Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana

Journal article

Jabre, I., Chaudhary, S. and Syed, N. 2021. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics. 113 (6). https://doi.org/https://doi.org/10.1016/j.ygeno.2021.08.006
AuthorsJabre, I., Chaudhary, S. and Syed, N.
Abstract

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.

KeywordsAlternative splicing ; Arabidopsis; Cold stress; DNA-methylation; epiRILs; Nucleosome occupancy
Year2021
JournalGenomics
Journal citation113 (6)
PublisherElsevier
ISSN0888-7543
Digital Object Identifier (DOI)https://doi.org/https://doi.org/10.1016/j.ygeno.2021.08.006
Official URLhttps://doi.org/10.1016/j.ygeno.2021.08.006
Publication dates
Online12 Aug 2021
PrintNov 2021
Publication process dates
Accepted10 Aug 2021
Deposited06 Sep 2021
Accepted author manuscript
License
Output statusPublished
Permalink -

https://repository.canterbury.ac.uk/item/8y776/epigenetic-differences-in-an-identical-genetic-background-modulate-alternative-splicing-in-a-thaliana

Download files

Accepted author manuscript
Manuscript_revised.pdf
License: CC BY-NC-ND 4.0

  • 139
    total views
  • 20
    total downloads
  • 2
    views this month
  • 0
    downloads this month

