Hanover, J. A., Krause, M. W. & Love, D. C. The hexosamine signaling pathway: O-GlcNAc cycling in feast or famine. Biochim. Biophys. Acta 1800, 80–95 (2010).
Hart, G. W., Slawson, C., Ramirez-Correa, G. & Lagerlof, O. Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease. Annu. Rev. Biochem. 80, 825–858 (2011).
Ma, J. & Hart, G. W. O-GlcNAc profiling: from proteins to proteomes. Clin. Proteom. 11, 8 (2014).
Yang, X. & Qian, K. Protein O-GlcNAcylation: emerging mechanisms and functions. Nat. Rev. Mol. Cell Biol. 18, 452–465 (2017).
Chen, P. H., Chi, J. T. & Boyce, M. Functional crosstalk among oxidative stress and O-GlcNAc signaling pathways. Glycobiology 28, 556–564 (2018).
Banerjee, P. S., Lagerlof, O. & Hart, G. W. Roles of O-GlcNAc in chronic diseases of aging. Mol. Asp. Med. 51, 1–15 (2016).
Jacobsen, S. E. & Olszewski, N. E. Mutations at the SPINDLY locus of Arabidopsis alter gibberellin signal transduction. Plant Cell 5, 887–896 (1993).
Liang, L. et al. SPINDLY is involved in ABA signaling bypassing the PYR/PYLs/RCARs-mediated pathway and partly through functional ABAR. Environ. Exp. Bot. 151, 43–54 (2018).
Hartweck, L. M., Scott, C. L. & Olszewski, N. E. Two O-linked N-acetylglucosamine transferase genes of Arabidopsis thaliana L. Heynh. have overlapping functions necessary for gamete and seed development. Genetics 161, 1279–1291 (2002).
Zentella, R. et al. The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat. Chem. Biol. 13, 479–485 (2017).
Zentella, R. et al. O-GlcNAcylation of master growth repressor DELLA by SECRET AGENT modulates multiple signaling pathways in Arabidopsis. Genes Dev. 30, 164–176 (2016).
Olszewski, N. E., West, C. M., Sassi, S. O. & Hartweck, L. M. O-GlcNAc protein modification in plants: evolution and function. Biochim. Biophys. Acta 1800, 49–56 (2010).
Xu, S. L. et al. Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis. Proc. Natl Acad. Sci. USA 114, E1536–E1543 (2017).
Murachelli, A. G., Ebert, J., Basquin, C., Le Hir, H. & Conti, E. The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat. Struct. Mol. Biol. 19, 378–386 (2012).
Wang, Z., Ballut, L., Barbosa, I. & Le Hir, H. Exon Junction Complexes can have distinct functional flavours to regulate specific splicing events. Sci. Rep. 8, 9509 (2018).
Schwerk, C. et al. ASAP, a novel protein complex involved in RNA processing and apoptosis. Mol. Cell. Biol. 23, 2981–2990 (2003).
Deka, B. & Singh, K. K. Multifaceted regulation of gene expression by the apoptosis- and splicing-associated protein complex and its components. Int. J. Biol. Sci. 13, 545–560 (2017).
Carvalho, R. F., Carvalho, S. D. & Duque, P. The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis. Plant Physiol. 154, 772–783 (2010).
Ali, G. S. et al. Regulation of plant developmental processes by a novel splicing factor. PLoS ONE 2, e471 (2007).
Ausin, I., Greenberg, M. V., Li, C. F. & Jacobsen, S. E. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis. Epigenetics 7, 29–33 (2012).
Zhang, X. N. et al. Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana. BMC Genomics 18, 772 (2017).
Xing, D., Wang, Y., Hamilton, M., Ben-Hur, A. & Reddy, A. S. 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 27, 3294–3308 (2015).
Chen, S. L. et al. Quantitative proteomics reveals a role for SERINE/ARGININE-rich 45 in regulating RNA metabolism and modulating transcriptional suppression via the ASAP complex in Arabidopsis thaliana. Front. Plant Sci. 10, 1116 (2019).
Hill, K., Wang, H. & Perry, S. E. A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. Plant J. 53, 172–185 (2008).
Song, C. P. & Galbraith, D. W. AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis. Plant Mol. Biol. 60, 241–257 (2006).
Questa, J. I., Song, J., Geraldo, N., An, H. L. & Dean, C. Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science 353, 485–488 (2016).
Aravind, L. & Koonin, E. V. SAP – a putative DNA-binding motif involved in chromosomal organization. Trends Biochem. Sci. 25, 112–114 (2000).
Whittaker, C. & Dean, C. The FLC Locus: a platform for discoveries in epigenetics and adaptation. Annu. Rev. Cell Dev. Biol. 33, 555–575 (2017).
Shaul, O. Unique Aspects of plant nonsense-mediated mRNA decay. Trends Plant Sci. 20, 767–779 (2015).
Hugouvieux, V., Kwak, J. M. & Schroeder, J. I. An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell 106, 477–487 (2001).
Hugouvieux, V. et al. Localization, ion channel regulation, and genetic interactions during abscisic acid signaling of the nuclear mRNA cap-binding protein, ABH1. Plant Physiol. 130, 1276–1287 (2002).
Kuhn, J. M., Hugouvieux, V. & Schroeder, J. I. mRNA cap binding proteins: effects on abscisic acid signal transduction, mRNA processing, and microarray analyses. Curr. Top. Microbiol. Immunol. 326, 139–150 (2008).
Kakei, Y. & Shimada, Y. AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles. Plant Cell Physiol. 56, e7 (2015).
Wang, Z. et al. ABA signalling is fine-tuned by antagonistic HAB1 variants. Nat. Commun. 6, 8138 (2015).
