Identification and characterization of CircRNA-associated CeRNA networks in moso bamboo under nitrogen stress | BMC Plant Biology

  • Grabowski P, Zaug A, Cech T. The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena. Cell. 1981;23(2):467–76.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ye C, Chen L, Liu C, Zhu Q, Fan L. Widespread noncoding circular RNAs in plants. New Phytol. 2015;208(1):88–95.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhao W, Cheng Y, Zhang C, You Q, Shen X, Guo W, et al. Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Sci Rep. 2017;7(1):5636.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang Y, Gao Y, Zhang H, Wang H, Liu X, Xu X, et al. Genome-wide profiling of circular RNAs in the rapidly growing shoots of moso bamboo (Phyllostachys edulis). Plant Cell Physiol. 2019;60(6):1354–73.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tan J, Zhou Z, Niu Y, Sun X, Deng Z. Identification and functional characterization of tomato circRNAs derived from genes involved in fruit pigment accumulation. Sci Rep. 2017;7(1):8594.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xu Y, Ren Y, Lin T, Cui D. Identification and characterization of circRNAs involved in the regulation of wheat root length. Biol Res. 2019;52(1):19.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xiang L, Cai C, Cheng J, Wang L, Wu C, Shi Y, et al. Identification of circular RNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq. PeerJ. 2018;6:e4500.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang P, Fan Y, Sun X, Chen L, Terzaghi W, Bucher E, et al. A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J. 2019;98(4):697–713.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li Y, Yang Y, Kong B, Song X, Gao Z, Li X. Identification and characterization of circRNAs under drought stress in moso bamboo (Phyllostachys edulis). Forests. 2022;13(3):426.

    Article 

    Google Scholar
     

  • von Wiren N, Lauter F, Ninnemann O, Gillissen B, Walch-Liu P, Engels C, et al. Differential regulation of three functional ammonium transporter genes by nitrogen in root hairs and by light in leaves of tomato. Plant J. 2000;21(2):167–75.

    Article 

    Google Scholar
     

  • Castro Marin I, Loef I, Bartetzko L, Searle I, Coupland G, Stitt M, et al. Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways. Planta. 2011;233(3):539–52.

    Article 
    PubMed 

    Google Scholar
     

  • Vidal E, Moyano T, Canales J, Gutierrez R. Nitrogen control of developmental phase transitions in Arabidopsis thaliana. J Exp Bot. 2014;65(19):5611–8.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nazish T, Arshad M, Jan S, Javaid A, Khan M, Naeem M, et al. Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.). Transgenic Res. 2022;31(1):23–42.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, et al. Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Mol Biol. 2006;60(5):617–31.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang H, Forde B. An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture. Science. 1998;279(5349):407–9.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Castaings L, Camargo A, Pocholle D, Gaudon V, Texier Y, Boutet-Mercey S, et al. The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis. Plant J. 2009;57(3):426–35.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rubin G, Tohge T, Matsuda F, Saito K, Scheible W. Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell. 2009;21(11):3567–84.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao M, Tai H, Sun S, Zhang F, Xu Y, Li W. Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency. PLoS ONE. 2012;7(1):e29669.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gutierrez L, Mongelard G, Flokova K, Pacurar D, Novak O, Staswick P, et al. Auxin controls Arabidopsis adventitious root initiation by regulating jasmonic acid homeostasis. Plant Cell. 2012;24(6):2515–27.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park B, Yao T, Seo J, Wong E, Mitsuda N, Huang C, et al. Arabidopsis nitrogen limitation adaptation regulates ORE1 homeostasis during senescence induced by nitrogen deficiency. Nat Plants. 2018;4(11):898–903.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ma P, Gao S, Zhang H, Li B, Zhong H, Wang Y, et al. Identification and characterization of circRNAs in maize seedlings under deficient nitrogen. Plant Biol. 2021;23(5):850–60.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nizampatnam N, Schreier S, Damodaran S, Adhikari S, Subramanian S. microRNA160 dictates stage-specific auxin and cytokinin sensitivities and directs soybean nodule development. Plant J. 2015;84(1):140–53.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang Y, Xu J, Ge M, Ning L, Hu M, Zhao H. High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize. BMC Genomics. 2020;21(1):353.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li Y, Feng P. Bamboo resources in china based on the ninth national forest inventory data. World Bamboo and Rattan. 2019;17(6):45–8.


