Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana

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dc.contributor.authorZhang, Xiao-Ning
dc.contributor.authorShi, Yifei
dc.contributor.authorPowers, Jordan J.
dc.contributor.authorGowda, Nikhil B.
dc.contributor.authorZhang, Chong
dc.contributor.authorIbrahim, Heba M. M.
dc.contributor.authorBall, Hannah B.
dc.contributor.authorChen, Samuel L.
dc.contributor.authorLu, Hua
dc.contributor.authorMount, Stephen M.
dc.date.accessioned2022-05-24T15:21:34Z
dc.date.available2022-05-24T15:21:34Z
dc.date.issued2017-10-11
dc.description.abstractBackground Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45–1 null mutant is viable. Narrow flower petals and reduced seed formation suggest that SR45 regulates genes involved in diverse processes, including reproduction. To understand how SR45 is involved in the regulation of reproductive processes, we studied mRNA from the wild-type and sr45–1 inflorescences using RNA-seq, and identified SR45-bound RNAs by immunoprecipitation. Results Using a variety of bioinformatics tools, we identified a total of 358 SR45 differentially regulated (SDR) genes, 542 SR45-dependent alternative splicing (SAS) events, and 1812 SR45-associated RNAs (SARs). There is little overlap between SDR genes and SAS genes, and neither set of genes is enriched for flower or seed development. However, transcripts from reproductive process genes are significantly overrepresented in SARs. In exploring the fate of SARs, we found that a total of 81 SARs are subject to alternative splicing, while 14 of them are known Nonsense-Mediated Decay (NMD) targets. Motifs related to GGNGG are enriched both in SARs and near different types of SAS events, suggesting that SR45 recognizes this motif directly. Genes involved in plant defense are significantly over-represented among genes whose expression is suppressed by SR45, and sr45–1 plants do indeed show enhanced immunity. Conclusion We find that SR45 is a suppressor of innate immunity. We find that a single motif (GGNGG) is highly enriched in both RNAs bound by SR45 and in sequences near SR45- dependent alternative splicing events in inflorescence tissue. We find that the alternative splicing events regulated by SR45 are enriched for this motif whether the effect of SR45 is activation or repression of the particular event. Thus, our data suggests that SR45 acts to control splice site choice in a way that defies simple categorization as an activator or repressor of splicing.en_US
dc.description.sponsorshipThis work was supported by National Science Foundation (DBI-1146300 to X. Zhang, IOS-1456140 to H. Lu, and DBI-1564785 to S. M. Mount), research fund in Department of Biology at St. Bonaventure University, and The Fulbright Scholar Program and The Council for International Exchange of Scholars to H. M. M. Ibrahim.en_US
dc.description.urihttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4183-7en_US
dc.format.extent17 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2ln4q-6uwh
dc.identifier.citationZhang, XN., Shi, Y., Powers, J.J. 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). https://doi.org/10.1186/s12864-017-4183-7en_US
dc.identifier.urihttps://doi.org/10.1186/s12864-017-4183-7
dc.identifier.urihttp://hdl.handle.net/11603/24713
dc.language.isoen_USen_US
dc.publisherBMCen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.*
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleTranscriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thalianaen_US
dc.typeTexten_US
dcterms.creatorhttps://orcid.org/0000-0002-7496-3200en_US

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