Zhan, X. et al. An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses. Nat. Commun. 6, 8139 (2015).
Liu, F., Marquardt, S., Lister, C., Swiezewski, S. & Dean, C. Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327, 94–97 (2010).
Marquardt, S. et al. Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol. Cell 54, 156–165 (2014).
Shen, H. et al. Light-induced phosphorylation and degradation of the negative regulator PHYTOCHROME-INTERACTING FACTOR1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes. Plant Cell 20, 1586–1602 (2008).
Hogg, R., McGrail, J. C. & O’Keefe, R. T. The function of the NineTeen Complex (NTC) in regulating spliceosome conformations and fidelity during pre-mRNA splicing. Biochem. Soc. Trans. 38, 1110–1115 (2010).
Monaghan, J. et al. Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity. PLoS Pathog. 5, e1000526 (2009).
Koncz, C., Dejong, F., Villacorta, N., Szakonyi, D. & Koncz, Z. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. Front. Plant Sci. 3, 9 (2012).
Reichow, S. L., Hamma, T., Ferre-D’Amare, A. R. & Varani, G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 35, 1452–1464 (2007).
Boehm, V. & Gehring, N. H. Exon junction complexes: supervising the gene expression assembly line. Trends Genet. 32, 724–735 (2016).
Le Hir, H., Sauliere, J. & Wang, Z. The exon junction complex as a node of post-transcriptional networks. Nat. Rev. Mol. Cell Biol. 17, 41–54 (2016).
Woodward, L. A., Mabin, J. W., Gangras, P. & Singh, G. The exon junction complex: a lifelong guardian of mRNA fate. Wiley Interdiscip. Rev. RNA 8, e1411 (2017).
Mahrez, W. et al. BRR2a affects flowering time via FLC splicing. PLoS Genet. 12, e1005924 (2016).
He, Y., Doyle, M. R. & Amasino, R. M. PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev. 18, 2774–2784 (2004).
Rodor, J., Pan, Q., Blencowe, B. J., Eyras, E. & Caceres, J. F. The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation. RNA 22, 1411–1426 (2016).
Vucetic, Z. et al. Acinus-S’ represses retinoic acid receptor (RAR)-regulated gene expression through interaction with the B domains of RARs. Mol. Cell. Biol. 28, 2549–2558 (2008).
Wang, F., Soprano, K. J. & Soprano, D. R. Role of Acinus in regulating retinoic acid-responsive gene pre-mRNA splicing. J. Cell Physiol. 230, 791–801 (2015).
Akin, D., Newman, J. R., McIntyre, L. M. & Sugrue, S. P. RNA-seq analysis of impact of PNN on gene expression and alternative splicing in corneal epithelial cells. Mol. Vis. 22, 40–60 (2016).
Pieczynski, M. et al. Down-regulation of CBP80 gene expression as a strategy to engineer a drought-tolerant potato. Plant Biotechnol. J. 11, 459–469 (2013).
Saez, A. et al. Gain-of-function and loss-of-function phenotypes of the protein phosphatase 2CHAB1reveal its role as a negative regulator of abscisic acid signalling. Plant J. 37, 354–369 (2004).
Vlad, F. et al. Protein phosphatases 2C regulate the activation of the Snf1-related kinase OST1 by abscisic acid in Arabidopsis. Plant Cell 21, 3170–3184 (2009).
Carvalho, R. F. et al. The Arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates SNF1-related protein kinase 1 stability. Plant Cell 28, 1910–1925 (2016).
Liu, Y. et al. Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy. PLoS ONE 6, e22241 (2011).
Tange, T. O., Shibuya, T., Jurica, M. S. & Moore, M. J. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11, 1869–1883 (2005).
Oldfield, C. J. & Dunker, A. K. Intrinsically disordered proteins and intrinsically disordered protein regions. Annu. Rev. Biochem. 83, 553–584 (2014).
Swain, S. M., Tseng, T. S. & Olszewski, N. E. Altered expression of SPINDLY affects gibberellin response and plant development. Plant Physiol. 126, 1174–1185 (2001).
Xing, L. et al. Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering. EMBO J. 37, e98115 (2018).
Tan, Z. W. et al. O-GlcNAc regulates gene expression by controlling detained intron splicing. Nucleic Acids Res. 48, 5656–5669 (2020).
Boutz, P. L., Bhutkar, A. & Sharp, P. A. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev. 29, 63–80 (2015).
Mauger, O., Lemoine, F. & Scheiffele, P. Targeted intron retention and excision for rapid gene regulation in response to neuronal activity. Neuron 92, 1266–1278 (2016).
Jia, J. et al. Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nat. Plants 6, 780–788 (2020).
Kim, T. W. et al. Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis. Preprint at bioRxiv https://doi.org/10.1101/636324 (2019).
Li, W. et al. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 43, W580–W584 (2015).
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
Ishida, T. & Kinoshita, K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res. 35, W460–W464 (2007).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Li, W., Lin, W. D., Ray, P., Lan, P. & Schmidt, W. Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiol. 162, 1750–1763 (2013).
Kojima, H. et al. Sugar-inducible expression of the nucleolin-1 gene of Arabidopsis thaliana and its role in ribosome synthesis, growth and development. Plant J. 49, 1053–1063 (2007).
Oh, E., Zhu, J. Y. & Wang, Z. Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–U864 (2012).
Ni, W. et al. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell 25, 2679–2698 (2013).
Fridy, P. C. et al. A robust pipeline for rapid production of versatile nanobody repertoires. Nat. Methods 11, 1253–1260 (2014).
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).
Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S. & Coon, J. J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteom. 11, 1475–1488 (2012).
Ni, W. et al. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat. Commun. 8, 15236 (2017).