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Journal Article

Optimization of ribosome profiling in plants including structural analysis of rRNA fragments

MPS-Authors
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Ting,  M. K. Y.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Gao,  Y.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Barahimipour,  R.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Ghandour,  R.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Liu,  J.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Martinez-Seidel,  F.       
Applied Metabolome Analysis, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Fischer,  A.
Cytoplasmic and Evolutionary Genetics, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Zoschke,  R.       
Translational Regulation in Plants, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Ting, M. K. Y., Gao, Y., Barahimipour, R., Ghandour, R., Liu, J., Martinez-Seidel, F., et al. (2024). Optimization of ribosome profiling in plants including structural analysis of rRNA fragments. Plant Methods, 20(1): 143. doi:10.1186/s13007-024-01267-3.


Cite as: https://hdl.handle.net/21.11116/0000-000F-DDFB-E
Abstract
Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are abundant rRNA fragments that are wastefully incorporated into the libraries and dramatically reduce sequencing depth. To remove these rRNA contaminants, it is common to perform preliminary trials to identify these fragments because they are thought to vary depending on nuclease treatment, tissue source, and plant species.