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Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

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Journal of Integrative Plant Biology 2020年第2期62卷 201-217页

作者： Pengfei Dong Xiaoyu Tu Haoxuan li Jianhua Zhang Donald Grierson pinghua li Silin Zhong State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityHangzhou 310058China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTai’an 271018China

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation,which is best studied in the mammalian models.Using in situ Hi-C,we have compared the 3D chromatin architectures of rice mesophyll and endosperm,foxtail millet bundle sheath and mesophyll,and maize bundle sheath,mesophyll and endosperm tissues.We found that their global A/B compartment partitions are stable across tissues,while local A/B compartment has tissue-specific dynamic associated with differential gene expression.Plant domains are largely stable across tissues,while new domain border formations are often associated with transcriptional activation in the region.Genes inside plant domains are not conserved across species,and lack significant co-expression behavior unlike those in mammalian TADs.Although we only observed chromatin loops between gene islands in the large genomes,the maize loop gene pairs’syntenic orthologs have shorter physical distances in small genome monocots,suggesting that loops instead of domains might have conserved biological function.Our study showed that plants’chromatin features might not have conserved biological functions as the mammalian ones.

关键词： plant chromatin domains Tissue-specific Hi-C analyses rice

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

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Molecular Plant 2017年第12期10卷 1497-1509页

作者： Pengfei Dong Xiaoyu Tu Po-Yu Chu Peitao Lu Ning Zhu Donald Grierson Baijuan Du pinghua li Silin Zhong State Key Laboratory of Crop Biology College of Agronomy Shandong Agricultural University Tai'an Shandong China State Key Laboratory of Agrobiotechnology School of Life Sciences The Chinese University of Hong Kong Hong Kong China Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang University Hangzhou Zhejiang China These authors contributed equally to this article.

The spatial organization of the genome plays an important role in the regulation of gene expression. How- ever, the core structural features of animal genomes, such as topologically associated domains （TADs） and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we examine the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin, and gene expression, of maize, tomato, sorghum, foxtail millet, and rice with genome sizes ranging from 0.4 to 2.4 Gb. We found that these plant genomes can be divided into mammalian-like A/B compartments. At higher resolution, the chromosomes of these plants can be further partitioned to local AJB compartments that reflect their euchromatin, heterochromatin, and polycomb status. Chromatins in all these plants are organized into domains that are not conserved across species. They show similarity to the Drosophila compartment domains, and are clustered into active, polycomb, repressive, and interme- diate types based on their transcriptional activities and epigenetic signatures, with domain border overlaps with the local A/B compartment junctions. In the large maize and tomato genomes, we observed extensive chromatin loops. However, unlike the mammalian chromatin loops that are enriched at the TAD border, plant chromatin loops are often formed between gene islands outside the repressive domains and are closely associated with active compartments. Our study indicates that plants have complex and unique 3D chromatin architectures, which require further study to elucidate their biological functions.

关键词： Hi-C chromatin loop compartment domain local compartment

Regulation of Leaf Angle by Auricle Development n Maize

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Molecular Plant 2017年第3期10卷 516-519页

作者： Fanying Kong Tingting Zhang Jisheng liu Siqi Heng Qingbiao Shi Haisen Zhang Zeli Wang Lei Ge pinghua li Xiaoduo Lu Gang li College of life Science State Key Laboratory of Crop Biology Shandong AgricuLtural University Tai'an Shandong 271018 China College of Agronomy Shandong Agricultural University Tai'an Shandong 271018 China Institute of Molecular Breeding for Maize Qilu Normal University Jinan Shandong 250200 China These authors contributed equally to this article.

In plants, the leaf angle （LA） affects how densely crops can be planted and thus is one of factors determining grain yield per acre. This complex quantitative trait is controlled by developmental signals, hormones, ... 详细信息

关键词： Regulation Leaf Angle Auricle Development in Maize

Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing

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Journal of Integrative Plant Biology 2018年第8期60卷 670-690页

作者： Yuling Zhang Rita Giuliani Youjun Zhang Yang Zhang Wagner Luiz Araujo Baichen Wang Peng liu Qi Sun Asaph Cousins Gerald Edwards Alisdair Fernie Thomas P. Brutnell pinghua li State Key Laboratory of Crop Biology College of Agronomic Sciences Shandong Agricultural University Tai'an 271018 China School of Biological Sciences Molecular Plant Sciences Washington State University Pullman WA 99164-4236 USA Max-Planck-lnsitut for Molekulare Pflanzenphysiologie Am Muhlenberg 1 Potsdam-Golm D-14476 Germany Department of Agronomy and Horticulture University of Nebraska-Lincoln Nebraska USA Photosynthesis Research Center Key Laboratory of Photobiology Institute of Botany Chinese Academy of Sciences No. 20 Nanxincun Xiangshan Beijing 100093 China Department of Statistics iowa State University Ames iowa 50011 USA Computational Biology Service Unit Life Sciences Core Laboratories Center Cornell University ithaca New York 14850 USA Donald Danforth Plant Science Center St. Louis Missouri 63132 USA

