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| 1 | A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice显示文摘Grain size is one of the most important factors that control rice yield,as it is associated with grain weight(GW).To date,dozens of rice genes that regulate grain size have been isolated;however,the regulatory mechanism underlying GW control is not fully understood.Here,the quantitative trait locus qGL5 for grain length(GL)and GW was identified in recombinant inbred lines of 9311 and Nipponbare(NPB)and fine mapped to a candidate gene,OsAUX3.Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW.RNA sequencing,gene expression quantification,dual-luciferase reporter assays,chromatin immunoprecipitation-quantitative PCR,and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3.OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter,covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung,and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells.Furthermore,we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing.Taken together,our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice,providing a potential target for the improvement of rice yield. | Jiyue Qiao Hongzhen Jiang Yuqing Lin Lianguang Shang Mei Wang Dongming Li Xiangdong Fu Markus Geisler Yanhua Qi Zhenyu Gao Qian Qian | 2021 | Molecular Plant2021，14，10： | 8 |
| 2 | Newborn screening with targeted sequencing:a multicenter investigation and a pilot clinical study in China显示文摘Different newborn screening(NBS) programs have been practiced in many countries since the 1960 s. It is of considerable interest whether next-generation sequencing is applicable in NBS. We have developed a panel of 465 causative genes for 596 early-onset, relatively high incidence, and potentially actionable severe inherited diseases in our Newborn Screening with Targeted Sequencing(NESTS) program to screen 11,484 babies in 8 Women and Children’s hospitals nationwide in China retrospectively. The positive rate from preliminary screening of NESTS was 7.85%(902/11,484). With 45.89%(414/902) follow-up of preliminary positive cases, the overall clinically confirmative diagnosis rate of monogenic disorders was 12.07%(50/414), estimating an average of 0.95%(7.85% × 12.07%) clinical diagnosis rate, suggesting that monogenic disorders account for a considerable proportion of birth defects. The disease/gene spectrum varied in different regions of China. NESTS was implemented in a hospital by screening 3923 newborns to evaluate its clinical application. The turn-around time of a primary report, including the sequencing period of < 7 days, was within 11 days by our automatic interpretation pipeline. Our results suggest that NESTS is feasible and cost-effective as a first-tier NBS program, which will change the status of current clinical practice of NBS in China. | Chanjuan Hao Ruolan Guo Xuyun Hu Zhan Qi Qi Guo Xuanshi Liu Yuanhu Liu Yanhua Sun Xiaofen Zhang Feng Jin Xiujie Wu Ren Cai Dingyuan Zeng Xijiang Hu Xiaohua Wang Xiaoping Ji Wenjie Li Quansheng Xing Lanfang Mu Xiulian Jiang Xue Yang Weimin Yang Yan Zhang Qianli Yin Xin Ni Wei Li | 2022 | Journal of Genetics and Genomics2022，49，1： | 7 |
| 3 | The chimeric genes in the hybrid lineage of Carassius auratus cuvieri(♀)×Carassius auratus red var.(♂)显示文摘Hybridization can combine the genomes of different strains or species, which leads to changes of genotype and phenotype in the hybrids. In this study, we aimed to investigate the genetic variations of hybrids(WR-F1 and WR-F2) derived from the intraspecific hybridization of white crucian carp(Carassius auratus cuvieri, WCC, ♀) and red crucian carp(Carassius auratus red var., RCC, ♂). Here, we compared the orthologous genes in the liver transcriptomes of hybrids with those of WCC and RCC, and classified the orthologous genes into eight gene patterns within three categories(chimera, mutant, and biparental origin genes).The results revealed 19.04%, 4.17% chimeric genes and 6.90%, 5.05% mutations of orthologous genes in WR-F1 and WR-F2 respectively. Seventeen of twenty-three characterized genes(77%) were confirmed to be the chimeras at the genomic DNA level.The GO classification discovered that some chimeric and mutant genes were related to metabolic process, immune system and developmental process in WR-F1. Our results provide the new evidence that hybridization can combine the parental genomes,leading to changes in the genotype of the resultant hybrids. This is the first report on the formation of chimeric genes from fish intraspecific hybridization, which is potentially interesting from the context of both evolution and the genetic breeding of fish. | Qingfeng Liu Yanhua Qi Qiuli Liang Xiujuan Xu Fangzhou Hu Jing Wang Jun Xiao Shi Wang Wuhui Li Min Tao Qinbo Qin Rurong Zhao Zhanzhou Yao Shaojun Liu | 2018 | Science China(Life Sciences)2018，61，9： | 6 |
