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PhD position in EU Training Network EpiDiverse

Posted on November 03, 2017

Highly motivated candidates from (epi)genetics/genomics, computational biology, bioinformatics! read more

EpiDiverse: Epigenetic Diversity in Ecology

RP14: Transgenerational epigenetic effects: role of small RNAs

Duration: 36 months • Fixed start date: 1 April 2018

Epigenetic mechanisms can establish a memory of previous stress exposure, allowing a plant to react more effectively upon repeated exposure to the same stress. In some cases, such memory may extend to the following generation. Prominent targets of stress-induced epigenetic changes are transposable elements. Their induced methylation can repress neighboring genes, and thus modify cellular output and stress response. Such changes may involve stress-induced small RNAs generated from and/or recognizing sequences found in transposable elements. 

Objective is to study the transgenerational aspect of epigenetic memory by integrating information on small RNA abundance and DNA methylation both within and between plant generations. Of particular interest will also be DNA sequence variation among related genotypes of the same species and its effects on stress memory. This may be caused by the absence of transposable elements, the absence of transposon repression through altered small RNA sequences, misregulation of small RNA abundances, or additional components of epigenetic control. Next generation sequencing, including data analysis, will be an integral part of the project. 

Qualifications

We are looking for motivated candidates with a genuine interest in plant epigenetics and relevant prior experience in molecular plant biology and/or Next Generation Sequencing data analysis. Our interactive, international and interdisciplinary work environment requires excellent oral and written communication skills in English, as well as the ability to work well both independently and in a team environment. Please include a 1-page motivation letter stating your interest in epigenetics, learning or applying tools for the analysis of Next Generation Sequencing data, as well as the lab; also include why your prior (scientific) experience makes you a good candidate.

Contact Detlef Weigel

The Max Planck Institute for Developmental Biology is one of more than 80 institutes of the Max Planck Society, and addresses fundamental questions of modern biology ranging from the atomic level (protein structure) to the organismal level (ecology and evolution). The position will be hosted in the Department of Molecular Biology, with a particular focus on the genetic and epigenetic determinants of plant adaptation to local environments. 

Congratulations, Dr. Giovanna Capovilla!

Posted on October 09, 2017

Giovanna successfully defended her PhD thesis entitled 'Exploring the role of temperature regulated alternative splicing in flowering time and morphogenesis' read more

Congratulations, Giovanna!

Maus Türöffner Tag

Posted on October 03, 2017

How we sequence DNA - teaching lab for kids read more

As big fans of Die Maus, we participated in this year's open house event and showed how DNA can be extracted, read and sequenced. 

Big thanks to all kids for a fun day!

6th bioRxiv of 2017: Massive field data from rain manipulation

Posted on September 11, 2017

Field experiment with 517 A. thaliana accessions in Madrid & Tübingen read more

A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions

Exposito-Alonso et al. https://doi.org/10.1101/186767

The gold standard for studying natural selection is to quantify lifetime fitness in individuals from natural populations that have been grown together under different field conditions. This has been widely done in ecology to measure phenotypic selection in nature for a wide range of organisms -- an evolutionary force that seems to be most determined by local precipitation patterns. Studies that include whole-genome data would enable the translation of coefficients of selection to the genetic level, but such studies are still scarce, even though this type of genetic knowledge will be critical to predict the effect of climate change in natural populations. Here we present such an experiment including rainfall-manipulation with the plant Arabidopsis thaliana. The experiment was carried out in a Mediterranean and a Central European field station with rainout shelters to simulate a high and low rainfall treatment within each location. For each treatment combination, we planted 7 pots with one individual and 5 pots with 30 counted seeds of 517 whole-genome sequenced natural accessions covering the global species distribution. Survival, germination, flowering time, and final seed output were measured for ca. 25,000 pots, which contained ca. 14,500 individual plants and over 310,00 plants growing in small populations. This high-throughput phenotyping was only possible thanks to image analysis techniques using custom-made scripts. To make the data and processing code available, we created an R package dryAR (http://github.com/MoisesExpositoAlonso/dryAR).

In Nature Plants: Prominent TADs in rice

Posted on August 29, 2017

Different from Arabidopsis, the 3D genome of rice has clear TADs read more

Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis

Chang Liu, Ying-Juan Cheng, Jia-Wei Wang & Detlef Weigel

The non-random three-dimensional organization of genomes is critical for many cellular processes. Recently, analyses of genome-wide chromatin packing in the model dicot plant Arabidopsis thaliana have been reported. At a kilobase scale, the A. thaliana chromatin interaction network is highly correlated with a range of genomic and epigenomic features. Surprisingly, topologically associated domains (TADs), which appear to be a prevalent structural feature of genome packing in many animal species, are not prominent in the A. thaliana genome. Using a genome-wide chromatin conformation capture approach, Hi-C , we report high-resolution chromatin packing patterns of another model plant, rice. We unveil new structural features of chromatin organization at both chromosomal and local levels compared to A. thaliana, with thousands of distinct TADs that cover about a quarter of the rice genome. The rice TAD boundaries are associated with euchromatic epigenetic marks and active gene expression, and enriched with a sequence motif that can be recognized by plant-specific TCP proteins. In addition, we report chromosome decondensation in rice seedlings undergoing cold stress, despite local chromatin packing patterns remaining largely unchanged. The substantial variation found already in a comparison of two plant species suggests that chromatin organization in plants might be more diverse than in multicellular animals.

In Genome Biology: 3D genome of interspecific hybrids

Posted on August 28, 2017

Altered chromatin compaction & histone methylation in an interspecific Arabidopsis hybrid read more

Wangsheng Zhu et al., Genome Biology 2017 18:157, doi.org/10.1186/s13059-017-1281-4

Background: The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization. However, the detailed mechanisms responsible for non-additive phenotypic novelty in hybrids remain elusive.

Results: In an interspecific hybrid between Arabidopsis thaliana and A. lyrata, the vast majority of genes that become upregulated or downregulated relative to the parents originate from A. thaliana. Among all differentially expressed A. thaliana genes, the majority is downregulated in the hybrid. To understand why parental origin affects gene expression in this system, we compare chromatin packing patterns and epigenomic landscapes in the hybrid and parents. We find that the chromatin of A. thaliana, but not that of A. lyrata, becomes more compact in the hybrid. Parental patterns of DNA methylation and H3K27me3 deposition are mostly unaltered in the hybrid, with the exception of higher CHH DNA methylation in transposon-rich regions. However, A. thaliana genes enriched for the H3K27me3 mark are particularly likely to differ in expression between the hybrid and parent.

Conclusions: It has long been suspected that genome-scale properties cause the differential responses of genes from one or the other parent to hybridization. Our work links global chromatin compactness and H3K27me3 histone modification to global differences in gene expression in an interspecific Arabidopsis hybrid.

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