Abstract
Flowering time is an important agronomic trait in Brassica rapa (B. rapa). However, our current understanding of the role of long noncoding RNAs (lncRNAs) in flowering time responded to vernalization is limited. The rapid development of the omics sequencing technology has facilitated the identification of thousands of lncRNAs in various plant species. Here, we used comparative transcriptome analysis between control and vernalized B. rapa to identify differentially expressed genes (DEGs) and lncRNAs (DELs). A total of 300 DEGs and 254 DELs were identified. Co-localization networks consisting of 128 DEGs and 127 DELs were established, followed by analyses of hierarchical categories, functional annotations, and correlation from mRNA-to-lncRNA. We found that the BraZF-HD21 (Bra026812) gene which responds to photoperiods and vernalization is correlated with lncRNA TCONS_00035129. The correlated genes that were mapped to the plant hormone signal transduction pathway and increased gibberellin A3 (GA3) content demonstrated that vernalization influences plant hormone levels. These findings suggest that vernalization alters the process of hormone biosynthesis, which in turn regulates flowering. This study provides an approach to elucidation of the regulatory mechanism of lncRNAs during vernalization in B. rapa.
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References
Aikawa S, Kobayashi MJ et al (2010) Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment. Proc Natl Acad Sci USA 107(25):11632–11637
Angel A, Song J et al (2011) A polycomb-based switch underlying quantitative epigenetic memory. Nature 476(7358):105–108
Bastow R, Mylne JS et al (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427(6970):164–167
Bernier JL, Henichart JP (1981) Extension of the Nenitzescu reaction to a cyclic enamino ketone: one-step synthesis of 6-hydroxy-9H-pyrimido[4,5-b]indole-2,4-dione. J Org Chem 46(21):4197–4198
Bolger AM, Lohse M et al (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120
Carrieri C, Cimatti L et al (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491(7424):454–457
Chouard P (2003) Vernalization and its relations to dormancy. Annu Rev Plant Physiol 11(1):191–238
De LF, Crevillen P et al (2008) A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci USA 105(44):16831–16836
Derrien T, Guigó R et al (2011) The long non-coding RNAs: a new (p)layer in the “dark matter”. Front Gene 2:107. https://doi.org/10.3389/fgene.2011.00107
Finnegan EJ, Dennis ES (2007) Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr Biol 17(22):1978–1983
Gendall AR, Levy YY et al (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107(4):525–535
Grabherr MG, Haas BJ et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652
Grob S, Schmid MW et al (2013) Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol. https://doi.org/10.1186/gb-2013-14-11-r129
Guil S, Esteller M (2012) Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol 19(11):1068–1075
Helliwell C, Wood C, M, et al (2006) The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J 46(2):183–192
Henderson IR, Shindo AC et al (2003) The need for winter in the switch to flowering. Annu Rev Genet 37(1):371–392
Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79
Kaneko S, Li G et al (2010) Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 24(23):2615–2620
Kaneko S, Bonasio R et al (2013) Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol Cell 53(2):290–300
Kim SY, Park BS et al (2007) Delayed flowering time in Arabidopsis and Brassica rapa by the overexpression of FLOWERING LOCUS C (FLC) homologs isolated from Chinese cabbage (Brassica rapa L. ssp. pekinensis). Plant Cell Rep 26(3):327–336
Koornneef M, Alonsoblanco C et al (2003) Genetic control of flowering time in Arabidopsis. Annu Rev Plant Physiol Plant Mol Biol 49(1):345–370
Levy YY, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297(5579):243–246
Li R, Yu C et al (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967
Lin S, Wang JG et al (2005) Differential regulation of FLOWERING LOCUS C expression by vernalization in cabbage and Arabidopsis. Plant Physiol 137(3):1037–1048
Mercer TR, Mattick JS (2013) Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20(3):300–307
Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11(5):949–956
Michaels SD, Amasino RM (2001) Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell 13(4):935–941
Michalczuk B, Przybyla A et al (1992) Effect of postharvest chemical treatment on longevity of different cultivars of cut Alstroemeria flowers. Acta Hort (325):199–206
Mortazavi A, Williams BA et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-SEq. Nat Methods 5(7):621–628