| 4 | Targeted disruption of tyrosinase causes melanin reduction in Carassius auratus cuvieri and its hybrid progeny显示文摘The white crucian carp(Carassius auratus cuvieri,WCC) not only is one of the most economically important fish in Asia,characterized by strong reproductive ability and rapid growth rates,but also represents a good germplasm to produce hybrid progenies with heterosis.Gene knockout technique provides a safe and acceptant way for fish breeding.Achieving gene knockout in WCC and its hybrid progeny will be of great importance for both genetic studies and hybridization breeding.Tyrosinase(TYR) is a key enzyme in melanin synthesis.Depletion of tyr in zebrafish and mice results in mosaic pigmentation or total albinism.Here,we successfully used CRISPR-Cas9 to target tyr in WCC and its hybrid progeny(WR) derived from the cross of WCC(♀) and red crucian carp(Carassius auratus red var.,RCC,♂).The level of TYR protein was significantly reduced in mutant WCC.Both the mutant WCC and the mutant WR showed different degrees of melanin reduction compared with the wild-type sibling control fish,resulting from different mutation efficiency ranging from 60% to 90%.In addition,the transcriptional expression profiles of a series of pivotal pigment synthesis genes,i.e.tyrp1,mitfa,mitfb,dct and sox10,were down-regulated in tyr-CRISPR WCC,which ultimately caused a reduction in melanin synthesis.These results demonstrated that tyr plays a key role in melanin synthesis in WCC and WR,and CRISPR-Cas9 is an effective tool for modifying the genome of economical fish.Furthermore,the tyr-CRISPR models could be valuable in understanding fundamental mechanisms of pigment formation in non-model fish. | Qingfeng Liu Yanhua Qi Qiuli Liang Jia Song Junmei Liu Wuhui Li Yuqin Shu Min Tao Chun Zhang Qinbo Qin Jing Wang Shaojun Liu | 2019 | Science China(Life Sciences)2019，62，9： | 4 |
| 5 | Primary root and root hair development regulation by OsAUX4 and its participation in the phosphate starvation response显示文摘Among the five members of AUX1/LAX genes coding for auxin carriers in rice,only OsAUX1 and OsAUX3 have been reported.To understand the function of the other AUX1/LAX genes,two independent alleles of osaux4 mutants,osaux4-1 and osaux4-2,were constructed using the CRISPR/Cas9 editing system.Homozygous osaux4-1 or osaux4-2 exhibited shorter primary root(PR)and longer root hair(RH)compared to the wild-type Dongjin(WT/DJ),and lost response to indoleacetic acid(IAA)treatment.OsAUX4 is intensively expressed in roots and localized on the plasma membrane,suggesting that OsAUX4 might function in the regulation of root development.The decreased meristem cell division activity and the downregulated expression of cell cycle genes in root apices of osaux4 mutants supported the hypothesis that OsAUX4 positively regulates PR elongation.OsAUX4 is expressed in RH,and osaux4 mutants showing longer RH compared to WT/DJ implies that OsAUX4 negatively regulates RH development.Furthermore,osaux4 mutants are insensitive to Pi starvation(-Pi)and OsAUX4 effects on the-Pi response is associated with altered expression levels of Pi starvation-regulated genes,and auxin distribution/contents.This study revealed that OsAUX4 not only regulates PR and RH development but also plays a regulatory role in crosstalk between auxin and-Pi signaling. | Rigui Ye Yunrong Wu Zhenyu Gao Hao Chen Lixia Jia Dongming Li Xugang Li Qian Qian Yanhua Qi | 2021 | Journal of Integrative Plant Biology2021，63，8： | 3 |
