriptional read-through （TRT）. By whole-genome strand- specific RNA sequencing, we identified and confirmed 43 endogenous TRTs between genes, transposable elements （TEs）, or genes and TEs in the ddml-10 mutant, which mainly occurred at heterochromatin regions. The DNA methylation analysis of these TRT regions revealed that TRT occurred frequently at the intergenic regions with a higher methylation level in wild type comparing to the regions where TRT did not occur. Our results suggest that the level of intergenic DNA methylation may involve in preventing aberrant gene TRT or producing new gene during evolution.

关键词： ArabidopsisDNA methylationIntergenic regionDDMITranscriptional read-through

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Genome-wide Transcription Factor Gene Prediction and their Expressional Tissue-Specificities in Maize

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Journal of Integrative Plant Biology 2012年第9期54卷 616-630页

作者： Yi Jiang Biao Zeng Hainan Zhao Mei Zhang Shaojun Xie jinsheng lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Transcription factors （TFs） are important regulators of gene expression. To better understand TFencoding genes in maize （Zea mays L.）, a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2 298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2014 （87.64%） TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues （including root, shoot, leaf, ear, tassel and kernel）. Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.

关键词： Genome-wide maize tissue-specific transcription factor.

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Genetic dissection of maize seedling root system architecture traits using an ultra-high density bin-map and a recombinant inbred line population

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Journal of Integrative Plant Biology 2016年第3期58卷 266-279页

作者： Weibin Song Baobao Wang Andrew L Hauck Xiaomei Dong Jieping Li jinsheng lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China Department of Plant Genetics and BreedingChina Agricultural University

Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（GBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.

关键词： Maize root system architecture QTL bin map genotyping by sequencing(GBS)

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MP3RNA-seq:Massively parallel 3’end RNA sequencing for high-throughput gene expression profiling and genotyping

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Journal of Integrative Plant Biology 2021年第7期63卷 1227-1239页

作者： Jian Chen Xiangbo Zhang Fei Yi Xiang Gao Weibin Song Haiming Zhao jinsheng lai State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China

Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression ***,its application tolarge‐scale experiments remains limited by costand labor *** we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this ***3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and ***3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also *** its utility,we applied MP3RNA‐seqto 477 double haploid lines of *** iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for *** with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative *** conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.

关键词： gene expression profiling genotyping maize MP3RNA‐seq quantitative trait loci

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Efficiency and Inheritance of Targeted Mutagenesis in Maize Using CRISPR-Cas9

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Journal of Genetics and Genomics 2016年第1期43卷 25-36页

作者： Jinjie Zhu Ning Song Silong Sun Weilong Yang Haiming Zhao Weibin Song jinsheng lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University

CRISPR/Cas （clustered regularly interspaced short palindromic repeats/CR1SPR-associated proteins） is an adaptive immune system in bacteria and archaea to defend against invasion from foreign DNA fragments. Recently, it has been developed as a powerful targeted genome editing tool for a wide variety of species. However, its application in maize has only been tested with transiently expressed somatic cells or with a limited number of stable transgenic To plants. The exact efficiency and specificity of the CRISPR/Cas system in the highly complex maize genome has not been documented yet. Here we report an extensive study of the well-studied type II CRISPR-Cas9 system for targeted genome editing in maize, with the codon-optimized Cas9 protein and the short non-coding guide RNA generated through a functional maize U6 snRNA promoter. Targeted gene mutagenesis was detected for 90 loci by maize protoplast assay, with an average cleavage efficiency of 10.67 %. Stable knockout transformants for maize phytoene synthase gene （PSYI） were obtained. Mutations occurred in germ ceils can be stably inherited to the next generation. Moreover, no off-target effect was detected at the computationally predicted putative off-target loci. No significant difference between the transcriptomes of the Cas9 expressed and non-expressed lines was detected. Our results confirmed that the CRISPR-Cas9 could be successfully applied as a robust targeted genome editing system in maize.

关键词： CRISPR-Cas9 Targeted mutagenesis Heritability Maize

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