In C4 photosynthesis, pyruvate orthophosphate dikinase （PPDK） catalyzes the regeneration of phospho- enolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we use the maize transposable elements Nlutator and Ds to generate multiple mutant alleles of PPDK. Loss-of- function mutants are seedling lethal, even when plants were grown under 2% CO2, and they show very low capacity for CO2 assimilation, indicating C4 photosynthesis is essential in maize. Using RNA-seq and GC-MS technologies, we exam- ined the transcriptional and metabolic responses to a deficiency in PPDK activity. These results indicate loss of PPDK results in downregulation of gene expression ofenzymes of the C4 cycle, the Calvin cycle, and components of photochemistry. Furthermore, the loss of PPDK did not change Kranz anatomy, indicating that this metabolic defect in the C4 cycle did not impinge on the morphological differentiation of C4 characters. However, sugar metabolism and nitrogen utilization were altered in the mutants. An interaction between light intensity and genotype was also detected from transcriptome profiling, suggesting altered transcriptional and metabolic responses to environmental and endogenous signals in the PPDK mutants.

关键词： Characterization of maize leaf pyruvate orthophosphate dikinase using high throughput sequencing

不同月龄苏淮育肥猪纤维表观消化率、肠道长度与微生物差异分析

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南京农业大学学报 2024年第1期47卷 105-112页

作者：杜陶然牛清蒲广李开军刘根盛牛培培张总平李强李平华黄瑞华南京农业大学养猪研究所江苏南京210095 南京农业大学淮安研究院江苏淮安223001 淮安新势畜牧服务有限公司江苏淮安223001 淮安市淮阴新淮种猪场江苏淮安223322 上海市农业科学院上海201106

[目的]本试验旨在探究不同月龄苏淮育肥猪耐粗饲特征(以纤维表观消化率为评定表型)、肠道发育及肠道微生物的差异,并分析肠道发育及微生物与纤维表观消化率的相关性。[方法]试验选取82头出生条件相近的苏淮猪,在相同饲养环境下饲养,分别... 详细信息

[目的]本试验旨在探究不同月龄苏淮育肥猪耐粗饲特征(以纤维表观消化率为评定表型)、肠道发育及肠道微生物的差异,并分析肠道发育及微生物与纤维表观消化率的相关性。[方法]试验选取82头出生条件相近的苏淮猪,在相同饲养环境下饲养,分别在7、8月龄时进行屠宰。采集结肠后端内容物样品并测定不同月龄结肠后段各营养成分的表观消化率;测定肠道长度、周长,分析不同月龄苏淮育肥猪肠道营养成分表观消化率和肠道发育差异,并进行消化率与肠道长度、周长的相关性分析。同时,分别在7、8月龄猪中选取高纤维消化率组和低纤维消化率组各5头进行盲肠、结肠内容物常见纤维分解菌的丰度分析。[结果]8月龄苏淮猪的粗纤维、中性洗涤纤维、酸性洗涤纤维、粗蛋白和粗脂肪的表观消化率均显著高于7月龄(P<0.05),但8月龄苏淮猪大肠、小肠及整个肠道长度、盲肠、结肠周长与7月龄间无显著差异。盲肠周长与粗纤维、酸性洗涤纤维和粗脂肪的表观消化率呈显著正相关(P<0.05)。7月龄和8月龄苏淮猪的盲肠、结肠白化瘤胃球菌和柔嫩梭菌的丰度在高、低纤维消化率组间均无显著差异。7月龄苏淮猪的结肠柔嫩梭菌丰度在高、低纤维消化组均显著高于盲肠(P<0.05)。8月龄苏淮猪结肠柔嫩梭菌丰度在低纤维消化率组显著低于7月龄(P<0.05)。[结论]不同月龄苏淮猪耐粗饲特征不同,随月龄的增加,苏淮猪的消化性能逐渐完善,8月龄苏淮猪各营养成分表观消化率显著高于7月龄,且其纤维消化率与盲肠周长呈显著正相关,但肠道内容物中白化瘤胃球菌和柔嫩梭菌可能不是影响其纤维消化的关键微生物。

关键词：苏淮猪耐粗饲日龄表观消化率肠道发育肠道微生物

猪繁殖与呼吸综合征病毒GS15株NSP2蛋白多位点缺失病毒的拯救与体外生长特性分析

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微生物学报 2024年第7期64卷 2307-2322页

