Non-Canonical Functions of Splicing Factors in RNA Metabolism

References

• Aitken, C. E. and Lorsch, J. R. 2012. A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 19: 568–576. doi:10.1038/nsmb.230
   PubMed Web of Science ®Google Scholar
• Albaqami, M. and Reddy, A. S. N. 2018. Development of an in vitro pre-mRNA splicing assay using plant nuclear extract. Plant Meth. 14: 1. doi:10.1186/s13007-017-0271-6
   PubMed Web of Science ®Google Scholar
• Ali, G. S., Golovkin, M., and Reddy, A. S. 2003. Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein. Plant J. 36: 883–893. doi:10.1046/j.1365-313x.2003.01932.x
   PubMed Web of Science ®Google Scholar
• Ali, G. S., Palusa, S. G., Golovkin, M., Prasad, J., Manley, J. L., and Reddy, A. S. 2007. Regulation of plant developmental processes by a novel splicing factor. PLoS One 2: e471. doi:10.1371/journal.pone.0000471
   PubMed Web of Science ®Google Scholar
• Ariel, F., Romero-Barrios, N., Jégu, T., Benhamed, M., and Crespi, M. 2015. Battles and hijacks: noncoding transcription in plants. Trends Plant Sci. 20: 362–371. doi:10.1016/j.tplants.2015.03.003
   PubMed Web of Science ®Google Scholar
• Ashwal-Fluss, R., Meyer, M., Pamudurti, N. R., Ivanov, A., Bartok, O., Hanan, M., Evantal, N., Memczak, S., Rajewsky, N., and Kadener, S. 2014. CircRNA biogenesis competes with pre-mRNA splicing. Mol. Cell 56: 55–66. doi:10.1016/j.molcel.2014.08.019
   PubMed Web of Science ®Google Scholar
• Ausin, I., Greenberg, M. V., Li, C. F., and Jacobsen, S. E. 2012. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis. Epigenetics 7: 29–33. doi:10.4161/epi.7.1.18782
   PubMed Web of Science ®Google Scholar
• Azam, S., Hou, S., Zhu, B., Wang, W., Hao, T., Bu, X., Khan, M., and Lei, H. 2019. Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus. RNA Biol. 16: 1001–1009. doi:10.1080/15476286.2019.1620061
   PubMed Web of Science ®Google Scholar
• Bao, P., Will, C. L., Urlaub, H., Boon, K. L., and Lührmann, R. 2017. The RES complex is required for efficient transformation of the precatalytic B spliceosome into an activated Bact complex. Genes Dev. 31: 2416–2429. doi:10.1101/gad.308163.117
   PubMed Web of Science ®Google Scholar
• Bardou, F., Ariel, F., Simpson, C. G., Romero-Barrios, N., Laporte, P., Balzergue, S., Brown, J. W. S., and Crespi, M. 2014. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev. Cell 30: 166–176. doi:10.1016/j.devcel.2014.06.017
   PubMed Web of Science ®Google Scholar
• Bazin, J., Romero, N., Rigo, R., Charon, C., Blein, T., Ariel, F., and Crespi, M. 2018. Nuclear speckle RNA binding proteins remodel alternative splicing and the non-coding Arabidopsis transcriptome to regulate a cross-talk between auxin and immune responses. Front Plant Sci. 9: 1209. doi:10.3389/fpls.2018.01209
   PubMed Web of Science ®Google Scholar
• Bose, R. and Ain, R. 2018. Regulation of transcription by circular RNAs. Adv. Exp. Med. Biol. 1087: 81–94. doi:10.1007/978-981-13-1426-1_7
   PubMed Web of Science ®Google Scholar
• Bouvrette, L. P. B., Cody, N., Bergalet, J., Lefebvre, F. A., Diot, C., Wang, X., Blanchette, M., and Lécuyern, E. 2018. CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells. RNA 24: 98–113. doi:10.1261/rna.063172.117
   PubMed Web of Science ®Google Scholar
• Brighty, D. W., and Rosenberg, M. A. 1994. Cis-acting repressive sequence that overlaps the Rev-responsive element of human immunodeficiency virus type 1 regulates nuclear retention of env mRNAs independently of known splice signals. Proc. Natl. Acad. Sci. USA. 91: 8314–8318. doi:10.1073/pnas.91.18.8314
   PubMed Web of Science ®Google Scholar
• Calixto, C. P. G., Tzioutziou, N. A., James, A. B., Hornyik, C., Guo, W., Zhang, R., Nimmo, H. G., and Brown, J. W. S. 2019. Cold-dependent expression and alternative splicing of Arabidopsis long non-coding RNAs. Front. Plant Sci. 10: 235. doi:10.3389/fpls.2019.00235
   PubMed Web of Science ®Google Scholar
• Campalans, A., Kondorosi, A., and Crespi, M. 2004. Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16: 1047–1059. doi:10.1105/tpc.019406
   PubMed Web of Science ®Google Scholar
• Chaabane, S. B., Liu, R., Chinnusamy, V., Kwon, Y., Park, J. H., Kim, S. Y., Zhu, J. K., Yang, S. W., and Lee, B. H. 2013. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res. 41: 1984–1997. doi:10.1093/nar/gks1309
   PubMed Web of Science ®Google Scholar
• Charon, C., Sousa, C., Crespi, M., and Kondorosi, A. 1999. Alteration of enod40 expression modifies medicago truncatula root nodule development induced by sinorhizobium meliloti. Plant Cell 11: 1953–1966. doi:10.1105/tpc.11.10.1953
   PubMed Web of Science ®Google Scholar
• Chen, G., Cui, J., Wang, L., Zhu, Y., Lu, Z., and Jin, B. 2017. Genome-wide identification of circular RNAs in Arabidopsis thaliana. Front. Plant Sci. 8: 1678. doi:10.3389/fpls.2017.01678
   PubMed Web of Science ®Google Scholar
• Chen, L., Zhang, P., Fan, Y., Lu, Q., Li, Q., Yan, J., Muehlbauer, G. J., Schnable, P. S., Dai, M., and Li, L. 2018. Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. New Phytol. 217: 1292–1306. doi:10.1111/nph.14901
   PubMed Web of Science ®Google Scholar
• Chen, M. X., Zhu, F. Y., Wang, F. Z., Ye, N. H., Gao, B., Chen, X., Zhao, S. S., Fan, T., Cao, Y. Y., Liu, T. Y., Su, Z. Z., Xie, L.J., Hu, Q. J., Wu, H. J., Xiao, S., Zhang, J., and Liu, Y. G. 2019. Alternative splicing and translation play important roles in hypoxic germination in rice. J. Exp. Bot. 70: 817–833. doi:10.1093/jxb/ery393
   PubMed Web of Science ®Google Scholar
• Chen, S. L., Rooney, T. J., Hu, A. R., Beard, H. S., Garrett, W. M., Mangalath, L. M., Powers, J. J., Cooper, B., and Zhang, X. N. 2019. 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. doi:10.3389/fpls.2019.01116
   PubMed Web of Science ®Google Scholar
• Chen, T., Cui, P., Chen, H., Ali, S., Zhang, S., and Xiong, L. 2013. A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis. PLoS Genet. 9: e1003875. doi:10.1371/journal.pgen.1003875
   PubMed Web of Science ®Google Scholar
• Chen, T., Cui, P., and Xiong, L. 2015. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res. 43: 8283–8298. doi:10.1093/nar/gkv751
   PubMed Web of Science ®Google Scholar
• Chen, Z., Wang, H. C., Shen, J., Sun, F., Wang, M., Xu, C., and Tan, B. C. 2019. PPR-SMR1 is required for the splicing of multiple mitochondrial introns, interacts with Zm-mCSF1, and is essential for seed development in maize. J. Exp. Bot. 70: 5245–5258. doi:10.1093/jxb/erz305
   PubMed Web of Science ®Google Scholar
• Cocquerelle, C., Mascrez, B., Hétuin, D., and Bailleul, B. 1993. Mis-splicing yields circular RNA molecules. FASEB J. 7: 155–160. doi:10.1096/fasebj.7.1.7678559
   PubMed Web of Science ®Google Scholar
• Conn, S. J., Pillman, K. A., Toubia, J., Conn, V. M., Salmanidis, M., Phillips, C. A., Roslan, S., Schreiber, A. W., Gregory, P. A., and Goodall, G. J. 2015. The RNA binding protein quaking regulates formation of circRNAs. Cell 160: 1125–1134. doi:10.1016/j.cell.2015.02.014
   PubMed Web of Science ®Google Scholar
• Conn, V. M., Hugouvieux, V., Nayak, A., Conos, S. A., Capovilla, G., Cildir, G., Jourdain, A., Tergaonkar, V., Schmid, M., Zubieta, C., and Conn, S. J. 2017. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat. Plants 3: 17053. doi:10.1038/nplants.2017.53
   PubMed Web of Science ®Google Scholar
• Crespi, M., Jurkevitchl, E., Poiret, M., Aubenton-Carafa, Y., Petrovics, G., Kondorosi, E., and Kondorosi, A. 1994. enod4O, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J. 13: 5099–5112. doi:10.1002/j.1460-2075.1994.tb06839.x
   PubMed Web of Science ®Google Scholar
• Das, R., Yu, J., Zhang, Z., Gygi, M. P., Krainer, A. R., Gygi, S. P., and Reed, R. 2007. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26: 867–881. doi:10.1016/j.molcel.2007.05.036
   PubMed Web of Science ®Google Scholar
• Deveson, I. W., Brunck, M. E., Blackburn, J., Tseng, E., Hon, T., Clark, T. A., Clark, M. B., Crawford, J., Dinger, M. E., Nielsen, L. K., Mattick, J. S., and Mercer, T. R. 2018. Universal alternative splicing of noncoding exons. Cell Syst. 6: 245–255. doi:10.1016/j.cels.2017.12.005
   PubMed Web of Science ®Google Scholar
• Dolata, J., Taube, M., Bajczyk, M., Jarmolowski, A., Szweykowska-Kulinska, Z., and Bielewicz, D. 2018. Regulation of plant microprocessor function in shaping microRNA landscape. Front. Plant Sci. 9: 753. doi:10.3389/fpls.2018.00753
   PubMed Web of Science ®Google Scholar