| 6 | Advances in structure and function of auxin response factor in plants显示文摘Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development.Auxin signal transduction is mainly controlled by two gene families:auxin response factor(ARF)and auxin/indole-3-acetic acid(Aux/IAA).ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxinresponsive genes.ARF proteins contain three conserved regions:a conserved N-terminal B3DNA-binding domain,a variable intermediate middle region domain that functions in activation or repression,and a C-terminal domain including the Phox and Bem1p region for dimerization,similar to theⅢandⅣelements of Aux/IAA,which facilitate protein–protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins.In the two decades following the identification of the first ARF,23 ARF members have been identified and characterized in Arabidopsis.Using whole-genome sequencing,22,25,23,25,and 36 ARF genes have been identified in tomato,rice,wheat,sorghum,and maize,respectively,in addition to which the related biofunctions of some ARFs have been reported.ARFs play crucial roles in regulating the growth and development of roots,leaves,flowers,fruits,seeds,responses to biotic and abiotic stresses,and phytohormone signal crosstalk.In this review,we summarize the research progress on the structures and functions of ARFs in Arabidopsis,tomato,and cereal crops,to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops. | Yonghui Li Shaqila Han Yanhua Qi | 2023 | Journal of Integrative Plant Biology2023，65，3： | 2 |
| 7 | RGS16 regulated by let-7c-5p promotes glioma progression by activating PI3K-AKT pathway显示文摘Gliomas are the most common central nervous system tumours;they are highly aggressive and have a poor prognosis. RGS16 belongs to the regulator of G-protein signalling (RGS) protein family, which plays an important role in promoting various cancers, such as breast cancer, pancreatic cancer, and colorectal cancer. Moreover, previous studies confirmed that let-7c-5p, a well-known microRNA, can act as a tumour suppressor to regulate the progression of various tumours by inhibiting the expression of its target genes. However, whether RGS16 can promote the progression of glioma and whether it is regulated by miR let-7c-5p are still unknown. Here, we confirmed that RGS16 is upregulated in glioma tissues and that high expression of RGS16 is associated with poor survival. Ectopic deletion of RGS16 significantly suppressed glioma cell proliferation and migration both in vitro and in vivo. Moreover, RGS16 was validated as a direct target gene of miR let-7c-5p. The overexpression of miR let-7c-5p obviously downregulated the expression of RGS16, and knocking down miR let-7c-5p had the opposite effect. Thus, we suggest that the suppression of RGS16 by miR let-7c-5p can promote glioma progression and may serve as a potential prognostic biomarker and therapeutic target in glioma. | Chaochao Wang Hao Xue Rongrong Zhao Zhongzheng Sun Xiao Gao Yanhua Qi Huizhi Wang Jianye Xu Lin Deng Gang Li | 2023 | Frontiers of Medicine2023，17，1： | 2 |
| 8 | Monitoring and identifying pendant droplets in microbottle resonators显示文摘Optofluidic resonators are capable of characterizing various fluidic media.Here,we propose an optofluidic microbottle resonator(OFMBR)that is applied to generate pendant droplets,whose maximum mass is related to the liquid surface tension.Mass and type of droplets forming along the OFMBR stem can be monitored in real time by spectrum variation.As a pendant droplet grows,increased droplet gravity introduces a decreased coupling gap and compressive force between the tapered fiber and OFMBR,leading to a resonance wavelength shift.The operation mechanism of the proposed sensors is validated by theoretical simulation and experimental results.From the experimental spectra,a liquid mass sensor with maximum sensitivity of−3.34pm/mg is obtained,and distilled water and alcohol can be identified.This scheme provides a new thread for droplet generation as well as fluidic properties characterization. | Zijie Wang Xiaobei Zhang Qi Zhang Yiqi Chen Yong Yang Yang Yu Yang Wang Yanhua Dong Yi Huang Tingyun Wang | 2022 | Photonics Research2022，10，3： | 2 |
| 9 | Identification of A Novel SBF2 Frameshift Mutation in Charcot–Marie–Tooth Disease Type 4B2 Using Whole-exome Sequencing显示文摘Charcot–Marie–Tooth disease type 4B2 with early-onset glaucoma(CMT4B2, OMIM604563) is a genetically-heterogeneous childhood-onset neuromuscular disorder. Here, we report the case of a 15-year-old male adolescent with lower extremity weakness, gait abnormalities, foot deformities and early-onset glaucoma. Since clinical diagnosis alone was insufficient for providing pathogenetic evidence to indicate that the condition belonged to a consanguineous family, we applied whole-exome sequencing to samples from the patient, his parents and his younger brother,assuming that the