Carvalho RF, Feijão CV, Duque P. On the physiological significance of alternative splicing events in higher plants. Protoplasma. 2013;250:639–50.
Article
CAS
PubMed
Google Scholar
Hubé F, Francastel C. Mammalian introns: when the junk generates molecular diversity. Int J Mol Sci. 2015;16:4429–52.
Article
PubMed
PubMed Central
Google Scholar
Santosh B, Varshney A, Yadava PK. Non‐coding RNAs: biological functions and applications. Cell Biochem Funct. 2015;33:14–22.
Article
CAS
PubMed
Google Scholar
Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell. 2013;25:3657–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res. 2015;25:995–1007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dubrovina A, Kiselev K, Zhuravlev YN. The role of canonical and noncanonical pre-mRNA splicing in plant stress responses. Biomed Res Int. 2012;2013.
Aghamirzaie D, Batra D, Heath LS, Schneider A, Grene R, Collakova E. Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics. 2015;16:1.
Article
Google Scholar
Trötschel C, Poetsch A. Current approaches and challenges in targeted absolute quantification of membrane proteins. Proteomics. 2015;15:915–29.
Article
PubMed
Google Scholar
Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics. 2009;9:1492–510.
Article
CAS
PubMed
Google Scholar
Boschetti E, Bindschedler LV, Tang C, Fasoli E, Righetti PG. Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price. J Chromatogr A. 2009;1216:1215–22.
Article
CAS
PubMed
Google Scholar
Valadkhan S, Jaladat Y. The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine. Proteomics. 2010;10:4128–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol. 2009;10:741–54.
CAS
PubMed
PubMed Central
Google Scholar
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A-C, Munschauer M. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010;141:129–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol. 2012;13:1–13.
Article
Google Scholar
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. Deciphering the splicing code. Nature. 2010;465:53–9.
Article
CAS
PubMed
Google Scholar
Leung MK, Xiong HY, Lee LJ, Frey BJ. Deep learning of the tissue-regulated splicing code. Bioinformatics. 2014;30:i121–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science. 2010;329:439–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 2011;12:R79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol. 2014;15:R20.
Article
PubMed
PubMed Central
Google Scholar
Gosai SJ, Foley SW, Wang D, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory BD. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Mol Cell. 2015;57:376–88.
Article
CAS
PubMed
Google Scholar
Schneider A, Aghamirzaie D, Elmarakeby H, Poudel AN, Koo AJ, Heath LS, Grene R, Collakova E. Potential targets of VIVIPAROUS1/ABI3‐LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J. 2015.
Baud S, Dubreucq B, Miquel M, Rochat C, Lepiniec L. Storage reserve accumulation in Arabidopsis: metabolic and developmental control of seed filling. The Arabidopsis Book. 2008;6:e0113.
Article
PubMed
PubMed Central
Google Scholar
Baud S, Boutin JP, Miquel M, Lepiniec L, Rochat C. An integrated overview of seed development in Arabidopsis thaliana ecotype WS. Plant Physiol Biochem. 2002;40:151–60.
Article
CAS
Google Scholar
Meinke DW. Molecular genetics of plant embryogenesis. Annu Rev Plant Biol. 1995;46:369–94.
Article
CAS
Google Scholar
Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E. Changes in RNA splicing in developing soybean (Glycine max) embryos. Biology. 2013;2:1311–37.
Article
PubMed
PubMed Central
Google Scholar
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2012;31:46–53.
Article
PubMed
Google Scholar
Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM. Long non-coding RNAs as a source of new peptides. Elife. 2014;3:e03523.
Article
PubMed
PubMed Central
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Day IS, Golovkin M, Palusa SG, Link A, Ali GS, Thomas J, Richardson DN, Reddy AS. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing. Plant J. 2012;71:936–47.
Article
CAS
PubMed
Google Scholar
Meyer K, Koester T, Staiger D. Pre-mRNA splicing in plants: in vivo functions of RNA-binding proteins implicated in the splicing process. Biomolecules. 2015;5:1717–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013;499:172–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pan HA, Lin YS, Lee KH, Huang JR, Lin YH, Kuo PL. Expression patterns of the DAZ-associated protein DAZAP1 in rat and human ovaries. Fertil Steril. 2005;84 Suppl 2:1089–94.
Article
CAS
PubMed
Google Scholar
Lin YT, Yen PH. A novel nucleocytoplasmic shuttling sequence of DAZAP1, a testis-abundant RNA-binding protein. RNA. 2006;12:1486–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu JX, Howell SH Managing the protein folding demands in the endoplasmic reticulum of plants. New Phytol. 2016.
Caceres JF, Misteli T. Division of labor: minor splicing in the cytoplasm. Cell. 2007;131:645–7.