作者：张兴民张婧孙普李娇阳崔占鼎李国秀王健李平花袁红李坤曹轶梅付元芳李冬赵志荀曾巧英卢曾军甘肃农业大学动物医学院甘肃兰州730070 中国农业科学院兰州兽医研究所/兰州大学动物医学与生物安全学院动物疫病防控全国重点实验室甘肃兰州730000 甘肃省病原生物学基础学科研究中心甘肃兰州730046

【目的】本实验室前期在高致病性毒株PRRSV/GSWW/2015的感染性克隆上,拯救获得了非结构蛋白(non-structural protein 2,NSP2)第519-565位和第628-747位氨基酸双缺失的工程病毒(r GS15-?2)。本研究旨在在双缺失病毒的感染性克隆上,构建... 详细信息

【目的】本实验室前期在高致病性毒株PRRSV/GSWW/2015的感染性克隆上,拯救获得了非结构蛋白(non-structural protein 2,NSP2)第519-565位和第628-747位氨基酸双缺失的工程病毒(r GS15-?2)。本研究旨在在双缺失病毒的感染性克隆上,构建拯救获得NSP2三个位点缺失的工程病毒。【方法】在前期双缺失病毒感染性克隆的基础上,利用融合PCR方法分别构建缺失NSP2第323-364位和第372-433位优势抗原表位的两个3个位点缺失的重组质粒。经脂质体介导,转染Marc-145细胞拯救病毒,通过电子显微镜观察、免疫荧光实验、测定病毒滴度、绘制生长曲线等方法对缺失病毒的生长特性进行分析。【结果】成功获得拯救病毒r GS15-?3-1和r GS15-?3-2。电子显微镜下可以观察到直径大小为50-80 nm的病毒粒子;免疫荧光实验检测表明,拯救病毒与亲本病毒GS15一致,都能检测到PRRSV N蛋白表达;缺失区域RT-PCR扩增鉴定,拯救病毒传至40代缺失标记稳定存在;r GS15-△3-1与r GS15-△3-2病毒滴度分别为2.00×10^(6.0)TCID_(50)/m L和2.25×10^(5.8)TCID50/m L,与亲本病毒相比病毒滴度差异显著(P<0.05);生长曲线分析表明拯救病毒复制水平低于亲本病毒达到最高滴度的培养时间比亲本病毒延迟24 h。【结论】本研究通过对PRRSV基因2型非结构蛋白NSP2多位点缺失病毒的体外生长特性分析,为研制新型PRRSV标记疫苗奠定了基础,也为猪繁殖与呼吸综合征的防控提供新的策略。

关键词：猪繁殖与呼吸综合征病毒感染性克隆非结构蛋白2(NSP2) 缺失标记生长特性

细胞自噬相关蛋白ATG9A对口蹄疫病毒侵入的影响

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中国兽医科学 2024年第3期54卷 285-291页

作者：邓欣雨袁红王涛宫晓华赵俊芳包慧芳李平花孙普付元芳李坤刘在新卢曾军白兴文中国农业科学院兰州兽医研究所兰州大学动物医学与生物安全学院动物疫病防控全国重点实验室甘肃兰州730000

为揭示细胞自噬相关蛋白9A(ATG9A)对口蹄疫病毒(FMDV)复制的影响,利用IFA、RT-qPCR和Western-blot等方法检测FMDV与ATG9A的共定位情况以及病毒感染对ATG9A的影响;通过构建ATG9A重组表达质粒和合成小干扰RNA,检测过表达及敲降ATG9A对FMD... 详细信息

为揭示细胞自噬相关蛋白9A(ATG9A)对口蹄疫病毒(FMDV)复制的影响,利用IFA、RT-qPCR和Western-blot等方法检测FMDV与ATG9A的共定位情况以及病毒感染对ATG9A的影响;通过构建ATG9A重组表达质粒和合成小干扰RNA,检测过表达及敲降ATG9A对FMDV吸附、内化、基因组复制、蛋白翻译、子代病毒粒子产生的影响。结果显示,FMDV感染后与ATG9A共定位且抑制ATG9A的表达;ATG9A不影响FMDV的吸附,但极显著地抑制FMDV的内化过程;同时,过表达(或干扰)ATG9A能够在RNA与蛋白水平显著降低(或提高)FMDV的增殖和子代病毒粒子产生的能力。结论,ATG9A抑制FMDV的复制,为深入认识FMDV在细胞内的复制周期提供了线索。

关键词：自噬相关蛋白9A 口蹄疫病毒内化复制

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口蹄疫O型重组病毒的构建及其免疫原性分析

微生物学报 2024年第7期64卷 2493-2501页

作者：黄书伦查晶晶孙普章兴赜李冬曹轶梅白兴文付元芳马雪青李坤袁红卢曾军刘在新李平花中国农业科学院兰州兽医研究所/兰州大学动物医学与生物安全学院动物疫病防控全国重点实验室甘肃兰州730000 甘肃省病原生物学基础学科研究中心甘肃兰州730046

