The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow
DNA codon frequencies and mRNA expression levels are the main predictors of protein abundance. In the absence of environmental perturbation neither gene-body methylation, tRNA abundance nor ribosome-associated transcript levels add appreciable information. The impact of constitutive gene-body methylation is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gene-body methylation by inflating differential expression variation. Our data show that the dogma holds only if both sequence and abundance information in mRNA are considered.
Authors
- Kathryn S. Lilley (ORCID: https://orcid.org/0000-0003-0594-6543)
- Chelsea A. Rundle (ORCID: https://orcid.org/0009-0008-0072-1082)
- Danny D. Nedialkova
- Nazanin P. Afsharyan (ORCID: https://orcid.org/0000-0003-0298-988X)
- Richard Mott (ORCID: https://orcid.org/0000-0002-1022-9330)
- Louise Arathoon (ORCID: https://orcid.org/0000-0003-1771-714X)
- Andrew Behrens (ORCID: https://orcid.org/0000-0001-9759-6207)
- Mark Bailey (ORCID: https://orcid.org/0000-0003-1843-9348)
- Keywan Hassani‐Pak (ORCID: https://orcid.org/0000-0001-9625-0511)
- Ziming Zhong (ORCID: https://orcid.org/0000-0002-1503-9456)
- Frederica L. Theodoulou (ORCID: https://orcid.org/0000-0002-8306-0716)
- Gancho T. Slavov (ORCID: https://orcid.org/0000-0001-8565-9098)
- B. B. Parker (ORCID: https://orcid.org/0009-0004-1157-5659)
- Xiaowei Li (ORCID: https://orcid.org/0009-0008-2436-7524)
- Yong‐In Kim (ORCID: https://orcid.org/0000-0002-2877-5110)
Institutions
- University of Cambridge (GB)
- Rothamsted Research (GB)
- Leibniz Centre for Agricultural Landscape Research (DE)
- Max Planck Institute of Neurobiology (DE)
- Institute of Biological, Environmental and Rural Sciences (GB)
- Max Planck Institute of Biochemistry (DE)
- University College London (GB)
- Technical University of Munich (DE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-09-29
- DOI
- https://doi.org/10.1186/s13059-025-03741-0
- Citations
- 3
- Primary Topic
- Plant nutrient uptake and metabolism
- Type
- article
- Field-Weighted Citation Impact
- 5.25
Funders
- Oxford Nanopore Technologies
- European Commission
- Max-Planck-Gesellschaft
- Biotechnology and Biological Sciences Research Council