Johanneslab
Population epigenetics and eigenomics
 | Technical University of Munich [TUM] Department of Plant Sciences [Home] Hans Eisenmann-Zentrum for Agricultural Sciences [HEZ] Liesel-Beckmann-Str. 2 85354 Freising, Germany Institute for Advanced Study [TUM-IAS] Lichtenbergstr. 2a 85748 Garching, Germany email: frank[at]johanneslab[dot]org email: f.johannes[at]tum[dot]de phone: +49 8161 71 4139 official page: http://www.epi.wzw.tum.de
|
Our main research interests
DNA stores heritable information in the form of a four letter code; A, C, G and T. Textbook genetics tells us that the code can be mutated (e.g. letter A turns into letter G), and that such mutations alter the functions of genes. In plants, it is becoming increasingly clear that heritable alterations in gene function can also be caused by meiotically stable epimutations, which arise independently of DNA changes. A well-known example of an epimutation is the accidental gain or loss of DNA methylation, the chemical modification of a cytosine (the letter C in the DNA code) into 5-methylcytosine.
We have previously shown that experimentally-induced as well as spontaneously occurring epimutations can be remarkably stable across generations, and can in some cases even contribute to the heritability of important plant traits. Because of these observations, epigenetic modifications - such as DNA methylation - have emerged as potentially important factors in plant evolution, and as possible molecular targets for the improvement of commercial crops.
Our group aims to explore the agricultural and evolutionary implications of heritable epimutations in plants. One major aspect of this work is the development of computational methods for the analysis of population-level epigenomic sequencing data. The goal is to find efficient ways to detect ‘epimutatable’ regions in plant genomes, and to characterize these regions in terms of epigenomic patterns of variation both within and across plant species. A second aspect of our work is to infer the sources, stability and phenotypic impact of heritable epimutations either by direct observation of multi-generational data, or indirectly by using inference methods from evolutionary genetics.
Key reviews and perspectives
Johannes F, Schmitz RJ (2018).
Spontaneous epimutations in plants.
New Phytologist https://doi.org/10.1111/nph.15434
New Phytologist https://doi.org/10.1111/nph.15434
Vidali A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F* (2016).
Methylome evolution in plants.
Genome Biology 17:264.Taudt A, Colomé-Tatché M, Johannes F*. (2016).
Genetic sources of population epigenomic variation.
Nature Reviews Genetics doi:10.1038/nrg.2016.45
Johannes F*, Colot V, Jansen RC (2008).
Epigenome dynamics: A quantitative genetic perspective.
Nature Reviews Genetics 9: 883-890.
Key findings
Nature Reviews Genetics doi:10.1038/nrg.2016.45
Johannes F*, Colot V, Jansen RC (2008).
Epigenome dynamics: A quantitative genetic perspective.
Nature Reviews Genetics 9: 883-890.
Key findings
Lauss K, Wardenaar R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M*,
Johannes F* (2017).
Parental DNA methylation states are associated with heterosis in Arabidopsis epigenetic hybrids.
Plant Physiology doi: https://doi.org/10.1104/pp.17.01054
Parental DNA methylation states are associated with heterosis in Arabidopsis epigenetic hybrids.
Plant Physiology doi: https://doi.org/10.1104/pp.17.01054
van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F* (2015).
Rate, spectrum and evolutionary dynamics of spontaneous epimutations.Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1424254112.
Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury J-M, Wincker P, Roudier F, Jansen RC, Colot V*, Johannes F* (2014).
Mapping the epigenetic basis of complex traits.
Science doi:10.1126/science.1248127.
Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F* (2012).
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.
Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.1212955109.
Johannes F, Porcher E, Teixeira F, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009).
Assessing the impact of transgenerational epigenetic variation on complex traits.
PLoS Genetics 5: e1000530.
Key computational methods
Taudt A, Roquis D, Vidalis A, Wardenaar R, Johannes F*, Colomé-Tatché M* (2018).
METHimpute: Imputation-guided construction of complete methylomes from WGBS data.BMC Genomics 19:444.
Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F (2015).
histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
BMC Bioinformatics 16:60.
Cortijo S, Wardenaar R, M. Colomé-Tatché M, Johannes F*, Colot V* (2014).
Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.
Methods in Molecular Biology 1112:125-49.
Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier R, Colot V (2012).
MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.
Bioinformatics doi:10.1093/bioinformatics/bts562.