【目的】利用反向遗传操作技术,构建含O型口蹄疫病毒(food-and-mouth disease virus,FMDV)3个拓扑型免疫优势结构蛋白基因的重组FMDV,评估其作为猪O型口蹄疫(food-and-mouth disease,FMD)疫苗候选株的潜力。【方法】通过基因合成,在FMD... 详细信息

【目的】利用反向遗传操作技术,构建含O型口蹄疫病毒(food-and-mouth disease virus,FMDV)3个拓扑型免疫优势结构蛋白基因的重组FMDV,评估其作为猪O型口蹄疫(food-and-mouth disease,FMD)疫苗候选株的潜力。【方法】通过基因合成,在FMD疫苗株O/HN/CHA/93(古典中国拓扑型)的基因中嵌合流行株O/NXYCh/CHA/2018(东南亚拓扑型)VP1结构蛋白的重组病毒骨架上,用O/TUR/5/2009疫苗株(中东-南亚拓扑型)VP1蛋白的G-H环基因替换其对等基因,构建含O型3个拓扑型FMDV结构蛋白基因的重组全长质粒,Not I线性化后转染表达T7 RNA聚合酶的BSR/T7细胞,拯救重组病毒。通过RT-PCR、序列测定、间接免疫荧光鉴定重组病毒;噬斑试验和一步生长曲线分析重组病毒的生物学特性。重组病毒制备疫苗免疫猪,用病毒中和试验分析其对当前流行的O型3个拓扑型FMDV的交叉反应性。【结果】成功拯救到含O型3个拓扑型FMDV结构蛋白基因的重组病毒,重组病毒与亲本病毒具有相似的生物学特性。亲本病毒和重组病毒制备的疫苗免疫猪,均能够对中东-南亚型(Middle East-South Asia,ME-SA)拓扑型和东南亚型(South-East Asia,SEA)拓扑型病毒株产生保护性平均中和抗体(>1.65log10);均不能对古典中国型(Cathay)拓扑型流行株产生保护性平均中和抗体(<1.65log10),但与亲本病毒相比,O/TUR/5/2009疫苗株G-H环基因的替换显著提高了对ME-SA和SEA拓扑型病毒株的交叉反应性(P<0.05)。【结论】本研究对未来FMD疫苗的设计具有重要的指导意义。

关键词：口蹄疫(FMD) 重组病毒构建免疫原性

一株羊肠道病毒的分离鉴定及其基因组特征分析

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中国兽医科学 2024年第4期54卷 511-518页

作者：张雨星马雪青李平花魏达礼李冬张婧王卉袁红王萌白兴文刘在新卢曾军曾巧英王桂荣孙普甘肃农业大学动物医学院甘肃兰州1730070 中国农业科学院兰州兽医研究所兰州大学动物医学与生物安全学院动物疫病防控全国重点实验室甘肃兰州730046 甘肃省病原生物学基础学科研究中心甘肃兰州730046

本研究利用宏基因组测序技术,从死亡湖羊淋巴组织中检测出小反刍兽疫病毒与羊肠道病毒混合感染,为了分离羊肠道病毒,采取病毒总RNA转染BHK21细胞方法,连续传代后,通过致细胞病变、测序、TCID_(50)测定和病毒一步生长曲线、电镜观察等鉴... 详细信息

本研究利用宏基因组测序技术,从死亡湖羊淋巴组织中检测出小反刍兽疫病毒与羊肠道病毒混合感染,为了分离羊肠道病毒,采取病毒总RNA转染BHK21细胞方法,连续传代后,通过致细胞病变、测序、TCID_(50)测定和病毒一步生长曲线、电镜观察等鉴定分离出病毒,并与参考毒株比对分析分离病毒的基因特征。结果显示,转染病毒总RNA的BHK21细胞传至第2代就出现了明显的致细胞病变效应,测序证明培养物中仅含羊肠道病毒,其基因组全长为7446 nt,其中5′UTR长821 nt,3′UTR长109 nt,ORF长6516 nt,与参考毒株比较可划分为G种肠道病毒,病毒粒子大小为20~30 nm,第6代细胞毒感染8 h时TCID_(50)值最高,为10^(-4.2)/0.1 mL,命名为JSNT/1/2022株。本研究首次利用组织病料RNA转染细胞的方法成功分离出1株羊肠道病毒,说明羊肠道病毒核酸具有感染性,为羊肠道病毒的分离鉴定探索了一种更为可靠的方法,也为羊肠道病毒相关基础与应用研究奠定了病原学基础。

关键词：羊肠道病毒分离鉴定 RNA感染性基因组