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Melatonin activates the OsbZIP79–OsABI5 module that orchestrates nitrogen and ROS homeostasis to alleviate nitrogen-limitation stress in rice

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Plant Communications 2023年第6期4卷 113-133页

作者： Meng Jiang Yue Song Ruifang Yang Chenfan Zheng Yunchao Zheng Huali Zhang Shan Li Yuanyuan Tan Jianzhong Huang Qingyao Shu Ruiqing Li Hainan Institute Zhejiang UniversityYazhou Bay Sci-Tech CitySanyaChina National key laboratory of rice breeding and Biology and Zhejiang provincial key laboratory of Crop Germplasm The Advanced Seed InstituteZhejiang UniversityHangzhouChina College of Agronomy Anhui Agricultural UniversityHefeiChina Crop breeding and Cultivation Research Institute Shanghai Academy of Agricultural SciencesShanghaiChina School of Life Sciences Westlake UniversityHangzhouChina State key laboratory of rice breeding and Biology and Chinese National Center for rice Improvement China National Rice Research InstituteHangzhouChina

Melatonin(Mel)has previously been reported to effectively alleviate nitrogen-limitation(N-L)stress and thus increase nitrogen-use efficiency(NUE)in several plants,but the underlying mechanism remains obscure.Here,we revealed that OsbZIP79(BASIC LEUCINE ZIPPER 79)is transcriptionally activated under N-L conditions,and its expression is further enhanced by exogenous Mel.By the combined use of omics,genetics,and biological techniques,we revealed that the OsbZIP79–OsABI5(ABSCISIC ACID INSENSITIVE 5)module stimulated regulation of reactive oxygen species(ROS)homeostasis and the uptake and metabolismof nitrogen under conditions of indoor nitrogen limitation(1/16 normal level).OsbZIP79 activated the transcription of OsABI5,and OsABI5 then bound to the promoters of target genes,including genes involved in ROS homeostasis and nitrogen metabolism,activating their transcription.This module was also indispensable for upregulation of several other genes involved in abscisic acid catabolism,nitrogen uptake,and assimilation under N-L and Mel treatment,although these genes were not directly transactivated by OsABI5.Field experiments demonstrated that Mel significantly improved rice growth under low nitrogen(L-N,half the normal level)by the same mechanism revealed in the nitrogen-limitation study.Mel application produced a 28.6%yield increase under L-N and thus similar increases in NUE.Also,two OsbZIP79-overexpression lines grown in L-N field plots had significantly higher NUE(+13.7%and+21.2%)than their wild types.Together,our data show that an OsbZIP79–OsABI5 module regulates the rice response to N insufficiency(N limitation or low N),which is important for increasing NUE in rice production.

关键词： melatonin peroxidase nitrogen starvation allantoinase ROS signaling

m^(6)A demethylase FTO regulate CTNNB1 to promote adipogenesis of chicken preadipocyte

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Journal of Animal Science and Biotechnology 2023年第2期14卷 578-592页

作者： Kan Li Weichen Huang Zhijun Wang Qinghua Nie Department of Animal genetics Breeding and ReproductionCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China National‑Local Joint Engineering Research Center for Livestock breeding Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breedingand Key Laboratory of Chicken GeneticsBreeding and ReproductionMinistry of AgricultureGuangzhou 510642China

Background:N6-methyladenosine(m^(6)A)is an abundant post-transcriptional RNA modification that affects various biological processes.The fat mass and obesity-associated(FTO)protein,a demethylase encoded by the FTO gene,has been found to regulate adipocyte development in an m^(6)A-dependent manner in multiple species.However,the effects of the m^(6)A methylation and FTO demethylation functions on chicken adipogenesis remain unclear.This study aims to explore the association between m^(6)A modification and chicken adipogenesis and the underlying mechanism by which FTO affects chicken preadipocyte development.Results:The association between m^(6)A modification and chicken lipogenesis was assessed by treating chicken pread-ipocytes with different doses of methyl donor betaine and methylation inhibitor cycloleucine.The results showed that betaine significantly increased methylation levels and inhibited lipogenesis,and the inverse effect was found in preadipocytes after cycloleucine treatment.Overexpression of FTO significantly inhibited m^(6)A levels and promoted proliferation and differentiation of chicken preadipocytes.Silencing FTO showed opposite results.Mechanistically,FTO overexpression increased the expression of catenin beta 1(CTNNB1)by improving RNA stability in an m^(6)A-dependent manner,and we proved that FTO could directly target CTNNB1.Furthermore,CTNNB1 may be a positive regulator of adipogenesis in chicken preadipocytes.Conclusions:m^(6)A methylation of RNA was negatively associated with adipogenesis of chicken preadipocytes.FTO could regulate CTNNB1 expression in a demethylation manner to promote lipogenesis.