patient's condition is transmitted in an autosomal recessive pattern. A frame-shift mutation, c.4571 del G(P.Gly1524Glufs*42), was revealed in the CMT4B2-related gene SBF2(also known as MTMR13, MIM 607697), and this mutation was found to be homozygous in the proband and heterozygous in his parents and younger brother. Together with the results of clinical diagnosis,this case was diagnosed as CMT4B2. Our finding further demonstrates the use of whole-exome sequencing in the diagnosis and treatment of rare diseases. | Meiyan Chen Jing Wu Ning Liang Lihui Tang Yanhua Chen Huishuang Chen Wei Wei Tianying Wei Hui Huang Xin Yi Ming Qi | 2014 | Genomics, Proteomics & Bioinformatics2014，12，5： | 1 |
| 10 | High performance Au/Ag core/shell bipyramids for determination of thiram based on surface‐enhanced Raman scattering显示文摘 | Xia Zheng Yanhua Chen Yang Chen Ning Bi Haibo Qi Meihong Qin Dan Song Hanqi Zhang Yuan Tian | 2012 | J Raman Spectrosc2012，，10： | 1 |
| 11 | Determination of mercury(II) by surface-enhanced Raman scattering spectroscopy based on thiol-functionalized silver nanoparticles显示文摘 | Yang Chen Lihang Wu Yanhua Chen Ning Bi Xia Zheng Haibo Qi Meihong Qin Xue Liao Hanqi Zhang Yuan Tian | 2012 | Microchimica Acta2012，，3： | 1 |
| 12 | Generation of cell-type-specific gene mutations by expressing the sgRNA of the CRISPR system from the RNA polymerase II promoters显示文摘 | Jiaqiang Wang (1) Xin Li (1) (2) Yanhua Zhao (1) Jingyu Li (1) Qi Zhou (1) (2) Zhonghua Liu (1) | 2015 | Protein & Cell2015，6，9： | 1 |
| 13 | Multiomics approach reveals the ubiquitination-specific processes hijacked by SARS-CoV-2显示文摘The Coronavirus Disease 2019(COVID-19)caused by Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2)is a global pandemic that seriously threatens health and socioeconomic development,but the existed antiviral drugs and vaccines still cannot yet halt the spread of the epidemic.Therefore,a comprehensive and profound understanding of the pathogenesis of SARS-CoV-2 is urgently needed to explore effective therapeutic targets.Here,we conducted a multiomics study of SARS-CoV-2-infected lung epithelial cells,including transcriptomic,proteomic,and ubiquitinomic.Multiomics analysis showed that SARS-CoV-2-infected lung epithelial cells activated strong innate immune response,including interferon and inflammatory responses.Ubiquitinomic further reveals the underlying mechanism of SARS-CoV-2 disrupting the host innate immune response.In addition,SARS-CoV-2 proteins were found to be ubiquitinated during infection despite the fact that SARS-CoV-2 itself didn’t code any E3 ligase,and that ubiquitination at three sites on the Spike protein could significantly enhance viral infection.Further screening of the E3 ubiquitin ligases and deubiquitinating enzymes(DUBs)library revealed four E3 ligases influencing SARS-CoV-2 infection,thus providing several new antiviral targets.This multiomics combined with high-throughput screening study reveals that SARS-CoV-2 not only modulates innate immunity,but also promotes viral infection,by hijacking ubiquitination-specific processes,highlighting potential antiviral and anti-inflammation targets. | Gang Xu Yezi Wu Tongyang Xiao Furong Qi Lujie Fan Shengyuan Zhang Jian Zhou Yanhua He Xiang Gao Hongxiang Zeng Yunfei Li Zheng Zhang | 2022 | Signal Transduction and Targeted Therapy2022，7，10： | 1 |
| 14 | Inhibitor of Growth 4 Induces Growth Suppression and Apoptosis in Glioma U87MG显示文摘 | Li Xiaomei Cai Limin Chen Hui Zhang Qingyuan Zhang Shujun Wang Yanhua Dong Yanyan Cheng Hui Qi Jiping | 2009 | Pathobiology2009，，4： | 1 |
| 15 | Identification and cloning of a submergence-induced gene OsGGT (glycogenin glucosyltransferase) from rice (Oryza sativa L.) by suppression subtractive hybridization显示文摘 | YanHua Qi Naoyoshi Kawano Yasuo Yamauchi JianQun Ling DeBao Li Kiyoshi Tanaka | 2005 | Planta2005，，3： | 1 |
