Adrian, J. et al. Cis-regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. Plant Cell 22, 1425–1440 (2010).
Cao, S. et al. A distal CCAAT/NUCLEAR FACTOR Y complex promotes chromatin looping at the FLOWERING LOCUS T promoter and regulates the timing of flowering in Arabidopsis. Plant Cell 26, 1009–1017 (2014).
Gnesutta, N. et al. CONSTANS imparts DNA sequence-specificity to the histone-fold NF-YB/NF-YC dimer. Plant Cell 29, 1516–1532 (2017).
Suárez-López, P. et al. Constans mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410, 1116–1120 (2001).
Ben-Naim, O. et al. The CCAAT binding factor can mediate interactions between constans-like proteins and DNA. Plant J. 46, 462–476 (2006).
Wenkel, S. et al. Constans and the ccaat box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell 18, 2971–2984 (2006).
Shlyueva, D., Stampfel, G. & Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 15, 272–286 (2014).
Weber, B., Zicola, J., Oka, R. & Stam, M. Plant enhancers: a call for discovery. Trends. Plant. Sci. 21, 974–987 (2016).
Liu, L. et al. Induced and natural variation of promoter length modulates the photoperiodic response of FLOWERING LOCUS T. Nat. Commun. 5, 4558 (2014).
Matzke, M. A. & Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394 (2014).
Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A. & Matzke, A. J. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194–5201 (2000).
Deng, S. et al. Transcriptional silencing of Arabidopsis endogenes by single-stranded RNAs targeting the promoter region. Plant Cell Physiol. 55, 823–833 (2014).
Deng S. & Chua, N.-H. Inverted-repeat RNAs targeting FT intronic regions promote FT expression in Arabidopsis. Plant Cell Physiol. 56, 1667–1678 (2015).
Hamilton, A., Voinnet, O., Chappell, L. & Baulcombe, D. Two classes of short interfering RNA in RNA silencing. EMBO J. 21, 4671–4679 (2002).
Melnyk, C. W., Molnar, A., Bassett, A. & Baulcombe, D. C. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr. Biol. 21, 1678–1683 (2011).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
Du, J. et al. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol. Cell 55, 495–504 (2014).
Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16, 519–532 (2015).
Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).
Zhang, W., Zhang, T., Wu, Y. & Jiang, J. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24, 2719–2731 (2012).
Pedmale, U. V. et al. Cryptochromes interact directly with PIFs to control plant growth in limiting blue light. Cell 164, 233–245 (2016).
Vaistij, F. E., Jones, L. & Baulcombe, D. C. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 14, 857–867 (2002).
Eamens, A., Vaistij, F. E. & Jones, L. Nrpd1a and nrpd1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis. Plant J. 55, 596–606 (2008).
Kanno, T. et al. A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation. Nat. Genet. 40, 670–675 (2008).
Daxinger, L. et al. A stepwise pathway for biogenesis of 24‐nt secondary siRNAs and spreading of DNA methylation. EMBO J. 28, 48–57 (2009).
Farrona, S. et al. Tissue-specific expression of FLOWERING LOCUS T in Arabidopsis is maintained independently of polycomb group protein repression. Plant Cell 23, 3204–3214 (2011).
Vaughn, M. W. et al. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 5, e174 (2007).
Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).
Mathieu, J., Yant, L. J., Mürdter, F., Küttner, F. & Schmid, M. Repression of flowering by the miR172 Target SMZ. PLoS Biol. 7, e1000148 (2009).
Takada, S. & Goto, K. Terminal flower2, an Arabidopsis homolog of heterochromatin protein1, counteracts the activation of FLOWERING LOCUS T by constans in the vascular tissues of leaves to regulate flowering time. Plant Cell 15, 2856–2865 (2003).
Barolo, S. Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy. BioEssays News Rev. Mol. Cell. Dev. Biol. 34, 135–141 (2012).
Lam, D. D. et al. Partially redundant enhancers cooperatively maintain mammalian pomc expression above a critical functional threshold. PLoS Genet. 11, e1004935 (2015).
Ruiz-Narváez, E. A. Redundant enhancers and causal variants in the TCF7L2 gene. Eur. J. Hum. Genet. 22, 1243–1246 (2014).
Hu, G., Codina, M. & Fisher, S. Multiple enhancers associated with ACAN suggest highly redundant transcriptional regulation in cartilage. Matrix Biol. J. Int. Soc. Matrix Biol. 31, 328–337 (2012).
Degenhardt, K. R. et al. Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expression. Dev. Biol. 339, 519–527 (2010).
Hellens, R. P., Edwards, E. A., Leyland, N. R., Bean, S. & Mullineaux, P. M. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol. Biol. 42, 819–832 (2000).
Kovalchuk, I. & Zemp, F. J. Plant Epigenetics: Methods and Protocols (Humana Press, New York, 2010).
Gruntman, E. et al. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics 9, 371 (2008).
Hetzl, J., Foerster, A. M., Raidl, G. & Scheid, O. M. CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J. 51, 526–536 (2007).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754–1760 (2009).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2014); http://www.R-project.org/
Reimer, J. J. & Turck, F. in Plant Epigenetics 631 (eds Kovalchuk, I. & Zemp, F. J.) 139–160 (Humana Press, New York, 2010).
Frazer, K. A., Pachter, L., Poliakov, A., Rubin, E. M. & Dubchak, I. Vista: computational tools for comparative genomics. Nucleic Acids Res. 32, W273–W279 (2004).