DNA damage and alternative splicing in plants
Abstract
There is an increasing evidence that post-transcriptional processes play an important role in gene expression regulation. Most messenger RNAs in higher eukaryotes are synthesized as precursors which contain intervening sequences, termed introns. Differential intron removal and splicing of the exons by alternative splicing (AS) may result in distinct protein isoforms or affect mRNA stability thus affecting transcriptome and proteome diversity in eukaryotic cells. Ser/Arg-rich (SR) proteins, a family of evolutionary highly conserved splicing factors, are one of the determinants of splicing patterns present in different cells and at specific developmental stages or conditions. Arabidopsis genome comprises 18 genes coding for SR proteins which is nearly double the number found in humans. Plant-specific SR proteins are particularly interesting as they might have evolved to serve plant oriented needs. Current estimates of the occurrence of alternative splicing entirely change the way we think about gene expression regulation in plants. Approximately 60% of intron-containing genes in Arabidopsis are alternatively spliced under normal growth conditions. This number is probably higher as it does not capture AS events specific for various environmental conditions that plants experience through their life cycle. Both environmental stresses and endogenous processes can induce DNA damage and impair genome stability. Cell response to DNA damage must be tightly regulated to ensure efficient repair on one side, and to prevent unnecessary and potentially harmful effects during normal cellular processes on the other side. Research of DNA damage response (DDR) both in plants and animals has focused on the transcriptional regulation by transcription factors, signaling pathways mediated by kinases and phosphatases, and lately on epigenetic regulation. Recent studies in animals have unexpectedly revealed that splicing factors and alternative splicing are important players in the DDR. Despite extensive studies of DDR and DNA repair pathways carried out in plants regulation at the level of alternative splicing has not been comprehensively addressed. In this project we will investigate the link between DNA damage, DNA repair and alternative splicing so far never explored in plants. Specifically, we will identify transcriptional and AS changes in response to DNA damage in Arabidopsis at the genome wide level. We will identify in vivo binding motifs and direct RNA targets of a plant-specific SR protein involved in AS regulation of DNA repair. We will perform small scale comparative studies in the moss Physcomitrella patens to gain evolutionary insights into the regulation of DNA damage response by SR proteins. Our project will contribute to understanding how alternative splicing can complement transcriptional/post-translational regulation of DNA repair and genotoxic stress response in plants.
Publikationen
A chloroplast retrograde signal regulates nuclear alternative splicing.
Autoren: Petrillo, E; Godoy Herz, MA; Fuchs, A; Reifer, D; Fuller, J; Yanovsky, MJ; Simpson, C; Brown, JW; Barta, A; Kalyna, M; Kornblihtt, AR; Jahr: 2014
Journal articles
Shedding light on the chloroplast as a remote control of nuclear gene expression.
Autoren: Godoy Herz, MA; Kornblihtt, AR; Barta, A; Kalyna, M; Petrillo, E; Jahr: 2014
Journal articles
Let there be light: Regulation of gene expression in plants.
Autoren: Petrillo, E; Godoy Herz, MA; Barta, A; Kalyna, M; Kornblihtt, AR; Jahr: 2014
Journal articles
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Autoren: Marquez, Y; Höpfler, M; Ayatollahi, Z; Barta, A; Kalyna, M; Jahr: 2015
Journal articles
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Autoren: Zhang, R; Calixto, CP; Tzioutziou, NA; James, AB; Simpson, CG; Guo, W; Marquez, Y; Kalyna, M; Patro, R; Eyras, E; Barta, A; Nimmo, HG; Brown, JW; Jahr: 2015
Journal articles
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
Autoren: Brown, JW; Simpson, CG; Marquez, Y; Gadd, GM; Barta, A; Kalyna, M; Jahr: 2015
Journal articles
Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms.
Autoren: Maronova, M; Kalyna, M; Jahr: 2016
Journal articles
AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data
Autoren: Runxuan Zhang, Cristiane P G Calixto, Yamile Marquez, Peter Venhuizen, Nikoleta A Tzioutziou, Wenbin Guo, Mark Spensley, Nicolas Frei dit Frey, Heribert Hirt, Allan B James, Hugh G Nimmo, Andrea Barta, Maria Kalyna, John W S Brown Jahr: 2016
Sonstige Werke
Remote control of alternative splicing in roots through TOR kinase
Autoren: Petrillo, E; Riegler, S; Fuchs, A; Servi, L; Godoy Herz, MA; Kubaczka, MG; Venhuizen, P; Schweighofer, A; Kornblihtt, AR; Simpson, C; Brown, JWS; Meyer, C; Kalyna, M; Barta A Jahr: 2018
Sonstige Werke
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Autoren: Jabre, I; Reddy, ASN; Kalyna, M; Chaudhary, S; Khokhar, W; Byrne, LJ; Wilson, CM; Syed, NH; Jahr: 2019
Journal articles
Auxin-dependent xyloglucan remodelling defines differential tissue expansion in Arabidopsis thaliana
Autoren: Velasquez, SM; Gallemi, M; Aryal, B; Venhuizen, P; Barbez, E; Dünser, K; Kalyna, M; Mouille, G; Benkova, E; Bhalerao, R; Kleine-Vehn, J Jahr: 2019
Sonstige Werke
Alternative Splicing and DNA Damage Response in Plants.
Autoren: Nimeth, BA; Riegler, S; Kalyna, M; Jahr: 2020
Journal articles
Current Challenges in Studying Alternative Splicing in Plants: The Case of
Autoren: Melo, JP; Kalyna, M; Duque, P; Jahr: 2020
Journal articles
A Collection of Pre-mRNA Splicing Mutants in
Autoren: Kanno, T; Venhuizen, P; Wu, MT; Chiou, P; Chang, CL; Kalyna, M; Matzke, AJM; Matzke, M; Jahr: 2020
Journal articles
Editorial: Alternative Splicing Regulation in Plants
Autoren: Petrillo, E; Kalyna, M; Mandadi, KK; Tu, SL; Simpson, CG Jahr: 2020
Journal articles
Alternative Splicing Regulation in Plants
Autoren: Petrillo, E; Kalyna, M; Simpson, CG; Tu, S-L; Mandadi, KK. Eds. Jahr: 2020
Editorial
Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana.
Autoren: Jabre, I; Chaudhary, S; Guo, W; Kalyna, M; Reddy, ASN; Chen, W; Zhang, R; Wilson, C; Syed, NH; Jahr: 2021
Journal articles
Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.
Autoren: Fuchs, A; Riegler, S; Ayatollahi, Z; Cavallari, N; Giono, LE; Nimeth, BA; Mutanwad, KV; Schweighofer, A; Lucyshyn, D; Barta, A; Petrillo, E; Kalyna, M; Jahr: 2021
Journal articles
Project staff
BOKU partners
External partners
Max Perutz Labs
Andrea Barta
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