Genome-wide identification of the CCCH gene family in rose (Rosa chinensis Jacq.) reveals its potential functions

References

• Dröge-Laser W, Snoek BL, Snel B, et al. The Arabidopsis bZIP transcription factor family-an update. Curr Opin Plant Biol. 2018;45(Pt A):36–49.
   PubMed Web of Science ®Google Scholar
• Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, et al. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 2010;38(Database issue):D822–827.
   PubMed Web of Science ®Google Scholar
• Gao G, Guo X, Goff SP. Inhibition of retroviral RNA production by ZAP, a CCCH-type zinc finger protein. Science. 2002;297(5587):1703–1706.
   PubMed Web of Science ®Google Scholar
• Li J, Jia D, Chen X. HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear RNA binding protein. Plant Cell. 2001;13(10):2269–2281.
   PubMed Web of Science ®Google Scholar
• Wang D, Guo Y, Wu C, et al. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics. 2008;9:44.
   PubMed Web of Science ®Google Scholar
• Bogamuwa S, Jang JC. The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination. Plant Cell Environ. 2013;36(8):1507–1519.
   PubMed Web of Science ®Google Scholar
• Kim DH, Yamaguchi S, Lim S, et al. SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5. Plant Cell. 2008;20(5):1260–1277.
   PubMed Web of Science ®Google Scholar
• Lin PC, Pomeranz MC, Jikumaru Y, et al. The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses. Plant J. 2011;65(2):253–268.
   PubMed Web of Science ®Google Scholar
• Lee SJ, Jung HJ, Kang H, et al. Arabidopsis zinc finger proteins AtC3H49/AtTZF3 and AtC3H20/AtTZF2 are involved in ABA and JA responses. Plant Cell Physiol. 2012;53(4):673–686.
   PubMed Web of Science ®Google Scholar
• Huang P, Ju H-W, Min J-H, et al. Molecular and physiological characterization of the Arabidopsis thaliana oxidation-related zinc finger 2, a plasma membrane protein involved in ABA and salt stress response through the ABI2-mediated signaling pathway. Plant Cell Physiol. 2012;53(1):193–203.
   PubMed Web of Science ®Google Scholar
• Maldonado-Bonilla LD, Eschen-Lippold L, Gago-Zachert S, et al. The Arabidopsis tandem zinc finger 9 protein binds RNA and mediates pathogen-associated molecular pattern-triggered immune responses. Plant Cell Physiol. 2014;55(2):412–425.
   PubMed Web of Science ®Google Scholar
• Jan A, Maruyama K, Todaka D, et al. OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol. 2013;161(3):1202–1216.
   PubMed Web of Science ®Google Scholar
• Guo YH, Yu YP, Wang D, et al. GhZFP1, a novel CCCH-type zinc finger protein from cotton, enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5. New Phytol. 2009;183(1):62–75. Epub 2009 Apr 15. PMID: 19402879.
   PubMed Web of Science ®Google Scholar
• Peng X, Zhao Y, Cao J, et al. CCCH-type zinc finger family in maize: genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PloS One . 2012;7(7):e40120
   PubMed Web of Science ®Google Scholar
• Pi B, He X, Ruan Y, et al. Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC Plant Biol. 2018;18(1):373
   PubMed Web of Science ®Google Scholar
• Liu S, Khan MR, Li Y, et al. Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization. Mol Genet Genomics. 2014;289(5):855–872.
   PubMed Web of Science ®Google Scholar
• Xu R. Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum. Mol Genet Genomics. 2014;289(5):965–979.
   PubMed Web of Science ®Google Scholar
• Chai G, Hu R, Zhang D, et al. Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC Genomics. 2012;13:253
   PubMed Web of Science ®Google Scholar
• Zhang C, Zhang H, Zhao Y, et al. Genome-wide analysis of the CCCH zinc finger gene family in Medicago truncatula. Plant Cell Rep. 2013;32(10):1543–1555.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Zhang WJ, Yin ZG, et al. Genome- and transcriptome-wide identification of C3Hs in common bean (Phaseolus vulgaris L.) and structural and expression-based analyses of their functions during the sprout stage under salt-stress conditions. Front Genet. 2020;11:564607
   PubMed Web of Science ®Google Scholar
• Raymond O, Gouzy J, Just J, et al. The Rosa genome provides new insights into the domestication of modern roses. Nat Genet. 2018;50(6):772–777.