关键词： Adipogenesis Chicken CTNNB1 FTO m^(6)A

circPTPN4 regulates myogenesis via the miR-499-3p/NAMPT axis

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Journal of Animal Science and Biotechnology 2022年第3期13卷 682-696页

作者： Bolin Cai Manting Ma Zhen Zhou Shaofen Kong Jing Zhang Xiquan Zhang Qinghua Nie State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642GuangdongChina Guangdong provincial key lab of Agro-Animal Genomics and Molecular breeding and Key Laboratory of Chicken GeneticsBreeding and ReproductionMinistry of AgricultureGuangzhou 510642GuangdongChina

Background:Circular RNAs(circ RNAs)are a novel class of endogenous nc RNA,which widely exist in the transcriptomes of different species and tissues.Recent studies indicate important roles for circ RNAs in the regulation of gene expression by acting as competing endogenous RNAs(ce RNAs).However,the specific role of circ RNAs in myogenesis is still poorly understood.In this study,we attempted to systematically identify the circ RNAs involved in myogenesis and analyze the biological functions of circ RNAs in chicken skeletal muscle development.Results:In total,532 circ RNAs were identified as being differentially expressed between pectoralis major(PEM)and soleus(SOL)in 7-week-old Xinghua chicken.Among them,a novel circ RNA(novel_circ_002621),generated by PTPN4 gene,was named circ PTPN4 and identified.circ PTPN4 is highly expressed in skeletal muscle,and its expression level is upregulated during myoblast differentiation.circ PTPN4 facilitates the proliferation and differentiation of myoblast.Moreover,circ PTPN4 suppresses mitochondria biogenesis and activates fast-twitch muscle phenotype.Mechanistically,circ PTPN4 can function as a ce RNA to regulate NAMPT expression by sponging mi R-499-3p,thus participating in AMPK signaling.Conclusions:circ PTPN4 functions as a ce RNA to regulate NAMPT expression by sponging mi R-499-3p,thus promoting the proliferation and differentiation of myoblast,as well as activating fast-twitch muscle phenotype.

关键词： Chicken Circ PTPN4 Circular RNA MiR-499-3p Myogenesis NAMPT The transformation of myofiber

MicroRNAs Involved in Skeletal Muscle Differentiation

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Journal of genetics and Genomics 2013年第3期40卷 107-116页

作者： Wen Luo Qinghua Nie Xiquan Zhang Guangdong provincial key lab of Agro-Animal Genomics and Molecular breeding and Key Lab of Chicken Genetics Breeding and Reproduction Ministry ofAgriculture South China Agricultural University

MicroRNAs （miRNAs） negatively regulate gene expression by promoting degradation of target mRNAs or inhibiting their translation. Previous studies have expanded our understanding that miRNAs play an important role in myogenesis and have a big impact on muscle mass, muscle fiber type and muscle-related diseases. The muscle-specific miRNAs, miR-206, miR-1 and miR-133, are among the most studied and best characterized miRNAs in skeletal muscle differentiation. They have a profound influence on multiple muscle differ- entiation processes, such as alternative splicing, DNA synthesis, and cell apoptosis. Many non-muscle-specific miRNAs are also required for the differentiation of muscle through interaction with myogenic factors. Studying the regulatory mechanisms of these miRNAs in muscle differentiation will extend our knowledge of miRNAs in muscle biology and will improve our understanding of the myogenesis regulation.

