Bewley JD. Seed germination and dormancy. Plant Cell. 1997;9:1055–66.
Bewley JD, Bradford K, Hilhorst H, Nonogaki H. Seeds: Physiology of development, germination and dormancy. 3rd ed. Springer; 2013.
Alonso-Peral MM, Li J, Li Y, Allen RS, Schnippenkoetter W, Ohms S, et al. The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol. 2010;154:757–71.
Das SS, Karmakar P, Nandi AK, Sanan-Mishra N. Small RNA mediated regulation of seed germination. Front Plant Sci. 2015;6:828.
Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J. 2007;52:133–46.
Stamm P, Topham AT, Mukhtar NK, Jackson MD, Tome DF, Beynon JL, et al. The transcription factor ATHB5 affects GA-mediated plasticity in hypocotyl cell growth during seed germination. Plant Physiol. 2017;173:907–17.
Xiao W, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, et al. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell. 2006;18:805–14.
Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, et al. Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol. 2009;149:961–80.
Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E. Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J. 2005;41:697–709.
Narsai R, Law SR, Carrie C, Xu L, Whelan J. In depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis thaliana. Plant Physiol. 2011;157(3):1342–62.
Silva AT, Ribone PA, Chan RL, Ligterink W, Hilhorst HW. A predictive coexpression network identifies novel genes controlling the seed-to-seedling phase transition in Arabidopsis thaliana. Plant Physiol. 2016;170:2218–31.
Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, et al. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J. 2010;62:39–51.
Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, et al. Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A. 2011;108:9709–14.
Hartmann L, Drewe-Boss P, Wiessner T, Wagner G, Geue S, Lee HC, et al. Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis. Plant Cell. 2016;28:2715–34.
Loraine AE, McCormick S, Estrada A, Patel K, Qin P. RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol. 2013;162:1092–109.
Shikata H, Shibata M, Ushijima T, Nakashima M, Kong SG, Matsuoka K, et al. The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction. Plant J. 2012;70:727–38.
Yan K, Liu P, Wu CA, Yang GD, Xu R, Guo QH, et al. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol Cell. 2012;48:521–31.
Rogers K, Chen X. Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell. 2013;25:2383–99.
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.
Baldrich P, San SB. MicroRNAs in rice innate immunity. Rice. 2016;9:6.
Curaba J, Singh MB, Bhalla PL. miRNAs in the crosstalk between phytohormone signalling pathways. J Exp Bot. 2014;65:1425–38.
Matzke MA, Mosher RA. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet. 2014;15:394–408.
Cuerda-Gil D, Slotkin RK. Non-canonical RNA-directed DNA methylation. Nat Plants. 2016;2:16163.
Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, et al. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nat Plants. 2016;2:16058.
Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell. 2012;151:194–205.
Ibarra CA, Feng X, Schoft VK, Hsieh TF, Uzawa R, Rodrigues JA, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337:1360–4.
Park K, Kim MY, Vickers M, Park JS, Hyun Y, Okamoto T, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci U S A. 2016;113:15138–43.
Deleris A, Halter T, Navarro L. DNA methylation and demethylation in plant immunity. Annu Rev Phytopathol. 2016;54:579–603.
Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, et al. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytol. 2017;214(2):808–19.
Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, et al. Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. Plant Cell. 2013;25:4285–304.
Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16:519–32.
Gouil Q, Baulcombe DC. DNA methylation signatures of the plant chromomethyltransferases. PLoS Genet. 2016;12:e1006526.
Portis E, Acquadro A, Comino C, Lanteri S. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci. 2004;166:169–78.
Meng FR, Li YC, Yin J, Liu H, Chen JX, Ni FZ, et al. Analysis of DNA methylation during the germination of wheat seeds. Biol Plant. 2012;56:269–75.
Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. Plant J. 2017;89:805–24.
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell. 2002;110:33–42.
Ruhl C, Stauffer E, Kahles A, Wagner G, Drechsel G, Ratsch G, et al. Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes. Plant Cell. 2012;24:4360–75.
Zhang XN, Mount SM. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol. 2009;150:1450–8.
Lopez-Molina L, Mongrand S, McLachlin DT, Chait BT, Chua NH. ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. Plant J. 2002;32:317–28.
Chiang GC, Barua D, Kramer EM, Amasino RM, Donohue K. Major flowering time gene, flowering locus C, regulates seed germination in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2009;106:11661–6.
Kendall SL, Hellwege A, Marriot P, Whalley C, Graham IA, Penfield S. Induction of dormancy in Arabidopsis summer annuals requires parallel regulation of DOG1 and hormone metabolism by low temperature and CBF transcription factors. Plant Cell. 2011;23:2568–80.
Carvalho RF, Carvalho SD, Duque P. The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis. Plant Physiol. 2010;154:772–83.
Xing D, Wang Y, Hamilton M, Ben-Hur A, Reddy AS. Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININE-RICH45 uncovers the unexpected roles of this RNA binding protein in RNA processing. Plant Cell. 2015;27:3294–308.
Schulze S, Schafer BN, Parizotto EA, Voinnet O, Theres K. LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems. Plant J. 2010;64:668–78.
Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol. 2012;6:104.
O’Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, et al. Cistrome and epicistrome features shape the regulatory DNA landscape. Cell. 2016;166:1598.
Olsen AN, Ernst HA, Leggio LL, Skriver K. NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 2005;10:79–87.