• Dou, K., Huang, C. F., Ma, Z. Y., Zhang, C. J., Zhou, J. X., Huang, H. W., Cai, T., Tang, K., Zhu, J. K., and He, X. J. 2013. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Nucleic Acids Res. 41: 8489–8502. doi:10.1093/nar/gkt639
   PubMed Web of Science ®Google Scholar
• Du, F., Gong, W., Bosca, S., Tucker, M., Vaucheret, H., and Laux, T. 2020. Dose-dependent AGO1-mediated inhibition of the miRNA165/166 pathway modulates stem cell maintenance in Arabidopsis shoot apical meristem. Plant Com. 1: 100002. doi:10.1016/j.xplc.2019.100002
   PubMedGoogle Scholar
• Dufu, K., Livingstone, M. J., Seebacher, J., Gygi, S. P., Wilson, S. A., and Reed, R. 2010. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev. 24: 2043–2053. doi:10.1101/gad.1898610
   PubMed Web of Science ®Google Scholar
• Dziembowski, A., Ventura, A. P., Rutz, B., Caspary, F., Faux, C., Halgand, F., Laprévote, O., and Séraphin, B. 2004. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J. 23: 4847–4856. doi:10.1038/sj.emboj.7600482
   PubMed Web of Science ®Google Scholar
• Eddy, A. C., Chapman, H., Brown, D. T., and George, E. M. 2020. Differential regulation of sFlt-1 splicing by U2AF65 and JMJD6 in placental-derived and endothelial cells. Biosci. Rep. 40: BSR20193252. doi:10.1042/BSR20193252
   PubMed Web of Science ®Google Scholar
• Ehrnsberger, H. F., Grasser, M., and Grasser, K. D. 2019. Nucleocytosolic mRNA transport in plants: export factors and their influence on growth and development. J. Exp. Bot. 70: 3757–3763. doi:10.1093/jxb/erz173
   PubMed Web of Science ®Google Scholar
• Ehrnsberger, H. F., Pfaff, C., Hachani, I., Flores-Tornero, M., Sørensen, B. B., Längst, G., Sprunck, S., Grasser, M., and Grasser, K. D. 2019. The UAP56-interacting export factors UIEF1 and UIEF2 function in mRNA export. Plant Physiol. 179: 1525–1536. doi:10.1104/pp.18.01476
   PubMed Web of Science ®Google Scholar
• Fang, Y. and Spector, D. L. 2007. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr. Biol. 17: 818–823. doi:10.1016/j.cub.2007.04.005
   PubMed Web of Science ®Google Scholar
• Fernandez, J. P., Moreno-Mateos, M. A., Gohr, A., Miao, L., Chan, S. H., Irimia, M., and Giraldez, A. J. 2018. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet. 14: e1007473. doi:10.1371/journal.pgen.1007473
   PubMed Web of Science ®Google Scholar
• Fiszbein, A., Godoy Herz, M. A., Gomez Acuña, L. I., and Kornblihtt, A. R. 2017. Interplay between chromatin and splicing. In Chromatin Regulation and Dynamics, Chapter 8; Göndör, A., Ed. Academic Press, pp 191–209. doi:10.1016/B978-0-12-803395-1.00008-3
   Google Scholar
• Fu, R., Zhang, M., Zhao, Y., He, X., Ding, C., Wang, S., Feng, Y., Song, X., Li, P., and Wang, B. 2017. Identification of salt tolerance-related microRNAs and their targets in maize (Zea mays L.) using high-throughput sequencing and degradome analysis. Front. Plant Sci. 8: 864. doi:10.3389/fpls.2017.00864
   PubMed Web of Science ®Google Scholar
• Gai, Y. P., Yuan, S. S., Zhao, Y. N., Zhao, H. N., Zhang, H. L., and Ji, X. L. 2018. A novel lncRNA, MuLnc1, associated with environmental stress in mulberry (Morus multicaulis). Front. Plant Sci. 9: 669. doi:10.3389/fpls.2018.00669
   PubMed Web of Science ®Google Scholar
• Galy, V., Gadal, O., Fromont-Racine, M., Romano, A., Jacquier, A., and Nehrbass, U. 2004. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 116: 63–73. doi:10.1016/S0092-8674(03)01026-2
   PubMed Web of Science ®Google Scholar
• Godoy Herz, M. A., Kubaczka, M. G., Brzyżek, G., Servi, L., Krzyszton, M., Simpson, C., Brown, J., Swiezewski, S., Petrillo, E., and Kornblihtt, A. R. 2019. Light regulates plant alternative splicing through the control of transcriptional elongation. Mol. Cell. 73: 1066–1074. doi:10.1016/j.molcel.2018.12.005
   PubMed Web of Science ®Google Scholar
• Granados-Riveron, J. T. and Aquino-Jarquin, G. 2016. The complexity of the translation ability of circRNAs. Biochim. Biophys. Acta 1859: 1245–1251. doi:10.1016/j.bbagrm.2016.07.009
   PubMed Web of Science ®Google Scholar
• Gu, B., Eick, D., and Bensaude, O. 2013. CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res. 41: 1591–1603. doi:10.1093/nar/gks1327
   PubMed Web of Science ®Google Scholar
• Guan, Q., Wen, C., Zeng, H., and Zhu, J. 2013. A KH domain-containing putative RNA-binding protein is critical for heat stress-responsive gene regulation and thermotolerance in Arabidopsis. Mol. Plant 6: 386–395. doi:10.1093/mp/sss119
   PubMed Web of Science ®Google Scholar
• Hackmann, A., Wu, H., Schneider, U. M., Meyer, K., Jung, K., and Krebber, H. 2014. Quality control of spliced mRNAs requires the shuttling SR proteins Gbp2 and Hrb1. Nat. Commun. 5: 3123. doi:10.1038/ncomms4123
   PubMed Web of Science ®Google Scholar
• Haïli, N., Planchard, N., Arnal, N., Quadrado, M., Vrielynck, N., Dahan, J., Des Francs-Small, C. C., and Mireau, H. 2016. The MTL1 pentatricopeptide repeat protein is required for both translation and splicing of the mitochondrial NADH DEHYDROGENASE SUBUNIT7 mRNA in Arabidopsis. Plant Physiol. 170: 354–366. doi:10.1104/pp.15.01591
   PubMed Web of Science ®Google Scholar
• Hall, M. P., Nagel, R. J., Fagg, W. S., Shiue, L., Cline, M. S., Perriman, R. J., Donohue, J. P., and Ares, M., Jr. 2013. Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. RNA. 19: 627–638. doi:10.1261/rna.038422.113
   PubMed Web of Science ®Google Scholar
• Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., and Kjems, J. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495: 384–388. doi:10.1038/nature11993
   PubMed Web of Science ®Google Scholar
• Hargous, Y., Hautbergue, G. M., Tintaru, A. M., Skrisovska, L., Golovanov, A. P., Stevenin, J., Lian, L. Y., Wilson, S. A., and Allain, F. H. 2006. Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8. EMBO J. 25: 5126–5137. doi:10.1038/sj.emboj.7601385
   PubMed Web of Science ®Google Scholar
• Henriques, R., Wang, H., Liu, J., Boix, M., Huang, L. F., and Chua, N. H. 2017. The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering. New Phytol. 216: 854–867. doi:10.1111/nph.14703
   PubMed Web of Science ®Google Scholar
• Herdt, O., Reich, S., Medenbach, J., Timmermann, B., Olofsson, D., Preußner, M., and Heyd, F. 2020. The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation. RNA Biol. 17: 843–856. doi:10.1080/15476286.2020.1732701
   PubMed Web of Science ®Google Scholar
• Houseley, J. M., Garcia-Casado, Z., Pascual, M., Paricio, N., O’Dell, K. M., Monckton, D. G., and Artero, R. D. 2006. Noncanonical RNAs from transcripts of the Drosophila muscleblind gene. J. Hered. 97: 253–260. doi:10.1093/jhered/esj037
   PubMed Web of Science ®Google Scholar
• Howard, J. M. and Sanford, J. R. 2015. The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley. Interdiscip. Rev. RNA. 6: 93–110. doi:10.1002/wrna.1260
   PubMed Web of Science ®Google Scholar
• Hu, Y., Gor, V., Morikawa, K., Nagata, K., and Kawaguchi, A. 2017. Cellular splicing factor UAP56 stimulates trimeric NP formation for assembly of functional influenza viral ribonucleoprotein complexes. Sci. Rep. 7: 14053. doi:10.1038/s41598-017-13784-4
   PubMed Web of Science ®Google Scholar
• Huang, C., Liang, D., Tatomer, D. C., and Wilusz, J. E. 2018. A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev. 32: 639–644. doi:10.1101/gad.314856.118
   PubMed Web of Science ®Google Scholar
• Huang, C. F., Miki, D., Tang, K., Zhou, H. R., Zheng, Z., Chen, W., Ma, Z. Y., Yang, L., Zhang, H., Liu, R., He, X. J., and Zhu, J. K. 2013. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet. 9: e1003779. doi:10.1371/journal.pgen.1003779
   PubMed Web of Science ®Google Scholar
• Huang, C. F. and Zhu, J. K. 2014. RNA splicing factors and RNA-directed DNA methylation. Biology 3: 243–254. doi:10.3390/biology3020243
   PubMedGoogle Scholar
• Huang, Y. and Steitz, J. A. 2001. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol. Cell 7: 899–905. doi:10.1016/S1097-2765(01)00233-7
   PubMed Web of Science ®Google Scholar
• Ivanov, A., Memczak, S., Wyle, R. E., Torti, F., Porath, H. T., Orejuela, M. R., Piechotta, M., Levanon, E. Y., Landthaler, M., Dieterich, C., and Rajewsky, N. 2015. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 10: 170–177. doi:10.1016/j.celrep.2014.12.019
   PubMed Web of Science ®Google Scholar
• Jabnoune, M., Secco, D., Lecampion, C., Robaglia, C., Shu, Q., and Poirier, Y. 2013. A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25: 4166–4182. doi:10.1105/tpc.113.116251