Export as

Related outputs

Stochastic variation in DNA methylation modulates nucleosome occupancy and alternative splicing in Arabidopsis thaliana
Jabre, Ibtissam, Chaudhary, S., Wilson, C., Staiger, D. and Syed, N. 2022. Stochastic variation in DNA methylation modulates nucleosome occupancy and alternative splicing in Arabidopsis thaliana. Plants. 11 (9), p. 1105. https://doi.org/10.3390/plants11091105
Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana.
Chaudhary, Saurabh, Jabre, Ibtissam and Syed, Naeem 2021. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics. 113 (6), pp. 3476-3486. https://doi.org/S0888-7543(21)00312-8
Targeting DNA methyltransferases in non-small-cell lung cancer
Al-Yozbaki, M., Jabre, I., Syed, N. and Wilson, C. 2021. Targeting DNA methyltransferases in non-small-cell lung cancer. Seminars in Cancer Biology. https://doi.org/10.1016/j.semcancer.2021.01.005
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Reddy, A. S. N., Huang, J., Syed, N., Ben-Hur, A., Dong, S. and Gu, L. 2020. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochemical Society Transactions. https://doi.org/10.1042/BST20190492
Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana
Jabre, I., Chaudhary, S., Guo, W., Kalyna, M., Reddy, A. S. N., Chen, W., Zhang, R., Wilson, C. and Syed, N. 2020. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana. New Phytologist. https://doi.org/10.1111/nph.17062
Perspective on alternative splicing and proteome complexity in plants
Chaudhary, S., Jabre, I., Reddy, A., Staiger, D. and Syed, N. 2019. Perspective on alternative splicing and proteome complexity in plants. Trends in Plant Science. 24 (6), pp. 496-506. https://doi.org/10.1016/j.tplants.2019.02.006
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Jabre, I., Reddy, A., Kalyna, M., Chaudhary, S., Khokhar, W., Byrne, L., Wilson, C. and Syed, N. 2019. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Research. 47 (6), pp. 2716-2726. https://doi.org/10.1093/nar/gkz121
Alternative splicing and protein diversity: plants versus animals
Chaudhry, S., Khokhar, W., Jabre, I., Reddy, A., Byrne, L., Wilson, C. and Syed, N. 2019. Alternative splicing and protein diversity: plants versus animals. Frontiers in Plant Science. 10 (708). https://doi.org/10.3389/fpls.2019.00708
Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana
Khokhar, W., Hassan, M., Reddy, A., Chaudhary, S., Jabre, I., Byrne, L. and Syed, N. 2019. Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana. Frontiers in Plant Science. 10 (1160). https://doi.org/10.3389/fpls.2019.01160
Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum
Ievina, B., Rostoks, N., Syed, N., Flavell, A. and Ievinsh, G. 2019. Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.. 73 (5), pp. 446-454. https://doi.org/10.2478/prolas-2019-0008
A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations
Syed, N. 2016. A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations. Journal of New Sciences: Agri & Biotech. 27 (8), pp. 1513-1518.
Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting
Prince, S., Joshi, T., Mutava, R., Syed, N., Joao Vitor, M., Patil, G., Song, L., Wang, J., Lin, L., Chen, W., Shannon, J., Valliyodan, B., Xu, D. and Nguyen, H. 2015. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science. 240, pp. 65-78. https://doi.org/10.1016/j.plantsci.2015.08.017
Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing
Ho, T., Cardle, L., Xu, X., Bayer, M., Prince, K., Mutava, R., Marshall, D. and Syed, N. 2014. Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing. Molecular Breeding. 34 (3), pp. 977-988. https://doi.org/10.1007/s11032-014-0090-7
Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean
Syed, N., Prince, S., Mutava, R., Patil, G., Li, S., Chen, W., Babu, V., Joshi, T., Khan, S. and Nguyen, H. 2015. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erv407
Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress
Mutava, R., Prince, S., Syed, N., Song, L., Valliyodan, B., Chen, W. and Nguyen, H. 2015. Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress. Plant physiology and biochemistry : PPB / Société française de physiologie végétale. 86, pp. 109-20. https://doi.org/10.1016/j.plaphy.2014.11.010
Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions
Syed, N. and Flavell, A. 2007. Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nature Protocols. 1 (6), pp. 2746-2752. https://doi.org/10.1038/nprot.2006.407
Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers
Sanz, A., Gonzalez, S., Syed, N., Suso, M., Saldaña, C. and Flavell, A. 2007. Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Molecular Genetics and Genomics. 278 (4), pp. 433-441. https://doi.org/10.1007/s00438-007-0261-x
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
Kalyna, M., Simpson, C., Syed, N., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H., Barta, A. and Brown, J. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research. 40 (6), pp. 2454-2469. https://doi.org/10.1093/nar/gkr932
Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes
James, A., Syed, N., Bordage, S., Marshall, J., Nimmo, G., Jenkins, G., Herzyk, P., Brown, J. and Nimmo, H. 2012. Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. The Plant Cell. 24 (3), pp. 961-981. https://doi.org/10.1105/tpc.111.093948
Alternative splicing in plants – coming of age
Syed, N., Kalyna, M., Marquez, Y., Barta, A. and Brown, J. 2012. Alternative splicing in plants – coming of age. Trends in Plant Science. 17 (10), pp. 616-623. https://doi.org/10.1016/j.tplants.2012.06.001
Thermoplasticity in the plant circadian clock: how plants tell the time-perature
James, A., Syed, N., Brown, J. and Nimmo, H. 2012. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signaling & Behavior. 7 (10), pp. 1219-1223. https://doi.org/10.4161/psb.21491
Inbred lines as testers for combining ability in cotton
Syed, W., Mehdi, S. and Syed, N. 1994. Inbred lines as testers for combining ability in cotton. Pakistan Journal of Scientific Research. 46, pp. 93-95.
Genetic study of lint percentage and staple length in cotton
Syed, W., Mehdi, S. and Syed, N. 1994. Genetic study of lint percentage and staple length in cotton. Pakistan Journal of Science. 46 (3-4), pp. 123-124.
Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)
Syed, N., Mehdi, S. and Syed, N. 1995. Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Pakistan Journal of Scientific Research. 47 (3-4), pp. 62-65.
Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)
Syed, N., Mehdi, S., Khan, I. and Syed, N. 1995. Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Science International (Lahore). 7, pp. 201-202.
Association of agronomic and economic characters of cotton
Syed, W., Mehdi, S. and Syed, N. 1995. Association of agronomic and economic characters of cotton. Pakistan Journal of Scientific Research. 47, pp. 46-49.
Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana
Virk, P., Pooni, H., Syed, N. and Kearsey, M. 1999. Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana. Theoretical and Applied Genetics. 98 (3-4), pp. 462-464. https://doi.org/10.1007/s001220051092
Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters
Hart, G., Schertz, K., Peng, Y. and Syed, N. 2001. Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theoretical and Applied Genetics. 103 (8), pp. 1232-1242. https://doi.org/10.1007/s001220100582
Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L.
Kiær, L., Felber, F., Flavell, A., Guadagnuolo, R., Guiatti, D., Hauser, T., Olivieri, A., Scotti, I., Syed, N., Vischi, M., Wiel, C. and Jørgensen, R. 2009. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L. Genetic Resources and Crop Evolution. 56 (3), pp. 405-419. https://doi.org/10.1007/s10722-008-9375-1
Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance
Vida, G., Gál, M., Uhrin, A., Veisz, O., Syed, N., Flavell, A., Wang, Z. and Bedő, Z. 2009. Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance. Euphytica. 170 (1-2), pp. 67-76. https://doi.org/10.1007/s10681-009-9945-0
Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.)
Levina, B., Syed, N., Flavell, A., Ievinsh, G. and Rostoks, N. 2010. Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.). Plant Genetic Resources. 8 (3), pp. 258-266. https://doi.org/10.1017/S1479262110000316
A hAT superfamily transposase recruited by the cereal grass genome
Muehlbauer, G., Bhau, B., Syed, N., Heinen, S., Cho, S., Marshall, D., Pateyron, S., Buisine, N., Chalhoub, B. and Flavell, A. 2006. A hAT superfamily transposase recruited by the cereal grass genome. Molecular Genetics and Genomics. 275 (6), pp. 553-563. https://doi.org/10.1007/s00438-006-0098-8
Genetics of quantitative traits in Arabidopsis thaliana
Kearsey, M., Pooni, H. and Syed, N. 2003. Genetics of quantitative traits in Arabidopsis thaliana. Heredity. 91 (5), pp. 456-464. https://doi.org/10.1038/sj.hdy.6800306
Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations
Syed, N., Pooni, H., Mei, M., Chen, Z. and Kearsey, M. 2004. Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations. Molecular Breeding. 13 (1), pp. 59-68. https://doi.org/10.1023/B:MOLB.0000012845.37366.b5
Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana
Syed, N. and Chen, Z. 2005. Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana. Heredity. 94 (3), pp. 295-304. https://doi.org/10.1038/sj.hdy.6800558
Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.)
Syed, N., Sureshsundar, S., Wilkinson, M., Bhau, B., Cavalcanti, J. and Flavell, A. 2005. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theoretical and Applied Genetics. 110 (7), pp. 1195-1202. https://doi.org/10.1007/s00122-005-1948-1
A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers
Syed, N., Sørensen, A., Antonise, R., Wiel, C., Linden, C., van 't Westende, W., Hooftman, D., Nijs, H. and Flavell, A. 2006. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theoretical and Applied Genetics. 112 (3), pp. 517-527. https://doi.org/10.1007/s00122-005-0155-4
Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium)
Mei, M., Syed, N., Gao, W., Thaxton, P., Smith, C., Stelly, D. and Chen, Z. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theoretical and Applied Genetics. 108 (2), pp. 280-291. https://doi.org/10.1007/s00122-003-1433-7