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Rules of epiallele switching

Posted on January 09, 2017

DNA sequence properties that predict susceptibility to epiallelic switching read more

Catoni, M., Griffiths, J., Becker, C., Zabet N. R., Bayon, C., Dapp, M., Liebermann-Lazarovich, M., Weigel, D., Paszkowski, J.

Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss?of?function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon?derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice.

 

 

easyGWAS paper in Plant Cell

Posted on December 21, 2016

A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies read more

Grimm, D. G., Roqueiro, D., Salomé, P. A., Kleeberger, S., Greshake, B., Zhu, W., Liu, C., Lippert, C., Stegle, O., Schölkopf, B., Weigel, D., and Borgwardt, K. M. 

The ever-growing availability of high quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, speciesindependent online resource for computing, storing, sharing, annotating and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and datasets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics, and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organism Arabidopsis thaliana, using flowering and growth-related traits. 

https://easygwas.ethz.ch/

Summer nights - 2016 WeigelWorld clip

Posted on December 19, 2016

Click to watch it... read more

EMBO fellowship awarded to Lei

Posted on December 07, 2016

Congrats to Lei for securing an EMBO Long Term Fellowship!

Methods for Genotyping-by-Sequencing

Posted on December 01, 2016

A guide to genotyping-by-sequencing, in Methods in Molecular Biology read more

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017).

A major goal for biologists is to understand the connection between genes and phenotypic traits, and genetic mapping in experimental populations remains a powerful approach for discovering the causal genes underlying phenotypes. For genetic mapping, the process of genotyping was previously a major rate-limiting step. Modern sequencing technology has greatly improved the resolution and speed of genetic mapping by reducing the time, labor, and cost per genotyping marker. In addition, the ability to perform genotyping-by-sequencing (GBS) has facilitated large-scale population genetic analyses by providing a simpler way to survey segregating genetic variation in natural populations. Here we present two protocols for GBS, using the Illumina platform, that can be applied to a wide range of genotyping projects in different species. The first protocol is for genotyping a subset of marker positions genome-wide using restriction digestion, and the second is for preparing inexpensive paired-end whole-genome libraries. We discuss the suitability of each approach for different genotyping applications and provide notes for adapting these protocols for use with a liquid-handling robot.

Farewell to Claude

Posted on November 29, 2016

We’re saying farewell to Claude; read more

after a very successful time in Weigelworld, he will move South and establish his own group at the GMI in Vienna

We wish you all the best! 

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