   PubMed Web of Science ®Google Scholar
• Jacewicz, A., Schwer, B., Smith, P., and Shuman, S. 2014. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic Acids Res. 42: 12885–12898. doi:10.1093/nar/gku930
   PubMed Web of Science ®Google Scholar
• Jang, Y. H., Park, H. Y., Lee, K. C., Thu, M. P., Kim, S. K., Suh, M. C., Kang, H., and Kim, J. K. 2014. A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana. Plant J. 78: 591–603. doi:10.1111/tpj.12491
   PubMed Web of Science ®Google Scholar
• Ji, X., Zhou, Y., Pandit, S., Huang, J., Li, H., Lin, C. Y., Xiao, R., Burge, C. B., and Fu, X. D. 2013. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153: 855–868. doi:10.1016/j.cell.2013.04.028
   PubMed Web of Science ®Google Scholar
• Jia, T., Zhang, B., You, C., Zhang, Y., Zeng, L., Li, S., Johnson, K. C. M., Yu, B., Li, X., and Chen, X. 2017. The Arabidopsis MOS4-associated complex promotes microRNA biogenesis and precursor messenger RNA splicing. Plant Cell 29: 2626–2643. doi:10.1105/tpc.17.00370
   PubMed Web of Science ®Google Scholar
• Jiang, J., Wang, B., Shen, Y., Wang, H., Feng, Q., and Shi, H. 2013. The Arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression. PLoS Genet. 9: e1003625. doi:10.1371/journal.pgen.1003625
   PubMed Web of Science ®Google Scholar
• Jiang, S. C., Mei, C., Liang, S., Yu, Y. T., Lu, K., Wu, Z., Wang, X. F., and Zhang, D. P. 2015. Crucial roles of the pentatricopeptide repeat protein SOAR1 in Arabidopsis response to drought, salt and cold stresses. Plant Mol. Biol. 88: 369–385. doi:10.1007/s11103-015-0327-9
   PubMed Web of Science ®Google Scholar
• Jiang, S. C., Mei, C., Wang, X. F., and Zhang, D. P. 2014. A hub for ABA signaling to the nucleus: significance of a cytosolic and nuclear dual-localized PPR protein SOAR1 acting downstream of Mg-chelatase H subunit. Plant Signal. Behav. 9: e972899. doi:10.4161/15592316.2014.972899
   PubMed Web of Science ®Google Scholar
• Kalyna, M., Lopato, S., and Barta, A. 2003. Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mboc. 14: 3565–3577. doi:10.1091/mbc.e03-02-0109
   Google Scholar
• Kanno, T., Venhuizen, P., Wu, M. T., Chiou, P., Chang, C. L., Kalyna, M., Matzke, A., and Matzke, M. 2020. A Collection of pre-mRNA splicing mutants in Arabidopsis thaliana. G3 10: 1983–1996. doi:10.1534/g3.119.400998
   Web of Science ®Google Scholar
• Katahira, J. 2012. mRNA export and the TREX complex. Biochim. Biophys. Acta 1819: 507–513. doi:10.1016/j.bbagrm.2011.12.001
   PubMed Web of Science ®Google Scholar
• Knop, K., Stepien, A., Barciszewska-Pacak, M., Taube, M., Bielewicz, D., Michalak, M., Borst, J. W., Jarmolowski, A., and Szweykowska-Kulinska, Z. 2017. Active 5’ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Res. 45: 2757–2775. doi:10.1093/nar/gkw895
   PubMed Web of Science ®Google Scholar
• Koga, M., Hayashi, M., and Kaida, D. 2015. Splicing inhibition decreases phosphorylation level of Ser2 in Pol II CTD. Nucleic Acids Res. 43: 8258–9267. doi:10.1093/nar/gkv740
   PubMed Web of Science ®Google Scholar
• Koncz, C., Dejong, F., Villacorta, N., Szakonyi, D., and Koncz, Z. 2012. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. Front. Plant Sci. 3: doi:10.3389/fpls.2012.00009
   PubMed Web of Science ®Google Scholar
• Kong, X., Zhang, M., Xu, X., Li, X., Li, C., and Ding, Z. 2014. System analysis of microRNAs in the development and aluminium stress responses of the maize root system. Plant Biotechnol. J. 12: 1108–1121. doi:10.1111/pbi.12218
   PubMed Web of Science ®Google Scholar
• Köster, T., Meyer, K., Weinholdt, C., Smith, L. M., Lummer, M., Speth, C., Grosse, I., Weigel, D., and Staiger, D. 2014. Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis. Nucleic Acids Res. 42: 9925–9936. doi:10.1093/nar/gku716
   PubMed Web of Science ®Google Scholar
• Kotake, Y., Sagane, K., Owa, T., Mimori-Kiyosue, Y., Shimizu, H., Uesugi, M., Ishihama, Y., Iwata, M., and Mizui, Y. 2007. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol. 23: 570–575. doi:10.1038/nchembio.2007.16
   Google Scholar
• Krämer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65: 367–409. doi:10.1146/annurev.bi.65.070196.002055
   PubMed Web of Science ®Google Scholar
• Kress, T. L., Krogan, N. J., and Guthrie, C. 2008. A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Mol. Cell 32: 727–734. doi:10.1016/j.molcel.2008.11.013
   PubMed Web of Science ®Google Scholar
• Kroeger, T. S., Watkins, K. P., Friso, G., van Wijk, K. J., and Barkan, A. 2009. A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc. Natl. Acad. Sci. USA. 106: 4537–4542. doi:10.1073/pnas.0812503106
   PubMed Web of Science ®Google Scholar
• Lai, X., Bazin, J., Webb, S., Crespi, M., Zubieta, C., and Conn, S.J. 2018. CircRNAs in plants. Adv. Exp. Med. Biol. 1087: 329–343. doi:10.1007/978-981-13-1426-1_26
   PubMed Web of Science ®Google Scholar
• Laloum, T., Martín, G., and Duque, P. 2018. Alternative splicing control of abiotic stress responses. Trends Plant Sci. 23: 140–150. doi:10.1016/j.tplants.2017.09.019
   PubMed Web of Science ®Google Scholar
• Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J. U., Rätsch, G., and Weigel, D. 2008. Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 105: 8795–8800. doi:10.1073/pnas.0802493105
   PubMed Web of Science ®Google Scholar
• Lee, B. H., Kapoor, A., Zhu, J., and Zhu, J. K. 2006. STABILIZED1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis. Plant Cell 18: 1736–1749. doi:10.1105/tpc.106.042184
   PubMed Web of Science ®Google Scholar
• Lee, K. C., Jang, Y. H., Kim, S. K., Park, H. Y., Thu, M. P., Lee, J. H., and Kim, J. K. 2017. RRM domain of Arabidopsis splicing factor SF1 is important for pre-mRNA splicing of a specific set of genes. Plant Cell Rep. 36: 1083–1095. doi:10.1007/s00299-017-2140-1
   PubMed Web of Science ®Google Scholar
• Legnini, I., Di Timoteo, G., Rossi, F., Morlando, M., Briganti, F., Sthandier, O., Fatica, A., Santini, T., Andronache, A., Wade, M., Laneve, P., Rajewsky, N., and Bozzoni, I. 2017. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Mol. Cell 66: 22–37. doi:10.1016/j.molcel.2017.02.017
   PubMed Web of Science ®Google Scholar
• Legrain, P. and Rosbash, M. 1989. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm. Cell 57: 573–583. doi:10.1016/0092-8674(89)90127-X
   PubMed Web of Science ®Google Scholar
• Li, J., Fu, J., Chen, Y., Fan, K., He, C., Zhang, Z., Li, L., Liu, Y., Zheng, J., Ren, D., and Wang, G. 2017. The U6 biogenesis-like 1 plays an important role in maize kernel and seedling development by affecting the 3’ end processing of U6 snRNA. Mol. Plant 10: 470–482. doi:10.1016/j.molp.2016.10.016
   PubMed Web of Science ®Google Scholar
• Li, L. J., Leng, R. X., Fan, Y. G., Pan, H. F., and Ye, D. Q. 2017. Translation of noncoding RNAs: focus on lncRNAs, pri-miRNAs, and circRNAs. Exp. Cell Res. 361: 1–8. doi:10.1016/j.yexcr.2017.10.010
   PubMed Web of Science ®Google Scholar
• Li, P., Tao, Z., and Dean, C. 2015. Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR. Genes Dev. 29: 696–701. doi:10.1101/gad.258814.115
   PubMed Web of Science ®Google Scholar
• Li, S., Li, M., Liu, K., Zhang, H., Zhang, S., Zhang, C., and Yu, B. 2020. MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities. Proc. Natl. Acad. Sci. USA. 117: 23982–23990. doi:10.1073/pnas.2008283117
   PubMed Web of Science ®Google Scholar
• Li, S., Liu, K., Zhou, B., Li, M., Zhang, S., Zeng, L., Zhang, C., and Yu, B. 2018. MAC3A and MAC3B, two core subunits of the MOS4-associated complex, positively influence miRNA biogenesis. Plant Cell 30: 481–494. doi:10.1105/tpc.17.00953
   PubMed Web of Science ®Google Scholar
• Li, S., Wang, Y., Zhao, Y., Zhao, X., Chen, X., and Gong, Z. 2019. Global Co-transcriptional splicing in Arabidopsis and the correlation with splicing regulation in mature RNAs. Mol. Plant 13: 266–277. doi:10.1016/j.molp.2019.11.003
   PubMed Web of Science ®Google Scholar
• Li, S., Xu, R., Li, A., Liu, K., Gu, L., Li, M., Zhang, H., Zhang, Y., Zhuang, S., Wang, Q., Gao, G., Li, N., Zhang, C., Li, Y., and Yu, B. 2018. SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis. Nucleic Acids Res. 46: 9148–9159. doi:10.1093/nar/gky591
   PubMed Web of Science ®Google Scholar
• Li, Y., Guo, Q., Zhang, C., Zhang, S., and Yan, K. 2019. Genome-Wide Analysis of mRNA splicing variants in higher plants. J. Hort. 6: 255.