Article
CAS
PubMed
Google Scholar
Parra-Rojas J, Moreno AA, Mitina I, Orellana A. The Dynamic of the Splicing of bZIP60 and the Proteins Encoded by the Spliced and Unspliced mRNAs Reveals Some Unique Features during the Activation of UPR in Arabidopsis thaliana. PLoS One. 2015;10:e0122936.
Article
PubMed
PubMed Central
Google Scholar
Howell SH. Endoplasmic reticulum stress responses in plants. Annu Rev Plant Biol. 2013;64:477–99.
Article
CAS
PubMed
Google Scholar
Iwata Y, Koizumi N. Plant transducers of the endoplasmic reticulum unfolded protein response. Trends Plant Sci. 2012;17:720–7.
Article
CAS
PubMed
Google Scholar
Qi Y, Tsuda K, Joe A, Sato M, Nguyen LV, Glazebrook J, Alfano JR, Cohen JD, Katagiri F. A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Mol Plant Microbe Interact. 2010;23:1573–83.
Article
CAS
PubMed
Google Scholar
Kim HS, Abbasi N, Choi SB. Bruno‐like proteins modulate flowering time via 3′ UTR‐dependent decay of SOC1 mRNA. New Phytologist. 2013;198:747–56.
Article
CAS
PubMed
Google Scholar
Srivastava R, Deng Y, Shah S, Rao AG, Howell SH. BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis. Plant Cell. 2013;25:1416–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song Z-T, Sun L, Lu S-J, Tian Y, Ding Y, Liu J-X. Transcription factor interaction with COMPASS-like complex regulates histone H3K4 trimethylation for specific gene expression in plants. Proc Natl Acad Sci. 2015;112:2900–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Severing EI, van Dijk AD, van Ham RC. Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data. BMC Plant Biol. 2011;11:82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Magistri M, Faghihi MA, St Laurent 3rd G, Wahlestedt C. Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet. 2012;28:389–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wight M, Werner A. The functions of natural antisense transcripts. Essays Biochem. 2013;54:91–101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Charon C, Moreno AB, Bardou F, Crespi M. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. Mol Plant. 2010;3:729–39.
Article
CAS
PubMed
Google Scholar
Hiller M, Huse K, Szafranski K, Rosenstiel P, Schreiber S, Backofen R, Platzer M. Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biol. 2006;7:R65.
Article
PubMed
PubMed Central
Google Scholar
Schindler S, Szafranski K, Hiller M, Ali GS, Palusa SG, Backofen R, Platzer M, Reddy AS. Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics. 2008;9:159.
Article
PubMed
PubMed Central
Google Scholar
Iida K, Shionyu M, Suso Y. Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals. Mol Biol Evol. 2008;25:709–18.
Article
CAS
PubMed
Google Scholar
Iancu OD, Colville A, Darakjian P, Hitzemann R. Coexpression and cosplicing network approaches for the study of mammalian brain transcriptomes. Int Rev Neurobiol. 2014;116:73–93.
Article
PubMed
Google Scholar
Deng Y, Humbert S, Liu J-X, Srivastava R, Rothstein SJ, Howell SH. Heat induces the splicing by IRE1 of a mRNA encoding a transcription factor involved in the unfolded protein response in Arabidopsis. Proc Natl Acad Sci. 2011;108:7247–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagashima Y, Mishiba K, Suzuki E, Shimada Y, Iwata Y, Koizumi N. Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor. Sci Rep. 2011;1:29.
Article
PubMed
PubMed Central
Google Scholar
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis. 2015;53:474–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walley J, Xiao Y, Wang J-Z, Baidoo EE, Keasling JD, Shen Z, Briggs SP, Dehesh K. Plastid-produced interorgannellar stress signal MEcPP potentiates induction of the unfolded protein response in endoplasmic reticulum. Proc Natl Acad Sci. 2015;112:6212–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deng Y, Srivastava R, Howell SH. Protein kinase and ribonuclease domains of IRE1 confer stress tolerance, vegetative growth, and reproductive development in Arabidopsis. Proc Natl Acad Sci. 2013;110:19633–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruberti C, Kim S-J, Stefano G, Brandizzi F. Unfolded protein response in plants: one master, many questions. Curr Opin Plant Biol. 2015;27:59–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Y, Brandizzi F. AtIRE1A/AtIRE1B and AGB1 independently control two essential unfolded protein response pathways in Arabidopsis. Plant J. 2012;69:266–77.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015. gkv007.
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V. Scikit-learn: machine learning in python. J Mach Learn Res. 2011;12:2825–30.
Google Scholar
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 2011;39:D225–9.
Article
CAS
PubMed
Google Scholar
Wang B-B, Brendel V. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 2004;5:R102.
Article
PubMed
PubMed Central
Google Scholar
Koncz C, Villacorta N, Szakonyi D, Koncz Z. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. Front Plant Sci. 2012;3:9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol. 2007;8:R24.
Article
PubMed
PubMed Central
Google Scholar