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1001 Epigenomes: DNA methylation diversity in Arabidopsis thaliana

Posted on July 15, 2016

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions read more

Kawakatsu, T., Huang, S.-S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R, Nery., J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C.-R., Wang, C., Bemm, F., Becker, C., O’Neil, R., O’Malley, R. C., Quarless, D. X., The 1001 Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R. 

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Quantitative trait response in ETI: Genetics paper with Dangl lab

Posted on July 15, 2016

Effector Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait read more

Iakovidis, M., Teixeira, P. J. P. L., Exposito-Alonso, M., Cowper, M. G., Law, T. F., Liu, Q., Vu, M. C., Dang, T. M., Corwin, J. A., Weigel, D., Dangl, J. L., Grant, S. R. 

We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome Wide Association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative Trait Locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1- dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors. 

2016 Campus Soccer Tournament

Posted on June 24, 2016

Two incredibly good department teams participated in this year’s Campus Soccer Tournament read more

Absolute winner spirit - we keep practicing to become next year’s champions! 

Thanks to our numerous fans for believing in us, and thanks to the PhD reps for organizing a fun event!

Teams SWAT (Swift Weigel Attack Team) and Darwin’s Posse: 

Temporal patterns of damage and decay of DNA from herbaria specimens

Posted on June 22, 2016

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens read more

Weiss, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., Burbano, H. A.

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66×10-4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

First major phase of 1001 Genomes Project concluded

Posted on June 10, 2016

1135 genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana read more

The 1001 Genome Consortium

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Epigenetic stress memory - elife paper with Gutierrez-Marcos lab

Posted on May 31, 2016

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. read more

Wibowo, A., Becker, C., Marconi, G., Durr, J., Price, J., Hagmann, J., Papareddy, R., Putra, H., Kageyama, J., Becker, J., Weigel, D., Gutierrez-Marcos J.

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

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Upcoming Events

Jul
25

Diep's thesis defense

July 25, 2pm
Room 2.034, Auf der Morgenstelle 15, Tübingen University

Diep will defend her PhD thesis entitled "Biochemical Basis of Autoactivity of a Pair of Plant NLR Immune Receptors".


Jul
26

Jorge's thesis defense

July 26, 3pm
A301, Sand 1, Tübingen University

Jorge will defend his PhD thesis entitled "Genome-wide analysis of organ-specific DNA methylation patterns in Arabidopsis thaliana".


Jul
29

Cris' thesis defense

July 29, 2pm
Room 7E02, Auf der Morgenstelle 16, Tübingen University

Cris will defend her PhD thesis entitled "Identification of genetic modifiers of ACCELERATED CELL DEATH 6 (ACD6) in natural Arabidopsis thaliana accessions".