   Google Scholar
• Li, Z., Kearse, M. G., and Huang, C. 2019. The nuclear export of circular RNAs is primarily defined by their length. RNA Biol. 16: 1–4. doi:10.1080/15476286.2018.1557498
   PubMed Web of Science ®Google Scholar
• Li, Z., Wang, S., Cheng, J., Su, C., Zhong, S., Liu, Q., Fang, Y., Yu, Y., Lv, H., Zheng, Y., and Zheng, B. 2016. Intron lariat RNA inhibits microRNA biogenesis by sequestering the dicing complex in Arabidopsis. PLoS Genet. 12: e1006422. doi:10.1371/journal.pgen.1006422
   PubMed Web of Science ®Google Scholar
• Liang, D., Tatomer, D. C., Luo, Z., Wu, H., Yang, L., Chen, L. L., Cherry, S., and Wilusz, J. E. 2017. The output of protein-coding genes shifts to circular RNAs when the pre-mRNA processing machinery is limiting. Mol. Cell 68: 940–954. doi:10.1016/j.molcel.2017.10.034
   PubMed Web of Science ®Google Scholar
• Lin, P. C. and Xu, R. M. 2012. Structure and assembly of the SF3a splicing factor complex of U2 snRNP. EMBO J. 31: 1579–1590. doi:10.1038/emboj.2012.7
   PubMed Web of Science ®Google Scholar
• Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S., and Fu, X. D. 2008. The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol. 15: 819–826. doi:10.1038/nsmb.1461
   PubMed Web of Science ®Google Scholar
• Liu, F., Marquardt, S., Lister, C., Swiezewski, S., and Dean, C. 2010. Targeted 3’ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327: 94–97. doi:10.1126/science.1180278
   PubMed Web of Science ®Google Scholar
• Liu, F., Xu, Y., Chang, K., Li, S., Liu, Z., Qi, S., Jia, J., Zhang, M., Crawford, N. M., and Wang, Y. 2019. The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis. New Phytol. 224: 117–131. doi:10.1111/nph.16038
   PubMed Web of Science ®Google Scholar
• Liu, J., Jung, C., Xu, J., Wang, H., Deng, S., Bernad, L., Arenas-Huertero, C., and Chua, N. H. 2012. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24: 4333–4345. doi:10.1105/tpc.112.102855
   PubMed Web of Science ®Google Scholar
• Liu, X., Hao, L., Li, D., Zhu, L., and Hu, S. 2015. Long non-coding RNAs and their biological roles in plants. Genom. Proteom. Bioinf. 13: 137–147. doi:10.1016/j.gpb.2015.02.003
   PubMed Web of Science ®Google Scholar
• Lopato, S., Forstner, C., Kalyna, M., Hilscher, J., Langhammer, U., Indrapichate, K., Lorković, Z. J., and Barta, A. 2002. Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors. J. Biol. Chem. 277: 39989–39998. doi:10.1074/jbc.M206455200
   PubMed Web of Science ®Google Scholar
• Lu, T., Cui, L., Zhou, Y., Zhu, C., Fan, D., Gong, H., Zhao, Q., Zhou, C., Zhao, Y., Lu, D., Luo, J., Wang, Y., Tian, Q., Feng, Q., Huang, T., and Han, B. 2015. Transcriptome-wide investigation of circular RNAs in rice. RNA. 21: 2076–2087. doi:10.1261/rna.052282.115
   PubMed Web of Science ®Google Scholar
• Lubelsky, Y. and Ulitsky, I. 2018. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 555: 107–111. doi:10.1038/nature25757
   PubMed Web of Science ®Google Scholar
• Lucero, L., Bazin, J., Rodriguez Melo, J., Ibañez, F., Crespi, M. D., and Ariel, F. 2020. Evolution of the small family of alternative splicing modulators nuclear speckle RNA-binding proteins in plants. Genes 11: 207. doi:10.3390/genes11020207
   Web of Science ®Google Scholar
• Ma, Y., Zhang, S., Bi, C., Mei, C., Jiang, S. C., Wang, X. F., Lu, Z. J., and Zhang, D. P. 2020. Arabidopsis exoribonuclease USB1, interacting with PPR-domain protein SOAR1, is negatively involved in abscisic acid signaling. J. Exp. Bot. 7: 837–5851. doi:10.1093/jxb/eraa315
   Google Scholar
• Manavski, N., Guyon, V., Meurer, J., Wienand, U., and Brettschneider, R. 2012. An essential pentatricopeptide repeat protein facilitates 5’ maturation and translation initiation of rps3 mRNA in maize mitochondria. Plant Cell 24: 3087–3105. doi:10.1105/tpc.112.099051
   PubMed Web of Science ®Google Scholar
• Marquardt, S., Raitskin, O., Wu, Z., Liu, F., Sun, Q., and Dean, C. 2014. Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol Cell 54: 156–165. doi:10.1016/j.molcel.2014.03.026
   PubMed Web of Science ®Google Scholar
• Maslon, M. M., Heras, S. R., Bellora, N., Eyras, E., and Cáceres, J. F. 2014. The translational landscape of the splicing factor SRSF1 and its role in mitosis. Elife 3: e02028. doi:10.7554/eLife.02028
   Web of Science ®Google Scholar
• Masuyama, K., Taniguchi, I., Kataoka, N., and Ohno, M. 2004. RNA length defines RNA export pathway. Genes Dev. 18: 2074–2085. doi:10.1101/gad.1216204
   PubMed Web of Science ®Google Scholar
• Matera, A. G. and Wang, Z. 2014. A day in the life of the spliceosome. Nat. Rev. Mol. Cell Biol. 15: 108–121. doi:10.1038/nrm3742
   PubMed Web of Science ®Google Scholar
• Matzke, M. A., and Mosher, R. A. 2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15: 394–408. doi:10.1038/nrg3683
   PubMed Web of Science ®Google Scholar
• McCloskey, A., Taniguchi, I., Shinmyozu, K., and Ohno, M. 2012. HnRNP C tetramer measures RNA length to classify RNA polymerase II transcripts for export. Science 335: 1643–1646. doi:10.1126/science.1218469
   PubMed Web of Science ®Google Scholar
• Mei, C., Jiang, S. C., Lu, Y. F., Wu, F. Q., Yu, Y. T., Liang, S., Feng, X. J., Portoles Comeras, S., Lu, K., Wu, Z., Wang, X. F., and Zhang, D. P. 2014. Arabidopsis pentatricopeptide repeat protein SOAR1 plays a critical role in abscisic acid signalling. J. Exp. Bot. 65: 5317–5330. doi:10.1093/jxb/eru293
   PubMed Web of Science ®Google Scholar
• Michlewski, G., Sanford, J. R., and Cáceres, J. F. 2008. The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol. Cell 30: 179–189. doi:10.1016/j.molcel.2008.03.013
   PubMed Web of Science ®Google Scholar
• Modrek, B. and Lee, C. 2002. A genomic view of alternative splicing. Nat. Genet. 30: 13–19. doi:10.1038/ng0102-13
   PubMed Web of Science ®Google Scholar
• Moehle, E. A., Braberg, H., Krogan, N. J., and Guthrie, C. 2014. Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol. 11: 313–319. doi:10.4161/rna.28646
   PubMed Web of Science ®Google Scholar
• Monaghan, J., Xu, F., Xu, S., Zhang, Y., and Li, X. 2010. Two putative RNA-binding proteins function with unequal genetic redundancy in the MOS4-associated complex. Plant Physiol. 154: 1783–1793. doi:10.1104/pp.110.158931
   PubMed Web of Science ®Google Scholar
• Morris, E. R., Chevalier, D., and Walker, J. C. 2006. DAWDLE, a forkhead-associated domain gene, regulates multiple aspects of plant development. Plant Physiol. 141: 932–941. doi:10.1104/pp.106.076893
   PubMed Web of Science ®Google Scholar
• Müller-McNicoll, M., Botti, V., de Jesus Domingues, A. M., Brandl, H., Schwich, O. D., Steiner, M. C., Curk, T., Poser, I., Zarnack, K., and Neugebauer, K. M. 2016. SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes Dev. 30: 553–566. doi:10.1101/gad.276477.115
   PubMed Web of Science ®Google Scholar
• Naftelberg, S., Schor, I. E., Ast, G., and Kornblihtt, A. R. 2015. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu. Rev. Biochem. 84: 165–198. doi:10.1146/annurev-biochem-060614-034242
   PubMed Web of Science ®Google Scholar