Mutasagöttgens E, Hedden P (2009) Gibberellin as a factor in floral regulatory networks. J Exp Bot 60(7):1979–1989
Negishi M, Wongpalee SP et al (2014) A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS ONE 9(4):e95216. https://doi.org/10.1371/journal.pone.0095216
Oliver SN, Finnegan EJ et al (2009) Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION 1 gene. Proc Natl Acad Sci USA 106(20):8386–8391
Oono Y, Seki M et al (2006) Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct Integr Genom 6(3):212–234
Parkhomchuk D, Borodina T et al (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37(18):e123
Pin PA, Benlloch R et al (2010) An antagonistic pair of FT homologs mediates the control of flowering time in sugar beet. Science 330(6009):1397–1400
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81(1):145
Schwabe WW (1987) Hormone involvement in daylength and vernalization control of reproductive development. In: Hoad GV (ed) Hormone action in plant development: acritical appraisal. Elsevier, Amsterdam, pp 217–230
Searle I, He Y et al (2006) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev 20(7):898
Sheldon CC, Burn JE et al (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant cell 11(3):445–458
Song X, Liu G et al (2014) Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Mol Genet Genom 289(4):541–551
Suge H (1977) Changes in ethylene production of vernalized plants. Plant Cell Physiol 18(5):1167–1171
Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427(6970):159–164
Sung S, He Y et al (2006) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet 38(6):706–710
Tadege M, Sheldon CC et al (2002) Control of flowering time by FLC orthologues in Brassica napus. Plant J 28(5):545–553
Vance KW, Ponting CP (2014) Transcriptional regulatory functions of nuclear long noncoding RNAs. Trends Genet 30(8):348
Wang R, Farrona S et al (2009) PEP1 regulates perennial flowering in Arabis alpina. Nature 459(7245):423–427
Wang W, Peng W et al (2016) Genome-wide analysis and expression patterns of ZF-HD transcription factors under different developmental tissues and abiotic stresses in Chinese cabbage. Mol Genet Genom 291(3):1451–1464
Wood CC, Robertson M et al (2006) The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes vernalization insensitive 3. Proc Natl Acad Sci USA 103(39):14631–14636
Yang TJ, Kim JS et al (2006) Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18(6):1339
Yang L, Duff MO et al (2011) Genome wide characterization of non-polyadenylated RNAs. Genome Biol 12(2):R16
Zhao J, Sun BK et al (2008) Polycomb proteins targeted by a short repeat RNA to the mouse × chromosome. Science 322(5902):750
Zhao J, Ohsumi TK et al (2010) Genome-wide Identification of Polycomb-Associated RNAs by RIP-sEq. Mol Cell 40(6):939–953
Zheng BB, Wu XM et al (2012) Comparative transcript profiling of a male sterile cybrid pummelo and its fertile type revealed altered gene expression related to flower development. PLoS ONE 7(8):e43758
Acknowledgements
This work was supported by the Fundamental Research Funds for the Central Universities (Y0201700179), the Natural science of Jiangsu Province (BK20171374), and the National Natural Science Foundation of China (No. 31330067). We thank Mr. Hua-wei Tan in Nanjing Hua-Seq Biotechnologies Co, Ltd., China for assistance on bioinformatics analysis.
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Tongkun Liu and Peng Wu contributed equally to this work.
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Supplementary Fig. 1
The statistical analysis for the composition of raw reads for each sample. The statistical data include the reads containing adapter, “N”, low quality and clean reads (JPG 389 KB)
Supplementary Fig. 2
The sequencing saturation of each sample in NHCC (JPG 787 KB)
Supplementary Fig. 3
Exon coverage statistics of each sample (JPG 681 KB)
Supplementary Fig. 4
Secondary structure of known pre-miRNA (JPG 296 KB)
Supplementary Fig. 5
The distribution of genes that were mapped to the pathway of plant hormone signal transduction in NHCC (JPG 762 KB)
Supplementary Fig. 6
Bioinformatics analysis pipeline of LncRNA (JPG 29 KB)
Supplementary Fig. 7
Expression leves of DEG and DEL under vernalization (JPG 368 KB)
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Liu, T., Wu, P., Wang, Q. et al. Comparative transcriptome discovery and elucidation of the mechanism of long noncoding RNAs during vernalization in Brassica rapa. Plant Growth Regul 85, 27–39 (2018). https://doi.org/10.1007/s10725-018-0371-y
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DOI: https://doi.org/10.1007/s10725-018-0371-y