关键词： MicroRNAs Skeletal muscle Differentiation Regulation

Advances on genetic and genomic studies of ALV resistance

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Journal of Animal Science and Biotechnology 2023年第1期14卷 1-14页

作者： Guodong Mo Ping Wei Bowen Hu Qinghua Nie Xiquan Zhang Guangdong provincial key laboratory of Agro‑Animal Genomics and Molecular breeding College of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642GuangdongChina key lab of Chicken genetics Breeding and ReproductionMinistry of AgricultureGuangzhou 510642GuangdongChina State key laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources South China Agricultural UniversityGuangzhou 510642GuangdongChina Institute for Poultry Science and Health Guangxi UniversityNanning 530001GuangxiChina.

Avian leukosis(AL)is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus(ALV).No vaccine or drug is currently available for the disease.Therefore,the disease can result in severe economic losses in poultry flocks.Increasing the resistance of poultry to ALV may be one effective strategy.In this review,we provide an overview of the roles of genes associated with ALV infection in the poultry genome,including endogenous retroviruses,virus receptors,interferon-stimulated genes,and other immune-related genes.Furthermore,some methods and techniques that can improve ALV resistance in poultry are discussed.The objectives are willing to provide some valuable references for disease resistance breeding in poultry.

关键词： Avian leukosis Endogenous retrovirus Gene editing Immunity Interferon-stimulated genes Receptor Resistant breeding

Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean

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Journal of Integrative Plant Biology 2023年第7期65卷 1636-1650页

作者： Wei Wei Long Lu Xiao-Hua Bian Qing-Tian Li Jia-Qi Han Jian-Jun Tao Cui-Cui Yin Yong-Cai Lai Wei Li Ying-Dong Bi Wei-Qun Man Shou-Yi Chen Jin-Song Zhang Wan-Ke Zhang State key lab of Plant Genomics Institute of Genetics and Developmental BiologyINASEEDChinese Academy of SciencesBeijing 100101China key lab of Ministry of Education for genetics Breeding and Multiple Utilization of CropsCollege of Crop SciencesFujian Agriculture and Forestry UniversityFuzhou 350002China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China Institute of Farming and Cultivation Heilongjiang Provincial Academy of Agricultural SciencesHarbin 150086China Institute of Soybean Research Heilongjiang Provincial Academy of Agricultural SciencesHarbin 150086China

Abiotic stress is one of the most important factors reducing soybean yield. It is essential to identify regulatory factors contributing to stress responses.A previous study found that the tandem CCCH zincfinger protein Gm ZF351 is an oil level regulator. In this study, we discovered that the Gm ZF351 gene is induced by stress and that the overexpression of Gm ZF351 confers stress tolerance to transgenic soybean. Gm ZF351 directly regulates the expression of Gm CIPK9 and Gm SnRK, leading to stomata closing, by binding to their promoter regions, which carry two CT(G/C)(T/A)AA elements.Stress induction of Gm ZF351 is mediated through reduction in the H3K27me3 level at the Gm ZF351locus.TwoJMJ30-demethylase-likegenes,Gm JMJ30-1 and Gm JMJ30-2, are involved in this demethylationprocess.Overexpressionof Gm JMJ30-1/2 in transgenic hairy roots enhances Gm ZF351 expression mediated by histone demethylation and confers stress tolerance to soybean.Yield-related agronomic traits were evaluated in stable Gm ZF351-transgenic plants under mild drought stress conditions. Our study reveals a new mode of Gm JMJ30-Gm ZF351 action in stress tolerance, in addition to that of Gm ZF351 in oil accumulation. Manipulation of the components in this pathway is expected to improve soybean traits and adaptation under unfavorable environments.