• Niedojadło, J., Dełeńko, K., and Niedojadło, K. 2016. Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia. RNA Biol. 13: 531–543. doi:10.1080/15476286.2016.1166331
   PubMed Web of Science ®Google Scholar
• Nimeth, B. A., Riegler, S., and Kalyna, M. 2020. Alternative splicing and DNA damage response in plants. Front. Plant Sci. 11: 91. doi:10.3389/fpls.2020.00091
   PubMed Web of Science ®Google Scholar
• Nussbacher, J. K. and Yeo, G. W. 2018. Systematic discovery of RNA binding proteins that regulate microRNA levels. Mol. Cell 69: 1005–1016. doi:10.1016/j.molcel.2018.02.012
   PubMed Web of Science ®Google Scholar
• Ostheimer, G. J., Williams-Carrier, R., Belcher, S., Osborne, E., Gierke, J., and Barkan, A. 2003. Group II intron splicing factors derived by diversification of an ancient RNA-binding domain. EMBO J. 22: 3919–3929. doi:10.1093/emboj/cdg372
   PubMed Web of Science ®Google Scholar
• Palangat, M., Anastasakis, D. G., Fei, D. L., Lindblad, K. E., Bradley, R., Hourigan, C. S., Hafner, M., and Larson, D. R. 2019. The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation. Genes Dev. 33: 482–497. doi:10.1101/gad.319590.118
   PubMed Web of Science ®Google Scholar
• Palazzo, A. F. and Lee, E. S. 2018. Sequence determinants for nuclear retention and cytoplasmic export of mRNAs and lncRNAs. Front. Genet. 9: 440. doi:10.3389/fgene.2018.00440
   PubMed Web of Science ®Google Scholar
• Pamudurti, N. R., Bartok, O., Jens, M., Ashwal-Fluss, R., Stottmeister, C., Ruhe, L., Hanan, M., Wyler, E., Perez-Hernandez, D., Ramberger, E., Shenzis, S., Samson, M., Dittmar, G., Landthaler, M., Chekulaeva, M., Rajewsky, N., and Kadener, S. 2017. Translation of circRNAs. Mol. Cell 66: 9–21. doi:10.1016/j.molcel.2017.02.021
   PubMed Web of Science ®Google Scholar
• Pamudurti, N. R., Konakondla-Jacob, V. V., Krishnamoorthy, A., Ashwal-Fluss, R., Bartok, O., Wüst, S., Seitz, K., Maya, R., Lerner, N., Patop, I. N., Rizzoli, S., Beautus, T., and Kadener, S. 2018. An in vivo knockdown strategy reveals multiple functions for circMbl. bioRxiv. doi:10.1101/483271.
   Google Scholar
• Park, H. Y., Lee, K. C., Jang, Y. H., Kim, S. K., Thu, M. P., Lee, J. H., and Kim, J. K. 2017. The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. Plant Cell Rep. 36: 1113–1123. doi:10.1007/s00299-017-2142-z
   PubMed Web of Science ®Google Scholar
• Park, M. Y., Wu, G., Gonzalez-Sulser, A., Vaucheret, H., and Poethig, R. S. 2005. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. USA. 102: 3691–3696. doi:10.1073/pnas.0405570102
   PubMed Web of Science ®Google Scholar
• Price, A. M., Görnemann, J., Guthrie, C., and Brow, D. A. 2014. An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8. RNA. 20: 46–60. doi:10.1261/rna.041970.113
   PubMed Web of Science ®Google Scholar
• Qi, H. D., Lin, Y., Ren, Q. P., Wang, Y. Y., Xiong, F., and Wang, X. L. 2019. RNA splicing of FLC modulates the transition to flowering. Front. Plant Sci. 10: 1625. doi:10.3389/fpls.2019.01625
   PubMed Web of Science ®Google Scholar
• Qu, S., Liu, Z., Yang, X., Zhou, J., Yu, H., Zhang, R., and Li, H. 2018. The emerging functions and roles of circular RNAs in cancer. Cancer Lett. 414: 301–309. doi:10.1016/j.canlet.2017.11.022
   PubMed Web of Science ®Google Scholar
• Raczynska, K. D., Stepien, A., Kierzkowski, D., Kalak, M., Bajczyk, M., McNicol, J., Simpson, C. G., Szweykowska-Kulinska, Z., Brown, J. W., and Jarmolowski, A. 2014. The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res. 42: 1224–1244. doi:10.1093/nar/gkt894
   PubMed Web of Science ®Google Scholar
• Raitskin, O., Cho, D. S., Sperling, J., Nishikura, K., and Sperling, R. 2001. RNA editing activity is associated with splicing factors in lnRNP particles: the nuclear pre-mRNA processing machinery. Proc. Natl. Acad. Sci. USA. 98: 6571–6576. doi:10.1073/pnas.111153798
   PubMed Web of Science ®Google Scholar
• Reed, R. and Hurt, E. 2002. A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 108: 523–531. doi:10.1016/S0092-8674(02)00627-X
   PubMed Web of Science ®Google Scholar
• Ren, R. C., Wang, L. L., Zhang, L., Zhao, Y. J., Wu, J. W., Wei, Y. M., Zhang, X. S., and Zhao, X. Y. 2020. DEK43 is a P-type pentatricopeptide repeat (PPR) protein responsible for the cis-splicing of nad4 in maize mitochondria. J. Integr. Plant Biol. 62: 299–313. doi:10.1111/jipb.12843
   PubMed Web of Science ®Google Scholar
• Rigo, R., Bazin, J. R. M., Crespi, M., and Charon, C. L. 2019. Alternative splicing in the regulation of plant-microbe interactions. Plant Cell Physiol. 60: 1906–1916. doi:10.1093/pcp/pcz086
   PubMed Web of Science ®Google Scholar
• Rodríguez-Cazorla, E., Ripoll, J. J., Andújar, A., Bailey, L. J., Martínez-Laborda, A., Yanofsky, M. F., and Vera, A. 2015. K-homology nuclear ribonucleoproteins regulate floral organ identity and determinacy in Arabidopsis. PLoS Genet. 11: e1004983. doi:10.1371/journal.pgen.1004983
   PubMed Web of Science ®Google Scholar
• Romero-Barrios, N., Legascue, M. F., Benhamed, M., Ariel, F., and Crespi, M. 2018. Splicing regulation by long noncoding RNAs. Nucleic Acids Res. 46: 2169–2184. doi:10.1093/nar/gky095
   PubMed Web of Science ®Google Scholar
• Rutz, B. and Séraphin, B. 2000. A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing. EMBO J. 19: 1873–1886. doi:10.1093/emboj/19.8.1873
   PubMed Web of Science ®Google Scholar
• Saldi, T., Cortazar, M. A., Sheridan, R. M., and Bentley, D. L. 2016. Coupling of RNA polymerase II transcription elongation with pre-mRNA splicing. J. Mol. Biol. 428: 2623–2635. doi:10.1016/j.jmb.2016.04.017
   PubMed Web of Science ®Google Scholar
• Salzman, J., Gawad, C., Wang, P. L., Lacayo, N., and Brown, P. O. 2012. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7: e30733. doi:10.1371/journal.pone.0030733
   PubMed Web of Science ®Google Scholar
• Sanford, J. R., Gray, N. K., Beckmann, K., and Caceres, J. F. 2004. A novel role for shuttling SR proteins in mRNA. Genes Dev. 18: 755–768. doi:10.1101/gad.286404
   PubMed Web of Science ®Google Scholar
• Schmitz-Linneweber, C., Williams-Carrier, R., and Barkan, A. 2005. RNA immunoprecipitation and microarray analysis show a chloroplast pentatricopeptide repeat protein to be associated with the 5’ region of mRNAs whose translation it activates. Plant Cell 17: 2791–2804. doi:10.1105/tpc.105.034454
   PubMed Web of Science ®Google Scholar
• Shanmugapriya, H. H. A., Vijayarathna, S., Oon, C. E., Chen, Y., Kanwar, J. R., Ng, M. L., and Sasidharan, S. 2018. Functional analysis of circular RNAs. Adv. Exp. Med. Biol. 1087: 95–105. doi:10.1007/978-981-13-1426-1_8
   PubMed Web of Science ®Google Scholar
• Shao, C., Dong, A. W., Ma, X., and Meng, Y. 2014. Is Argonaute 1 the only effective slicer of small RNA-mediated regulation of gene expression in plants? J. Exp. Bot. 65: 6293–6299. doi:10.1093/jxb/eru382
   PubMed Web of Science ®Google Scholar
• Shao, C., Yang, B., Wu, T., Huang, J., Tang, P., Zhou, Y., Zhou, J., Qiu, J., Jiang, L., Li, H., Chen, G., Sun, H., Zhang, Y., Denise, A., Zhang, D. E., and Fu, X. D. 2014. Mechanisms for U2AF to define 3’ splice sites and regulate alternative splicing in the human genome. Nat. Struct. Mol. Biol. 21: 997–1005. doi:10.1038/nsmb.2906