   PubMed Web of Science ®Google Scholar
• Prakash A, Jeffryes M, Bateman A, et al. The HMMER web server for protein sequence similarity search. Curr Protoc Bioinformatics. 2017;60:3.15.1–13.15.23.
   PubMedGoogle Scholar
• El-Gebali S, Mistry J, Bateman A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47(D1):D427–d432.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–1549.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Johnson J, Grant CE, et al. The MEME Suite. Nucleic Acids Res. 2015;43(W1):W39–49.
   PubMed Web of Science ®Google Scholar
• Hu B, Jin J, Guo AY, et al. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–1297.
   PubMed Web of Science ®Google Scholar
• Chen Y, Li Y, Narayan R, et al. Gene expression inference with deep learning. Bioinformatics. 2016;32(12):1832–1839.
   PubMed Web of Science ®Google Scholar
• Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–1202.
   PubMed Web of Science ®Google Scholar
• Baek JH, Kim J, Kim CK, et al. MultiSyn: A webtool for multiple synteny detection and visualization of user’s sequence of interest compared to public plant species. Evol Bioinform Online. 2016;12:193–199.
   PubMed Web of Science ®Google Scholar
• Pradhan S, Kant C, Verma S, et al. Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.). PloS One . 2017;12(7):e0180469
   PubMed Web of Science ®Google Scholar
• Yuan S, Xu B, Zhang J, et al. Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass. BMC Genomics. 2015;16:129
   PubMed Web of Science ®Google Scholar
• Gaudet P, Livstone MS, Lewis SE, et al. Phylogenetic-based propagation of functional annotations within the gene ontology consortium. Brief Bioinform. 2011;12(5):449–462.
   PubMed Web of Science ®Google Scholar
• Bach-Pages M, Homma F, Kourelis J, et al. Discovering the RNA-binding proteome of plant leaves with an improved RNA interactome capture method. Biomolecules. 2020;10(4):661.
   PubMed Web of Science ®Google Scholar
• Yan Z, Jia J, Yan X, et al. Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence. Plant Mol Biol. 2017;95(6):549–565.
   PubMed Web of Science ®Google Scholar
• Sun J, Jiang H, Xu Y, et al. The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant Cell Physiol. 2007;48(8):1148–1158.
   PubMed Web of Science ®Google Scholar
• Lee TA, Bailey-Serres J. Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress. Plant Cell. 2019;31(11):2573–2595.
   PubMed Web of Science ®Google Scholar
• Jing Y, Shi L, Li X, et al. OXS2 is required for salt tolerance mainly through associating with salt inducible genes, CA1 and Araport11, in Arabidopsis. Sci Rep. 2019;9(1):20341
   PubMed Web of Science ®Google Scholar
• Reichel M, Liao Y, Rettel M, et al. In planta determination of the mRNA-binding proteome of arabidopsis etiolated seedlings. Plant Cell. 2016;28(10):2435–2452.
   PubMed Web of Science ®Google Scholar
• Zhang H, Zhang Z, Xiong T, et al. Corrigendum "The CCCH-type transcription factor BnZFP1 is a positive regulator to control oleic acid levels through the expression of diacylglycerol O-acyltransferase 1 gene in Brassica napus". Plant Physiol Biochem. 2018;133:158.
   PubMed Web of Science ®Google Scholar
• Xie Z, Lin W, Yu G, et al. Improved cold tolerance in switchgrass by a novel CCCH-type zinc finger transcription factor gene, PvC3H72, associated with ICE1-CBF-COR regulon and ABA-responsive genes. Biotechnol Biofuels. 2019;12:224.
   PubMed Web of Science ®Google Scholar