关键词： abiotic stress histone demethylation JMJ30 soybean TZF protein

Genome-wide analyses of nonsyndromic cleft lip with or without palate identify 20 new risk loci in the Chinese Han population

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Journal of genetics and Genomics 2022年第9期49卷 903-905页

作者： Bao Li Liang Yong Yafen Yu Yanqin Yu Qi Zhen Huiyao Ge Yiwen Mao Weiwei Chen Yanxia Yu Yirui Wang Zhuo Li Wencheng Fan Chang Zhang Xia Hu Ruixue Zhang Lu Cao Hao Liu Zhuan Bian Miao He Liangdan Sun Department of Dermatology The First Affiliated Hospital of Anhui Medical UniversityHefeiAnhui 230022China Institute of Dermatology Anhui Medical UniversityHefeiChina key laboratory of Dermatology Ministry of EducationAnhui Medical UniversityHefeiAnhui 230022China Inflammation and Immune Mediated Diseases laboratory of anhui Province HefeiAnhui 230022China anhui provincial Institute of Translational Medicine HefeiAnhui 230022China The State key laboratory breeding Base of Basic Science of Stomatology(Hubei-MOST)and key laboratory of Oral Biomedicine Ministry of Education School and Hospital of StomatologyWuhan UniversityWuhanHubei 430079China

Orofacial clefts(OFCs),particularly cleft lip with or without cleft palate(CL/P)and cleft palate only(CPO),are among the most common birth defects in humans(Mossey et al.,2009;Dixon et al.,2011).The birth prevalence r... 详细信息

关键词： al. palate Dixon

A cost-effective ts CUT&Tag method for profiling transcription factor binding landscape

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Journal of Integrative Plant Biology 2022年第11期64卷 2033-2038页

作者： Leiming Wu Zi Luo Yanni Shi Yizhe Jiang Ruonan Li Xinxin Miao Fang Yang Qing Li Han Zhao Jiquan Xue Shutu Xu Tifu Zhang Lin Li National key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China The National Engineering laboratory of Crop Resistance breeding School of Life SciencesAnhui Agricultural UniversityHefei 230036China Jiangsu provincial key laboratory of Agrobiology Institute of Germplasm Resources and BiotechnologyJiangsu Academy of Agricultural SciencesNanjing 210014China The key laboratory of Biology and genetics Improvement of Maize in Arid Area of Northwest Region Ministry of AgricultureNorthwest A&F UniversityYangling 712100China Hubei Hongshan laboratory Wuhan 430070China

Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic traits.However,a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants.Here,we developed a transient and simplified cleavage under targets and tagmentation(tsCUT&Tag)that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction.Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq.Furthermore,we developed a strategy combining tsCUT&Tag with machine learning,which has great potential for profiling the TFBL across plant development.

关键词： binding sites ChIP-seq CUT&Tag machine learning transcription factor transient expression

Determination of Residual Feed Intake and Its Associations with Single Nucleotide Polymorphism in Chickens

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Journal of Integrative Agriculture 2014年第1期13卷 148-157页

作者： XU Zhen-qiang CHEN Jie ZHANG Yan JI Cong-liang ZHANG De-xiang ZHANG Xi-quan Guangdong provincial key lab of Agro-Animal Genomics and Molecular breeding/key lab of Chicken genetics Breeding and ReproductionMinistry of Agriculture/South China Agricultural University Wens Nanfang Poultry breeding Co.Ltd.

Marker assisted selection （MAS） for residual feed intake （RFI） is considered to be one of the powerful means to improve feed conversion efficiency, and therefore reduce production costs. To test the inner relationship among body compositions, growth traits and RFI, four models were proposed to assess the extensively explanatory variables accounting for partial variables in feed intake besides metabolic body weight and growth rate. As a result, the original model （Koch＇s model） had the lowest R2 （80.78%） and the highest Bayesian information criterion （1 323.3） value among the four models. Moreover, the effects on RFI caused by single nucleotide polymorphisms （SNPs） were assessed in this study. Twelve SNPs from 7 candidate genes were genotyped in 2 Chinese native strains, rs14743490 of RPLP2 gene showed suggestively significant association with initial body weight in both strains （P〈0.10）. rs15047274 of TAF15 was significantly associated with growth weight, final weight, and feed intake （P〈0.05） in N301 strain, in contrast, it was only suggestively significant associated with feed intake （P〈0.10） in N414 strain, rs15869967 was significantly associated with RFI in N414 strain but not in N301 strain. This study has identified potential genetic markers suitable for MAS in improving the above mentioned traits, but these associations need to be rectified in other larger populations in future.

关键词： RFI model SNPs growth traits association