    Google Scholar
     

  • Hou D, Lu H, Zhao Z, Pei J, Yang H, Wu A, et al. Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature. Food Chem. 2022;368:130822.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yang K, Li L, Lou Y, Zhu C, Li X, Gao Z. A regulatory network driving shoot lignification in rapidly growing bamboo. Plant Physiol. 2021;187(2):900–16.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li Y, Zhang D, Zhang S, Lou Y, An X, Jiang Z, et al. Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots. Plant Physiol. 2022;188(4):2182–98.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Song X, Peng C, Ciais P, Li Q, Xiang W, Xiao W, et al. Nitrogen addition increased CO2 uptake more than non-CO2 greenhouse gases emissions in a moso bamboo forest. Sci Adv. 2020;6(12):eaaw5790.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xin W, Zhang L, Zhang W, Gao J, Yi J, Zhen X, et al. An integrated analysis of the rice transcriptome and metabolome reveals differential regulation of carbon and nitrogen metabolism in response to nitrogen availability. Int J Mol Sci. 2019;20(9):2349.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen H, Huang X, Shi W, Kronzucker H, Hou L, Yang H, et al. Coordination of nitrogen uptake and assimilation favours the growth and competitiveness of moso bamboo over native tree species in high-NH4+ environments. J Plant Physiol. 2021;266:153508.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li Z, Yuan T, Zhu C, Yang K, Song X, Gao Z. Molecular characteristics and patterns of gene expression of ammonium transporter in moso bamboo. Scientia Silvae Sinicae. 2021;57(7):71–9.


    Google Scholar
     

  • Yuan T, Zhu C, Li Z, Song X, Gao Z. Identification of NLP transcription factors of Phyllostachys edulis and their expression patterns in response to nitrogen. Forests Res. 2021;34(5):39–48.


    Google Scholar
     

  • Yuan T, Zhu C, Yang K, Song X, Gao Z. Identification of nitrate transporter gene family PeNPFs and their expression analysis in Phyllostachys edulis. Forests Res. 2021;34(3):1–12.


    Google Scholar
     

  • Liu H, Yu W, Wu J, Li Z, Li H, Zhou J, et al. Identification and characterization of circular RNAs during wood formation of poplars in acclimation to low nitrogen availability. Planta. 2020;251:47.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhou J, Yang L, Jia C, Shi W, Deng S, Luo Z. Identification and functional prediction of poplar root circRNAs involved in treatment with different forms of nitrogen. Front Plant Sci. 2022;13:941380.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yuan T, Zhu C, Li G, Liu Y, Yang K, Li Z, et al. An integrated regulation network of mRNAs, microRNAs, and lncRNAs involved in nitrogen metabolism of moso bamboo. Front Genet. 2022;13:854346.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao H, Gao Z, Wang L, Wang J, Wang S, Fei B, et al. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). GigaScience. 2018;7(10):giy115.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang Y, Yang M, Wei S, Qin F, Zhao H, Suo B. Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress. Front Plant Sci. 2016;7:2024.

