Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Journal article


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.
AuthorsJabre, I., Chaudhary, S., Guo, W., Kalyna, M., Reddy, A. S. N., Chen, W., Zhang, R., Wilson, C. and Syed, N.
Abstract

• Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood.
• Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS.
• Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns pointing to their distinct regulation.
• Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold.

KeywordsAlternative Splicing; Arabidopsis thaliana; Cold stress; Co-transcriptional Splicing; Exitrons; Nucleosome Positioning
Year2020
JournalNew Phytologist
PublisherWiley
ISSN0028-646X
1469-8137
Publication process dates
Accepted24 Oct 2020
Deposited29 Oct 2020
Accepted author manuscript
File Access Level
Restricted
Output statusIn press
Permalink -

https://repository.canterbury.ac.uk/item/8w8zq/differential-nucleosome-occupancy-modulates-alternative-splicing-in-arabidopsis-thaliana

  • 4
    total views
  • 0
    total downloads
  • 4
    views this month
  • 0
    downloads this month

Export as

Related outputs

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Syed, N. 2020. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochemical Society Transactions.
Applications and strategies in nanodiagnosis and nanotherapy in lung cancer
Woodman, C., Vundu, G., George, A. and Wilson, C. 2020. Applications and strategies in nanodiagnosis and nanotherapy in lung cancer. Seminars in Cancer Biology. https://doi.org/10.1016/j.semcancer.2020.02.009
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
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
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.. 0 (0). https://doi.org/10.2478/prolas-2019-0008
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
Understanding the epigenetics of alternative splicing in Arabidopsis thaliana
Jabre, I. 2019. Understanding the epigenetics of alternative splicing in Arabidopsis thaliana. PhD Thesis Canterbury Christ Church University Faculty of Social and Applied Sciences
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.
The role of endoproteolytic processing in neurodegeneration
Wilson, C., Mushtaq, G., Kamal, M. and Terro, F. 2016. The role of endoproteolytic processing in neurodegeneration. CNS and Neurological Disorders Drug Targets. 15. https://doi.org/10.2174/1871527315666160922163511
Challenges and strategies in precision medicine for non-small cell lung cancer
Wilson, C., Al-Akhrass, A. and Sacco, J. 2016. Challenges and strategies in precision medicine for non-small cell lung cancer. Current Pharmaceutical Design. 22. https://doi.org/10.2174/1381612822666160603014932
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
A resource aware MapReduce based parallel SVM for large scale image classification
Guo, W., Khalid, N., Liu, Y., Li, M., Qi, M., Guo, W., Khalid, N., Liu, Y., Li, M. and Qi, M. 2015. A resource aware MapReduce based parallel SVM for large scale image classification. Neural Processing Letters. 44 (1), pp. 161-184.
Sortilin mediates the release and transfer of exosomes in concert with two tyrosine kinase receptors
Wilson, C., Naves, T., Vincent, F., Lalloue, F. and Jauberteau, M. 2015. Sortilin mediates the release and transfer of exosomes in concert with two tyrosine kinase receptors.
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
Sortilin mediates the release and transfer of exosomes in concert with two tyrosine kinase receptors.
Wilson, C., Naves, T., Vincent, F., Melloni, B., Bonnaud, F., Lalloue, F. and Jauberteau, M. 2014. Sortilin mediates the release and transfer of exosomes in concert with two tyrosine kinase receptors. Journal of Cell Science (JCS). 127 (18), pp. 3983-3997. https://doi.org/10.1242/jcs.149336
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