   PubMed Web of Science ®Google Scholar
• Shen, H. 2009. UAP56- a key player with surprisingly diverse roles in pre-mRNA splicing and nuclear export. BMB Rep. 42: 185–188. doi:10.5483/BMBRep.2009.42.4.185
   PubMed Web of Science ®Google Scholar
• Shi, Y. 2017. Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat. Rev. Mol. Cell Biol. 18: 655–670. doi:10.1038/nrm.2017.86
   PubMed Web of Science ®Google Scholar
• Shiimori, M., Inoue, K., and Sakamoto, H. 2013. A specific set of exon junction complex subunits is required for the nuclear retention of unspliced RNAs in Caenorhabditis elegans. Mol. Cell Biol. 33: 444–456. doi:10.1128/MCB.01298-12
   PubMed Web of Science ®Google Scholar
• Shukla, C. J., McCorkindale, A. L., Gerhardinger, C., Korthauer, K. D., Cabili, M. N., Shechner, D. M., Irizarry, R. A., Maass, P. G., and Rinn, J. L. 2018. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 37: e98452. doi:10.15252/embj.201798452
   PubMed Web of Science ®Google Scholar
• Singh, A., Gautam, V., Singh, S., Sarkar Das, S., Verma, S., Mishra, V., Mukherjee, S., and Sarkar, A. K. 2018. Plant small RNAs: advancement in the understanding of biogenesis and role in plant development. Planta 248: 545–558. doi:10.1007/s00425-018-2927-5
   PubMed Web of Science ®Google Scholar
• Singh, A. K., Tamrakar, A., Jaiswal, A., Kanayama, N., and Kodgire, P. 2020. SRSF1-3, a splicing and somatic hypermutation regulator, controls transcription of IgV genes via chromatin regulators SATB2, UBN1 and histone variant H3.3. Mol. Immunol. 119: 69–82. doi:10.1016/j.molimm.2020.01.005
   PubMed Web of Science ®Google Scholar
• Solomon, O., Oren, S., Safran, M., Deshet-Unger, N., Akiva, P., Jacob-Hirsch, J., Cesarkas, K., Kabesa, R., Amariglio, N., Unger, R., Rechavi, G., and Eyal, E. 2013. Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). RNA. 19: 591–604. doi:10.1261/rna.038042.112
   PubMed Web of Science ®Google Scholar
• Song, Y., Gao, F., Peng, Y., and Yang, X. 2020. Long non-coding RNA DBH-AS1 promotes cancer progression in diffuse large B-cell lymphoma by targeting FN1 via RNA-binding protein BUD13. Cell Biol. Int. 44: 1331–1340. doi:10.1002/cbin.11327
   PubMed Web of Science ®Google Scholar
• Sørensen, B. B., Ehrnsberger, H. F., Esposito, S., Pfab, A., Bruckmann, A., Hauptmann, J., Meister, G., Merkl, R., Schubert, T., Längst, G., Melzer, M., Grasser, M., and Grasser, K. D. 2017. The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events. Plant Mol. Biol. 93: 283–298. doi:10.1007/s11103-016-0561-9
   PubMed Web of Science ®Google Scholar
• Stankovic, N., Schloesser, M., Joris, M., Sauvage, E., Hanikenne, M., and Motte, P. 2016. Dynamic distribution and interaction of the Arabidopsis SRSF1 subfamily splicing factors. Plant Physiol. 170: 1000–1013. doi:10.1104/pp.15.01338
   PubMed Web of Science ®Google Scholar
• Stepien, A., Knop, K., Dolata, J., Taube, M., Bajczyk, M., Barciszewska-Pacak, M., Pacak, A., Jarmolowski, A., and Szweykowska-Kulinska, Z. 2017. Posttranscriptional coordination of splicing and miRNA biogenesis in plants. Wiley Interdiscip. Rev. RNA. 8: doi:10.1002/wrna.1403
   PubMed Web of Science ®Google Scholar
• Sträßer, K., Masuda, S., Mason, P., Pfannstiel, J., Oppizzi, M., Rodriguez-Navarro, S., Rondón, A. G., Aguilera, A., Struhl, K., Reed, R., and Hurt, E. 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417: 304–308. doi:10.1038/nature746
   PubMed Web of Science ®Google Scholar
• Streitner, C., Danisman, S., Wehrle, F., Schöning, J. C., Alfano, J. R., and Staiger, D. 2008. The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana. Plant J. 56: 239–250. doi:10.1111/j.1365-313X.2008.03591.x
   PubMed Web of Science ®Google Scholar
• Streitner, C., Köster, T., Simpson, C. G., Shaw, P., Danisman, S., Brown, J. W., and Staiger, D. 2012. An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res. 40: 11240–11255. doi:10.1093/nar/gks873
   PubMed Web of Science ®Google Scholar
• Sun, H. X. and Chua, N. H. 2019. Bioinformatics approaches to studying plant long noncoding RNAs (lncRNAs): identification and functional interpretation of lncRNAs from RNA-Seq data sets. Methods Mol. Biol. 1933: 197–205. doi:10.1007/978-1-4939-9045-0_11
   PubMedGoogle Scholar
• Sun, X., Wang, L., Ding, J., Wang, Y., Wang, J., Zhang, X., Che, Y., Liu, Z., Zhang, X., Ye, J., Wang, J., Sablok, G., Deng, Z., and Zhao, H. 2016. Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA. FEBS Lett. 590: 3510–3516. doi:10.1002/1873-3468.12440
   PubMed Web of Science ®Google Scholar
• Sun, Y. M., Wang, W. T., Zeng, Z. C., Chen, T. Q., Han, C., Pan, Q., Huang, W., Fang, K., Sun, L. Y., Zhou, Y. F., Luo, X. Q., Luo, C., Du, X., and Chen, Y. Q. 2019. CircMYBL2, a circRNA from MYBL2, regulates FLT3 translation by recruiting PTBP1 to promote FLT3-ITD AML progression. Blood 134: 1533–1546. doi:10.1182/blood.2019000802
   PubMed Web of Science ®Google Scholar
• Swiezewski, S., Liu, F., Magusin, A., and Dean, C. 2009. Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462: 799–802. doi:10.1038/nature08618
   PubMed Web of Science ®Google Scholar
• Szakonyi, D. and Duque, P. 2018. Alternative splicing as a regulator of early plant development. Front. Plant Sci. 9: 1174. doi:10.3389/fpls.2018.01174
   PubMed Web of Science ®Google Scholar
• Takemura, R., Takeiwa, T., Taniguchi, I., McCloskey, A., and Ohno, M. 2011. Multiple factors in the early splicing complex are involved in the nuclear retention of pre-mRNAs in mammalian cells. Genes Cells 16: 1035–1049. doi:10.1111/j.1365-2443.2011.01548.x
   PubMed Web of Science ®Google Scholar
• Thatcher, L. F., Kamphuis, L. G., Hane, J. K., Oñate-Sánchez, L., and Singh, K. B. 2015. The Arabidopsis KH-Domain RNA-binding protein ESR1 functions in components of jasmonate signalling, unlinking growth restraint and resistance to stress. PLoS One 10: e0126978. doi:10.1371/journal.pone.0126978
   PubMed Web of Science ®Google Scholar
• Thatcher, S. R., Zhou, W., Leonard, A., Wang, B.-B., Beatty, M., Zastrow-Hayes, G., Zhao, X., Baumgarten, A., and Li, B. 2014. Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation. Plant Cell 26: 3472–3487. doi:10.1105/tpc.114.130773
   PubMed Web of Science ®Google Scholar
• Tian, Y., Chen, M. X., Yang, J. F., Achala, H. H. K., Gao, B., Hao, G. F., Yang, G. F., Dian, Z. Y., Hu, Q. J., Zhang, D., Zhang, J., and Liu, Y. G. 2019. Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species. Planta 249: 583–600. doi:10.1007/s00425-018-3026-3
   PubMed Web of Science ®Google Scholar
• Tillemans, V., Leponce, I., Rausin, G., Dispa, L., and Motte, P. 2006. Insights into nuclear organization in plants as revealed by the dynamic distribution of Arabidopsis SR splicing factors. Plant Cell 18: 3218–3234. doi:10.1105/tpc.106.044529
   PubMed Web of Science ®Google Scholar
• Trowitzsch, S., Weber, G., Lührmann, R., and Wahl, M. C. 2009. Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex. J. Mol. Biol. 385: 531–541. doi:10.1016/j.jmb.2008.10.087
   PubMed Web of Science ®Google Scholar
