Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data

Denton AK, Mass J, Külahoglu C, Lercher MJ, Bräutigam A, Weber APM (2017)
Journal of Experimental Botany 68(2): 147-160.

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The high efficiency of C-4 photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C-4 tissues along a developing leaf gradient. This method treats both C-4 tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set. Meta-analysis of this and the previous studies highlights the strengths and weaknesses of different C-4 tissue separation techniques. While the method reported here achieves the least enrichment, it is the only one that shows neither strong 3' (degradation) bias, nor different severity of 3' bias between samples. The meta-analysis highlighted previously unappreciated observations, such as an accumulation of evidence that aspartate aminotransferase is more mesophyll specific than expected from the current NADP-ME C-4 cycle model, and a shift in enrichment of protein synthesis genes from bundle sheath to mesophyll during development. The full comparative dataset is available for download, and a web visualization tool (available at http://www.plant-biochemistry.hhu.de/resources.html) facilitates comparison of the the Z. mays bundle sheath and mesophyll studies, their consistencies and their conflicts.
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Journal of Experimental Botany
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68
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2
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147-160
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Denton AK, Mass J, Külahoglu C, Lercher MJ, Bräutigam A, Weber APM. Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. Journal of Experimental Botany. 2017;68(2):147-160.
Denton, A. K., Mass, J., Külahoglu, C., Lercher, M. J., Bräutigam, A., & Weber, A. P. M. (2017). Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. Journal of Experimental Botany, 68(2), 147-160. doi:10.1093/jxb/erw463
Denton, A. K., Mass, J., Külahoglu, C., Lercher, M. J., Bräutigam, A., and Weber, A. P. M. (2017). Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. Journal of Experimental Botany 68, 147-160.
Denton, A.K., et al., 2017. Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. Journal of Experimental Botany, 68(2), p 147-160.
A.K. Denton, et al., “Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data”, Journal of Experimental Botany, vol. 68, 2017, pp. 147-160.
Denton, A.K., Mass, J., Külahoglu, C., Lercher, M.J., Bräutigam, A., Weber, A.P.M.: Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. Journal of Experimental Botany. 68, 147-160 (2017).
Denton, Alisandra K., Mass, Janina, Külahoglu, Canan, Lercher, Martin J., Bräutigam, Andrea, and Weber, Andreas P. M. “Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data”. Journal of Experimental Botany 68.2 (2017): 147-160.
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2017-12-15T10:15:13Z

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Maize leaf PPDK regulatory protein isoform-2 is specific to bundle sheath chloroplasts and paradoxically lacks a Pi-dependent PPDK activation activity.
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C4 photosynthesis: 50 years of discovery and innovation.
von Caemmerer S, Ghannoum O, Furbank RT., J Exp Bot 68(2), 2017
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