| 16 | UPLC-QTOF/MS Method for Screening and Determination of 59 Non-labeled Components in Veterinary Drug Preparations显示文摘[Objectives]This study was conducted to provide an accurate and reliable method for rapid high-throughput screening of veterinary drug preparations.[Methods]For the matrixes of veterinary drug preparations,high-performance liquid chromatography-high resolution quadrupole time-of-flight mass spectrometry(UPLC-QTOF/MS)was used to establish a fast screening method for 59 non-standard components in five categories of antiviral agents,aminoglycosides,quinolones,sulfonamides,and tetracyclines in veterinary drugs.The target drugs were separated by a Waters ACQUITY UPLC HSS T3 chromatographic column(50 mm×2.1 mm,1.8μm),and data were collected in the positive ion mode.Good separation of the 59 drugs was achieved within 7 min.[Results]In the concentration range of 0-100 ng/ml,each drug showed a good linear relationship,and the correlation coefficients were all greater than 0.999.The detection limits of the 59 drugs were in the range of 0.1-0.5 mg/ml,and the recovery under the addition concentration of 5 mg/ml was in the range of 85.2%-103.8%.[Conclusions]The method is fast,simple,accurate,and highly sensitive,and is suitable for high-throughput screening and qualitative identification of non-standard components in veterinary drug preparations. | Xueliang PANG Lei WANG Biao QI Sining TANG Yanhua YAN Xuesong WANG Lixue DONG Yi ZHANG Aijun LI | 2022 | Agricultural Biotechnology2022，11，1： | 1 |
| 17 | An atypical phenojpe of Reis-B ü cklers comeal dystrophy caused by the G623D mutation in TGFBI显示文摘 | Dandan Li Yanhua Qi Wang Li | 2008 | Mol Vis2008，14，： | 1 |
| 18 | Discovery of potential anti-SARS-CoV-2 drugs based on large-scale screening in vitro and effect evaluation in vivo显示文摘The coronavirus disease 2019(COVID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARSCoV-2)is a global crisis.Clinical candidates with high efficacy,ready availability,and that do not develop resistance are in urgent need.Despite that screening to repurpose clinically approved drugs has provided a variety of hits shown to be effective against SARS-CoV-2 infection in cell culture,there are few confirmed antiviral candidates in vivo.In this study,94 compounds showing high antiviral activity against SARS-CoV-2 in Vero E6 cells were identified from 2,580 FDA-approved small-molecule drugs.Among them,24 compounds with low cytotoxicity were selected,and of these,17 compounds also effectively suppressed SARS-CoV-2 infection in He La cells transduced with human ACE2.Six compounds disturb multiple processes of the SARSCoV-2 life cycle.Their prophylactic efficacies were determined in vivo using Syrian hamsters challenged with SARS-CoV-2infection.Seven compounds reduced weight loss and promoted weight regain of hamsters infected not only with the original strain but also the D614G variant.Except for cisatracurium,six compounds reduced hamster pulmonary viral load,and IL-6 and TNF-αm RNAwhen assayed at 4 d postinfection.In particular,sertraline,salinomycin,and gilteritinib showed similar protective effects as remdesivir in vivo and did not induce antiviral drug resistance after 10 serial passages of SARS-CoV-2 in vitro,suggesting promising application for COVID-19 treatment. | Haoran Peng Cuiling Ding Liangliang Jiang Wanda Tang Yan Liu Lanjuan Zhao Zhigang Yi Hao Ren Chong Li Yanhua He Xu Zheng Hailin Tang Zhihui Chen Zhongtian Qi Ping Zhao | 2022 | Science China(Life Sciences)2022，65，6： | 1 |
| 19 | OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice显示文摘Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root(PR) absorbs mineral nutrients and provides mechanical support;however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4(Os RLR4), osrlr4-1 and osrlr4-2 with longer PR, and three Os RLR4 overexpression lines, OE-Os RLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung(WT/HY), were identified. Os RLR4 isone of five members of the PRAF subfamily of the regulator chromosome condensation1(RCC1) family. Phylogenetic analysis of Os RLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. Os RLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that Os RLR4 functions directly upstream of the auxin transporter Os AUX1. Moreover, Os RLR4 interacts with the TRITHORAX-like protein Os Trx1 to promote H3 K4 me3 deposition at the Os AUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding. | Chendong Sun Dongming Li Zhenyu Gao Lei Gao Lianguang Shang Mei Wang Jiyue Qiao Shilin Ding Chuanyou Li Markus Geisler Dean Jiang Yanhua Qi Qian Qian | 2022 | Journal of Integrative Plant Biology2022，64，1： | 0 |
| 20 | Erratum to: Generation of cell-type-specfic gene mutations by expressing the sgRNA of the CRISPR system from the RNA polymerase II promoters显示文摘 | Jiaqiang Wang Xin Li Yanhua Zhao Jingyu Li Qi Zhou Zhonghua Liu | 2015 | Protein & Cell2015，6，12： | 0 |
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