• Uyttewaal, M., Mireau, H., Rurek, M., Hammani, K., Arnal, N., Quadrado, M., and Giegé, P. 2008. PPR336 is associated with polysomes in plant mitochondria. J. Mol. Biol. 375: 626–636. doi:10.1016/j.jmb.2007.11.011
   PubMed Web of Science ®Google Scholar
• Valencia, P., Dias, A. P., and Reed, R. 2008. Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc. Natl. Acad. Sci. USA. 105: 3386–3391. doi:10.1073/pnas.0800250105
   PubMed Web of Science ®Google Scholar
• Vicente-Crespo, M., Pascual, M., Fernandez-Costa, J. M., Garcia-Lopez, A., Monferrer, L., Miranda, M. E., Zhou, L., and Artero, R. D. 2008. Drosophila muscleblind is involved in troponin T alternative splicing and apoptosis. PLoS One 3: e1613. doi:10.1371/journal.pone.0001613
   PubMed Web of Science ®Google Scholar
• Voith von Voithenberg, L., Sánchez-Rico, C., Kang, H. S., Madl, T., Zanier, K., Barth, A., Warner, L. R., Sattler, M., and Lamb, D. C. 2016. Recognition of the 3’ splice site RNA by the U2AF heterodimer involves a dynamic population shift. Proc. Natl. Acad. Sci. USA. 113: E7169–E7175. doi:10.1073/pnas.1605873113
   PubMed Web of Science ®Google Scholar
• Wallace, E. W. J. and Beggs, J. D. 2017. Extremely fast and incredibly close: cotranscriptional splicing in budding yeast. RNA. 23: 601–610. doi:10.1261/rna.060830.117
   PubMed Web of Science ®Google Scholar
• Wan, R., Yan, C., Bai, R., Huang, G., and Shi, Y. 2016. Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. Science 353: 895–904. doi:10.1126/science.aag2235
   PubMed Web of Science ®Google Scholar
• Wan, R., Yan, C., Bai, R., Lei, J., and Shi, Y. 2017. Structure of an intron lariat spliceosome from saccharomyces cerevisiae. Cell 171: 120–132. doi:10.1016/j.cell. 2017.08.029
   PubMed Web of Science ®Google Scholar
• Wan, Y. and Hopper, A. K. 2018. Size matters: conserved proteins function in length-dependent nuclear export of circular RNAs. Genes Dev. 32: 600–601. doi:10.1101/gad.316216.118
   PubMed Web of Science ®Google Scholar
• Wang, H., Wang, H., Zhang, H., Liu, S., Wang, Y., Gao, Y., Xi, F., Zhao, L., Liu, B., Reddy, A. S. N., Lin, C., and Gu, L. 2019. The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics 35: 3119–3126. doi:10.1093/bioinformatics/btz038
   PubMed Web of Science ®Google Scholar
• Wang, H. V. and Chekanova, J. A. 2017. Long noncoding RNAs in plants. Adv. Exp. Med. Biol. 1008: 133–154. doi:10.1007/978-981-10-5203-3_5
   PubMed Web of Science ®Google Scholar
• Wang, K., Yin, C., Du, X., Chen, S., Wang, J., Zhang, L., Wang, L., Yu, Y., Chi, B., Shi, M., Wang, C., Reed, R., Zhou, Y., Huang, J., and Cheng, H. 2019. A U2-snRNP-independent role of SF3b in promoting mRNA export. Proc. Natl. Acad. Sci. USA. 16: 7837–7846. doi:10.1073/pnas.1818835116
   Google Scholar
• Wang, Q., Zhang, L., Lynn, B., and Rymond, B. C. 2008. A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast. Nucleic Acids Res. 36: 2787–2798. doi:10.1093/nar/gkn144
   PubMed Web of Science ®Google Scholar
• Wang, Y., Liu, J., Huang, B. O., Xu, Y. M., Li, J., Huang, L. F., Lin, J., Zhang, J., Min, Q. H., Yang, W. M., and Wang, X. Z. 2015. Mechanism of alternative splicing and its regulation. Biomed. Rep. 3: 152–158. doi:10.3892/br.2014.407
   PubMed Web of Science ®Google Scholar
• Wang, Y., Xiong, Z., Li, Q., Sun, Y., Jin, J., Chen, H., Zou, Y., Huang, X., and Ding, Y. 2019. Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition. BMC. Plant Biol. 19: 340. doi:10.1186/s12870-019-1944-2
   PubMed Web of Science ®Google Scholar
• Wang, Y. Y., Xiong, F., Ren, Q. P., and Wang, X. L. 2020. Regulation of flowering transition by alternative splicing: the role of the U2 auxiliary factor. J. Exp. Bot. 71: 751–758. doi:10.1093/jxb/erz416
   PubMed Web of Science ®Google Scholar
• Watkins, K. P., Rojas, M., Friso, G., van Wijk, K. J., Meurer, J., and Barkan, A. 2011. APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain. Plant Cell 23: 1082–1092. doi:10.1105/tpc.111.084335
   PubMed Web of Science ®Google Scholar
• Wei, X., Li, H., Yang, J., Hao, D., Dong, D., Huang, Y., Lan, X., Plath, M., Lei, C., Lin, F., Bai, Y., and Chen, H. 2017. Circular RNA profiling reveals an abundant circLMO7 that regulates myoblasts differentiation and survival by sponging miR-378a-3p. Cell Death Dis. 8: e3153. doi:10.1038/cddis.2017.541
   PubMed Web of Science ®Google Scholar
• Wilk, R., Hu, J., Blotsky, D., and Krause, H. M. 2016. Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs. Genes Dev. 30: 594–609. doi:10.1101/gad.276931.115
   PubMed Web of Science ®Google Scholar
• Will, C. L. and Lührmann, R. 2011. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3: a003707. doi:10.1101/cshperspect.a003707
   PubMed Web of Science ®Google Scholar
• Wilusz, J. E. 2018. A 360° view of circular RNAs: from biogenesis to functions. Wires. RNA. 9: e1478. doi:10.1002/wrna.1478
   Google Scholar
• Wu, Y., Guo, J., Cai, Y., Gong, X., Xiong, X., Qi, W., Pang, Q., Wang, X., and Wang, Y. 2016. Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance. Physiol. Plantarum 157: 453–468. doi:10.1111/ppl.12419
   PubMed Web of Science ®Google Scholar
• Wu, Z., Zhu, D., Lin, X., Miao, J., Gu, L., Deng, X., Yang, Q., Sun, K., Zhu, D., Cao, X., Tsuge, T., Dean, C., Aoyama, T., Gu, H., and Qu, L. J. 2016. RNA binding proteins RZ-1B and RZ-1C play critical roles in regulating pre-mRNA splicing and gene expression during development in Arabidopsis. Plant Cell 28: 55–73. doi:10.1105/tpc.15.00949
   PubMed Web of Science ®Google Scholar
• Wysoczanski, P., and Zweckstetter, M. 2016. Retention and splicing complex (RES) - the importance of cooperativity. RNA Biol. 13: 128–133. doi:10.1080/15476286.2015.1096484
   PubMed Web of Science ®Google Scholar
• Xiao, M. S., Ai, Y., and Wilusz, J. E. 2020. Biogenesis and functions of circular RNAs come into focus. Trends Cell Biol. 30: 226–240. doi:10.1016/j.tcb.2019.12.004
   PubMed Web of Science ®Google Scholar
• Xiong, F., Liu, H. H., Duan, C. Y., Zhang, B. K., Wei, G., Zhang, Y., and Li, S. 2019. Arabidopsis JANUS regulates embryonic pattern formation through Pol II-Mediated transcription of WOX2 and PIN7. iScience 19: 1179–1188. doi:10.1016/j.isci.2019.09.004
   PubMed Web of Science ®Google Scholar
• Xiong, F., Ren, J. J., Yu, Q., Wang, Y. Y., Kong, L. J., Otegui, M. S., and Wang, X. L. 2019. AtBUD13 affects pre-mRNA splicing and is essential for embryo development in Arabidopsis. Plant J. 98: 714–726. doi:10.1111/tpj.14268
   PubMed Web of Science ®Google Scholar
• Xiong, F., Ren, J. J., Yu, Q., Wang, Y. Y., Lu, C. C., Kong, L. J., Otegui, M. S., and Wang, X. L. 2019. AtU2AF65b functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in Arabidopsis. New Phytol. 223: 277–292. doi:10.1111/nph.15756
   PubMed Web of Science ®Google Scholar
• Xiong, F., Zhang, B. K., Liu, H. H., Wei, G., Wu, J. H., Wu, Y. N., and Zhang, Y. L. S. 2020. Transcriptional regulation of PLETHORA1 in the root meristem through an importin and its two antagonistic cargos. Plant Cell 32: 3812–3824. doi:10.1105/tpc.20.00108
   Web of Science ®Google Scholar
