Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana |
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| Affiliation: | 1. School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK;2. Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK;3. Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK;1. Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima str. 10, 10-748 Olsztyn, Poland;2. INRAE, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France;3. Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany;4. Sigenae, UR875, INRAE, 31326 Castanet-Tolosan, France;5. Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Poland;6. Department of Salmonid Research, The Stanislaw Sakowicz Inland Fisheries Institute, Olsztyn, Poland;7. University of Lorraine, INRAE, UR AFPA, F-54000 Nancy, France;1. Department of General Surgery, Nanchang University, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China;2. Taizhou Central Hospital, China;3. Taizhou University Affiliated Hospital, China;1. Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China;2. School of Public Health, Southwest Medical University, Luzhou 646000, China;3. Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China;4. Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China |
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| Abstract: | How stable and temperature-dependent variations in DNA methylation and nucleosome occupancy influence alternative splicing (AS) remains poorly understood in plants. To answer this, we generated transcriptome, whole-genome bisulfite, and MNase sequencing data for an epigenetic Recombinant Inbred Line (epiRIL) of A. thaliana at normal and cold temperature. For comparative analysis, the same data sets for the parental ecotype Columbia (Col-0) were also generated, whereas for DNA methylation, previously published high confidence methylation profiles of Col-0 were used. Significant epigenetic differences in an identical genetic background were observed between Col-0 and epiRIL lines under normal and cold temperatures. Our transcriptome data revealed that differential DNA methylation and nucleosome occupancy modulate expression levels of many genes and AS in response to cold. Collectively, DNA methylation and nucleosome levels exhibit characteristic patterns around intron-exon boundaries at normal and cold conditions, and any perturbation in them, in an identical genetic background is sufficient to modulate AS in Arabidopsis. |
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