Finkelstein RR, Lynch TJ. The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell. 2000;12:599–609.
Huang Y, Feng CZ, Ye Q, Wu WH, Chen YF. Arabidopsis WRKY6 transcription factor acts as a positive regulator of abscisic acid signaling during seed germination and early seedling development. PLoS Genet. 2016;12:e1005833.
Johannesson H, Wang Y, Hanson J, Engstrom P. The Arabidopsis thaliana homeobox gene ATHB5 is a potential regulator of abscisic acid responsiveness in developing seedlings. Plant Mol Biol. 2003;51:719–29.
Choi H, Jeong S, Kim DS, Na HJ, Ryu JS, Lee SS, et al. The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling. Physiol Plant. 2014;150:308–20.
Yanagisawa S. Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol. 2004;45:386–91.
Santopolo S, Boccaccini A, Lorrai R, Ruta V, Capauto D, Minutello E, et al. DOF AFFECTING GERMINATION 2 is a positive regulator of light-mediated seed germination and is repressed by DOF AFFECTING GERMINATION 1. BMC Plant Biol. 2015;15:72.
Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci. 2010;15:247–58.
Rueda-Romero P, Barrero-Sicilia C, Gomez-Cadenas A, Carbonero P, Onate-Sanchez L. Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot. 2012;63:1937–49.
O’Malley RC, Barragan CC, Ecker JR. A User’s guide to the Arabidopsis T-DNA insertion mutant collections. In: Alonso JM, Stepanova AN, editors. Plant functional genomics: methods and protocols. New York: Springer New York; 2015. p. 323–42.
Bueso E, Munoz-Bertomeu J, Campos F, Brunaud V, Martinez L, Sayas E, et al. ARABIDOPSIS THALIANA HOMEOBOX25 uncovers a role for Gibberellins in seed longevity. Plant Physiol. 2014;164:999–1010.
Skirycz A, Radziejwoski A, Busch W, Hannah MA, Czeszejko J, Kwasniewski M, et al. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J. 2008;56:779–92.
Willemsen V, Bauch M, Bennett T, Campilho A, Wolkenfelt H, Xu J, et al. The NAC domain transcription factors FEZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells. Dev Cell. 2008;15:913–22.
Green KA, Prigge MJ, Katzman RB, Clark SE. CORONA, a member of the class III homeodomain leucine zipper gene family in Arabidopsis, regulates stem cell specification and organogenesis. Plant Cell. 2005;17:691–704.
Martinez G, Kohler C. Role of small RNAs in epigenetic reprogramming during plant sexual reproduction. Curr Opin Plant Biol. 2017;36:22–8.
Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016;44:D239–247.
Jha A, Shankar R. MiRNAting control of DNA methylation. J Biosci. 2014;39:365–80.
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol. 2008;26:941–6.
Meinke D, Muralla R, Sweeney C, Dickerman A. Identifying essential genes in Arabidopsis thaliana. Trends Plant Sci. 2008;13:483–91.
Zhao JH, Fang YY, Duan CG, Fang RX, Ding SW, Guo HS. Genome-wide identification of endogenous RNA-directed DNA methylation loci associated with abundant 21-nucleotide siRNAs in Arabidopsis. Sci Rep. 2016;6:36247.
Nonogaki H. MicroRNA gene regulation cascades during early stages of plant development. Plant Cell Physiol. 2010;51:1840–6.
Penfield S, Springthorpe V. Understanding chilling responses in Arabidopsis seeds and their contribution to life history. Philos Trans R Soc Lond B Biol Sci. 2012;367:291–7.
Law SR, Narsai R, Taylor NL, Delannoy E, Carrie C, Giraud E, et al. Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination. Plant Physiol. 2012;158:1610–27.
Jiang Z, Xu G, Jing Y, Tang W, Lin R. Phytochrome B and REVEILLE1/2-mediated signalling controls seed dormancy and germination in Arabidopsis. Nat Commun. 2016;7:12377.
Neff MM. Light-mediated seed germination: connecting phytochrome B to gibberellic acid. Dev Cell. 2012;22:687–8.
Bourbousse C, Mestiri I, Zabulon G, Bourge M, Formiggini F, Koini MA, et al. Light signaling controls nuclear architecture reorganization during seedling establishment. Proc Natl Acad Sci U S A. 2015;112:E2836–2844.
Yu H, Kumar PP. Post-transcriptional gene silencing in plants by RNA. Plant Cell Rep. 2003;22:167–74.
Xu R, Wang Y, Zheng H, Lu W, Wu C, Huang J, et al. Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis. J Exp Bot. 2015;66:5997–6008.
Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2003;301:653–7.
Ulker B, Li Y, Rosso MG, Logemann E, Somssich IE, Weisshaar B. T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants. Nat Biotechnol. 2008;26:1015–7.
Baulcombe DC, Saunders GR, Bevan MW, Mayo MA, Harrison BD. Expression of biologically active viral satellite RNA from the nuclear genome of transformed plants. Nature. 1986;321:446.
Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, et al. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.). DNA Res. 2015;22:19–27.
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–19.
Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinforma. 2016;17:490.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562–78.
Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinforma. 2010;11:237.
Axtell MJ. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA. 2013;19:740–51.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc. 2015;10:475–83.
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571–2.
Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, et al. Genome-wide demethylation of Arabidopsis endosperm. Science. 2009;324:1451–4.
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21:64–72.