    PubMed 

    Google Scholar
     

  • Wang Z, Liu Y, Li D, Li L, Zhang Q, Wang S, et al. Identification of circular RNAs in kiwifruit and their species-specific response to bacterial canker pathogen invasion. Front Plant Sci. 2017;8:413.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ren Y, Yue H, Li L, Xu Y, Wang Z, Xin Z, et al. Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat. Biol Res. 2018;51(1):43.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yi D, Zhang H, Lai B, Liu L, Pan X, Ma Z, et al. Integrative analysis of the coloring mechanism of red longan pericarp through metabolome and transcriptome analyses. J Agric Food Chem. 2021;69(6):1806–15.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tong W, Yu J, Hou Y, Li F, Zhou Q, Wei C, et al. Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). Planta. 2018;248(6):1417–29.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang G, Diao S, Zhang T, Chen D, He C, Zhang J. Identification and characterization of circular RNAs during the sea buckthorn fruit development. RNA Biol. 2019;16(3):354–61.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang Y, Zhang X, Chen T, Xiang J, Yin Q, Xing Y, et al. Circular intronic long noncoding RNAs. Mol Cell. 2013;51(6):792–806.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zuo J, Wang Q, Zhu B, Luo Y, Gao L. Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun. 2016;479(2):132–8.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–83.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, et al. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet. 2013;45(4):456–61 (461e451-452).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zou N, Shi W, Hou L, Kronzucker H, Huang L, Gu H, et al. Superior growth, N uptake and NH4+ tolerance in the giant bamboo Phyllostachys edulis over the broad-leaved tree Castanopsis fargesii at elevated NH4+ may underlie community succession and favor the expansion of bamboo. Tree Physiol. 2020;40(11):1606–22.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lu T, Cui L, Zhou Y, Zhu C, Fan D, Gong H, et al. Transcriptome-wide investigation of circular RNAs in rice. RNA. 2015;21(12):2076–87.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Conn V, Hugouvieux V, Nayak A, Conos S, Capovilla G, Cildir G, et al. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants. 2017;3:17053.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li H, Deng Y, Wu T, Subramanian S, Yu O. Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol. 2010;153(4):1759–70.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trevisan S, Nonis A, Begheldo M, Manoli A, Palme K, Caporale G, et al. Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings. Plant, Cell Environ. 2012;35(6):1137–55.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zuluaga D, Liuzzi V, Curci P, Sonnante G. MicroRNAs in durum wheat seedlings under chronic and short-term nitrogen stress. Funct Integr Genomics. 2018;18(6):645–57.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hansen T, Jensen T, Clausen B, Bramsen J, Finsen B, Damgaard C, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–8.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meng X, Zhang P, Chen Q, Wang J, Chen M. Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development. BMC Genomics. 2018;19(1):607.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang B, Hao Z, Zhu Y, Zhang H, Li G. Genome-wide identification and functional analysis of circRNAs in Zea mays. PLoS ONE. 2018;13(12):e0202375.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Han B, Chao J, Yao H. Circular RNA and its mechanisms in disease: From the bench to the clinic. Pharmacol Ther. 2018;187:31–44.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu J, Zhang Z, Xia J, Alfatih A, Song Y, Huang Y, et al. Rice NIN-LIKE PROTEIN 4 plays a pivotal role in nitrogen use efficiency. Plant Biotechnol J. 2021;19(3):448–61.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J. 2011;17:10–2.

    Article 

    Google Scholar
     

  • Zhao H, Peng Z, Fei B, Li L, Hu T, Gao Z, et al. BambooGDB: a bamboo genome database with functional annotation and an analysis platform. Database. 2014;2014:bau006.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim D, Salzberg S. TopHat-fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011;12:R72.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015;16:4.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang X, Dong R, Zhang Y, Zhang J, Luo Z, Zhang J, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26:1277–87.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shumate A, Wong B, Pertea G, Pertea M. Improved transcriptome assembly using a hybrid of long and short reads with StringTie. PLoS Comput Biol. 2022;18(6):e1009730.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson M, McCarthy D, Smyth G. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li Y, Wei W, An S, Jiang J, He J, Zhang H, et al. Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage. PeerJ. 2021;9:e10529.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bo X, Wang S. TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatics. 2005;21(8):1401–2.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dou C, Cao Z, Yang B, Ding N, Hou T, Luo F, et al. Changing expression profiles of lncRNAs, mRNAs, circRNAs and miRNAs during osteoclastogenesis. Sci Rep. 2016;6:21499.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fan C, Ma J, Guo Q, Li X, Wang H, Lu M. Selection of reference genes for quantitative real-time PCR in bamboo (Phyllostachys edulis). PLoS ONE. 2013;8(2):e56573.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ding Y, Chen Z, Zhu C. Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot. 2011;62(10):3563–73.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Read more here: Source link