• Yan, K., Liu, P., Wu, C. A., Yang, G. D., Xu, R., Guo, Q. H., Huang, J. G., and Zheng, C. C. 2012. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol. Cell 48: 521–531. doi:10.1016/j.molcel.2012.08.032
   PubMed Web of Science ®Google Scholar
• Yan, Q., Xia, X., Sun, Z., and Fang, Y. 2017. Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes. PLoS Genet. 13: e1006663. doi:10.1371/journal.pgen.1006663
   PubMed Web of Science ®Google Scholar
• Yang, G., Li, Y., Wu, B., Zhang, K., Gao, L., and Zheng, C. 2019. MicroRNAs transcriptionally regulate promoter activity in Arabidopsis thaliana. J. Integr. Plant Biol. 61: 1128–1133. doi:10.1111/jipb.12775
   PubMed Web of Science ®Google Scholar
• Yang, X., Zhang, H., and Li, L. 2012. Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J. 70: 421–431. doi:10.1111/j.1365-313X.2011.04882.x
   PubMed Web of Science ®Google Scholar
• Yang, Y., Fan, X., Mao, M., Song, X., Wu, P., Zhang, Y., Jin, Y., Yang, Y., Chen, L. L., Wang, Y., Wong, C. C., Xiao, X., and Wang, Z. 2017. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 27: 626–641. doi:10.1038/cr.2017.31
   PubMed Web of Science ®Google Scholar
• Ye, C. Y., Chen, L., Liu, C., Zhu, Q. H., and Fan, L. 2015. Widespread noncoding circular RNAs in plants. New Phytol. 208: 88–95. doi:10.1111/nph.13585
   PubMed Web of Science ®Google Scholar
• Yin, Y., Lu, J. Y., Zhang, X., Shao, W., Xu, Y., Li, P., Hong, Y., Cui, L., Shan, G., Tian, B., Zhang, Q. C., and Shen, X. 2020. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature 580: 147–150. doi:10.1038/s41586-020-2105-3
   PubMed Web of Science ®Google Scholar
• Yu, D., Tang, Z., Shao, C., Ma, X., Xiang, T., Fan, Z., Wang, H., and Meng, Y. 2018. Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow. Brief. Bioinform. 19: 1317–1324. doi:10.1093/bib/bbx069
   PubMed Web of Science ®Google Scholar
• Zhan, X., Yan, C., Zhang, X., Lei, J., and Shi, Y. 2018. Structure of a human catalytic step I spliceosome. Science 359: 537–545. doi:10.1126/science.aar6401
   PubMed Web of Science ®Google Scholar
• Zhang, B., Gunawardane, L., Niazi, F., Jahanbani, F., Chen, X., and Valadkhan, S. 2014. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol. Cell Biol. 34: 2318–2329. doi:10.1128/MCB.01673-13
   PubMed Web of Science ®Google Scholar
• Zhang, C. J., Zhou, J. X., Liu, J., Ma, Z. Y., Zhang, S. W., Dou, K., Huang, H. W., Cai, T., Liu, R., Zhu, J. K., and He, X. J. 2013. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. EMBO J. 32: 1128–1140. doi:10.1038/emboj.2013.49
   PubMed Web of Science ®Google Scholar
• Zhang, H., Tang, K., Qian, W., Duan, C. G., Wang, B., Zhang, H., Wang, P., Zhu, X., Lang, Z., Yang, Y., and Zhu, J. K. 2014. An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol. Cell 54: 418–430. doi:10.1016/j.molcel.2014.03.019
   PubMed Web of Science ®Google Scholar
• Zhang, P., Fan, Y., Sun, X., Chen, L., Terzaghi, W., Bucher, E., Li, L., and Dai, M. 2019. A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J. 98: 697–713. doi:10.1111/tpj.14267
   PubMed Web of Science ®Google Scholar
• Zhang, S., Dou, Y., Li, S., Ren, G., Chevalier, D., Zhang, C., and Yu, B. 2018. DAWDLE interacts with DICER-LIKE proteins to mediate small RNA biogenesis. Plant Physiol. 177: 1142–1151. doi:10.1104/pp.18.00354
   PubMed Web of Science ®Google Scholar
• Zhang, S., Liu, Y., and Yu, B. 2014. PRL1, an RNA-binding protein, positively regulates the accumulation of miRNAs and siRNAs in Arabidopsis. PLoS Genet. 10: e1004841. doi:10.1371/journal.pgen.1004841
   PubMed Web of Science ®Google Scholar
• Zhang, S., Liu, Y., and Yu, B. 2015. New insights into pri-miRNA processing and accumulation in plants. Wiley Interdiscip. Rev. RNA. 6: 533–545. doi:10.1002/wrna.1292
   PubMed Web of Science ®Google Scholar
• Zhang, S., Xie, M., Ren, G., and Yu, B. 2013. CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts. Proc. Natl. Acad. Sci. USA. 110: 17588–17593. doi:10.1073/pnas.1310644110
   PubMed Web of Science ®Google Scholar
• Zhang, X., Zhang, Y., Wang, T., Li, Z., Cheng, J., Ge, H., Tang, Q., Chen, K., Liu, L., Lu, C., Guo, J., Zheng, B., and Zheng, Y. 2019. A comprehensive map of intron branchpoints and lariat RNAs in plants. Plant Cell 31: 956–973. doi:10.1105/tpc.18.00711
   PubMed Web of Science ®Google Scholar
• Zhang, X. O., Dong, R., Zhang, Y., Zhang, J. L., Luo, Z., Zhang, J., Chen, L. L., and Yang, L. 2016. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 26: 1277–1287. doi:10.1101/gr.202895.115
   PubMed Web of Science ®Google Scholar
• Zhang, Y. C., Liao, J. Y., Li, Z. Y., Yu, Y., Zhang, J. P., Li, Q. F., Qu, L. H., Shu, W. S., and Chen, Y. Q. 2014. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol. 15: 512. doi:10.1186/s13059-014-0512-1
   PubMed Web of Science ®Google Scholar
• Zhao, X., Li, J., Lian, B., Gu, H., Li, Y., and Qi, Y. 2018. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nat. Commun. 9: 5056. doi:10.1038/s41467-018-07500-7
   PubMed Web of Science ®Google Scholar
• Zhou, Y., Chen, C., and Johansson, M. J. 2013. The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression. Nucleic Acids Res. 41: 5669–5678. doi:10.1093/nar/gkt269
   PubMed Web of Science ®Google Scholar
• Zhu, D., Mao, F., Tian, Y., Lin, X., Gu, L., Gu, H., Qu, L. J., Wu, Y., and Wu, Z. 2020. The features and regulation of co-transcriptional splicing in Arabidopsis. Mol. Plant 13: 278–294. doi:10.1016/j.molp.2019.11.004
   PubMed Web of Science ®Google Scholar
• Zhu, F. Y., Chen, M. X., Ye, N. H., Shi, L., Ma, K. L., Yang, J. F., Cao, Y. Y., Zhang, Y., Yoshida, T., Fernie, A. R., Fan, G. Y., Wen, B., Zhou, R., Liu, T.Y., Fan, T., Gao, B., Zhang, D., Hao, G. F., Xiao, S., Liu, Y. G., and Zhang, J. 2017. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. Plant J. 91: 518–533. doi:10.1111/tpj.13571
   PubMed Web of Science ®Google Scholar
• Zhu, J., Li, Y., Lin, J., Wu, Y., Guo, H., Shao, Y., Wang, F., Wang, X., Mo, X., Zheng, S., Yu, H., and Mao, C. 2019. CRD1, an Xpo1 domain protein, regulates miRNA accumulation and crown root development in rice. Plant J. 100: 328–342. doi:10.1111/tpj.14445
   PubMed Web of Science ®Google Scholar
• Zmudjak, M., Colas Des Francs-Small, C., Keren, I., Shaya, F., Belausov, E., Small, I., and Ostersetzer-Biran, O. 2013. MCSF1, a nucleus-encoded CRM protein required for the processing of many mitochondrial introns, is involved in the biogenesis of respiratory complexes I and IV in Arabidopsis. New Phytol. 199: 379–394. doi:10.1111/nph.12282
   PubMed Web of Science ®Google Scholar
• Zoschke, R., Kroeger, T., Belcher, S., Schöttler, M. A., Barkan, A., and Schmitz-Linneweber, C. 2012. The pentatricopeptide repeat-SMR protein ATP4 promotes translation of the chloroplast atpB/E mRNA. Plant J. 72: 547–558. doi:10.1111/j.1365-313X.2012.05081.x
   PubMed Web of Science ®Google Scholar
• Zoschke, R., Watkins, K. P., Miranda, R. G., and Barkan, A. 2016. The PPR-SMR protein PPR53 enhances the stability and translation of specific chloroplast RNAs in maize. Plant J. 85: 594–606. doi:10.1111/tpj.13093
   PubMed Web of Science ®Google Scholar