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Research Paper

Identification and characterization of long non-coding RNAs involved in embryo development of Ginkgo biloba

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Article: 1674606 | Received 04 Aug 2019, Accepted 26 Sep 2019, Published online: 09 Oct 2019

References

  • Xu W, Yang T, Wang B, Han B, Zhou H, Wang Y, Li D, Liu A. Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds. Plant J. 2018;95:1–8. doi:10.1111/tpj.13953.
  • Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, Lavabre-Bertrand T, Commes T, Lemaître JM, Boureux A, et al. Long non-coding RNAs in human early embryonic development and their potential in ART. Hum Reprod Update. 2016;23:19–40. doi:10.1093/humupd/dmw035.
  • Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505:344–352. doi:10.1038/nature12986.
  • Zhu M, Zhang M, Xing L, Li W, Jiang H, Wang L, Xu M. Transcriptomic analysis of long non-coding RNAs and coding genes uncovers a complex regulatory network that is involved in maize seed development. Genes (Basel). 2017:8. doi:10.3390/genes8100274.
  • Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol. 2014;15:512. doi:10.1186/s13059-014-0512-1.
  • Kiegle EA, Garden A, Lacchini E, Kater MM. A genomic view of alternative splicing of long non-coding rnas during rice seed development reveals extensive splicing and lncRNA gene families. Front Plant Sci. 2018:9. doi:10.3389/fpls.2018.00115.
  • Shen E, Zhu X, Hua S, Chen H, Ye C, Zhou L, Liu Q, Zhu Q, Fan L, Chen X. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. BMC Genomics. 2018;19:1–13. doi:10.1186/s12864-018-5117-8.
  • Yin DD, Li SS, Shu QY, Gu ZY, Wu Q, Feng CY, Xu WZ, Wang LS. Identification of microRNAs and long non-coding RNAs involved in fatty acid biosynthesis in tree peony seeds. Gene. 2018;666:72–82. doi:10.1016/j.gene.2018.05.011.
  • Baskin JM, Baskin CC. A classification system for seed dormancy. Seed Sci Res. 2004;14:1–16. doi:10.1079/SSR2003150.
  • Liu Y, Fang J, Xu F, Chu C, Schläppi MR, Wang Y, Chu C. Expression patterns of ABA and GA metabolism genes and hormone levels during rice seed development and imbibition: A comparison of dormant and non-dormant rice cultivars. J Genet Genomics. 2014;41:327–338. doi:10.1016/j.jgg.2014.04.004.
  • Penfield S, Hall A. A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis. Plant Cell Online. 2009;21:1722–1732. doi:10.1105/tpc.108.064022.
  • Footitt S, Ölçer-Footitt H, Hambidge AJ, Finch-Savage WE. A laboratory simulation of Arabidopsis seed dormancy cycling provides new insight into its regulation by clock genes and the dormancy-related genes DOG1, MFT, CIPK23 and PHYA. Plant Cell Environ. 2017;40:1474–1486. doi:10.1111/pce.12940.
  • Adams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA. Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. New Phytol. 2018;220:893–907. doi:10.1111/nph.15415.
  • Liu S, Wu L, Qi H, Xu M. LncRNA/circRNA–miRNA–mRNA networks regulate the development of root and shoot meristems of populus. Ind Crops Prod. 2019;133:333–347. doi:10.1016/j.indcrop.2019.03.048.
  • Zhao YT, Wang M, Fu SX, Yang WC, Qi CK, Wang XJ. Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production-and development-correlated expression and new small RNA classes. Plant Physiol. 2012;158(2):813–823. doi:10.1104/pp.111.187666.
  • Reyes JL, Chua NH. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J. 2007;49:592–606. doi:10.1111/j.1365-313X.2006.02980.x.
  • Nonogaki H. microRNA gene regulation cascades during early stages of plant development. Plant Cell Physiol. 2010;51(11):1840–1846. doi:10.1093/pcp/pcq154.
  • Das SS, Karmakar P, Nandi AK, Sanan-Mishra N. Small RNA mediated egulation of seed germination. Front Plant Sci. 2015;6:828. doi:10.3389/fpls.2015.00828.
  • Nodine MD, Bartel DP. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev. 2010;24(23):2678–2692. doi:10.1101/gad.1986710.
  • Zhou X, Liu J, Wang W. Construction and investigation of breast-cancer-specific ceRNA network based on the mRNA and miRNA expression data. IET Syst Biol. 2014;8:96–103. doi:10.1049/iet-syb.2013.0025.
  • Wang L, Xia X, Jiang H, Lu Z, Cui J, Cao F, Jin B. Genome-wide identification and characterization of novel lncRNAs in Ginkgo biloba. Trees - Struct Funct. 2018;32:1429–1442. doi:10.1007/s00468-018-1724-x.
  • Liu Y, Li M, Bo X, Li T, Ma L, Zhai T, Huang T. Systematic analysis of long non-coding RNAs and mRNAs in the ovaries of duroc pigs during different follicular stages using RNA sequencing. Int J Mol Sci. 2018:19. doi:10.3390/ijms19061722.
  • Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011;147:1537–1550. doi:10.1016/j.cell.2011.11.055.
  • Ghosh S, Sati S, Sengupta S, Scaria V. Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long noncoding RNAs. J Genet. 2015;94:17–25. doi:10.1007/s12041-015-0484-2.
  • Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013;20:300–307. doi:10.1038/nsmb.2480.
  • Baroux C, Pien S, Grossniklaus U. Chromatin modification and remodeling during early seed development. Curr Opin Genet Dev. 2007;17:473–479. doi:10.1016/j.gde.2007.09.004.
  • Fan Z, Zhao M, Joshi PD, Li P, Zhang Y, Guo W, Xu Y, Wang H, Zhao Z, Yan J. A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation. Nucleic Acids Res. 2017;45:5720–5738. doi:10.1093/nar/gkx156.

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