Latest News

Congratulations, Dr. Dominik Grimm!

Posted on November 19, 2015

Dominik successfully defended his PhD thesis today. read more

Dominik worked with Karsten Borgwardt (now ETH Zürich) and among other things developed easyGWAS:

eLife paper on assessing ancient DNA authenticity from low-coverage da...

Posted on November 03, 2015

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data read more

Weiss, C..L., Dannemann, M., Pruefer K., Burbano, H.A.

Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

Read Nature News Article

Plant-plant competition through HDAC inhibitors

Posted on November 03, 2015

Plants release precursors of histone deacetylase inhibitors to suppress growth of competitors read more

Venturelli, S., Belz, R., Kämper, A., Berger, A., von Horn, K., Wegner, A.,  Böcker, A., Zabulon, G.,  Langenecker, T.,  Kohlbacher, O., Barneche, F.,  Weigel, D.,  Lauer, U., Bitzer, M, Becker, C.

To secure their access to water, light, and nutrients, many plant species have developed allelopathic strategies to suppress competitors. To this end, they release into the rhizosphere phytotoxic substances that inhibit the germination and growth of neighbors. Despite the importance of allelopathy in shaping natural plant communities and for agricultural production, the underlying molecular mechanisms are largely unknown. Here, we report that allelochemicals derived from the common class of cyclic hydroxamic acid root exudates directly affect the chromatin-modifying machinery in Arabidopsis thaliana. These allelochemicals inhibit histone deacetylases both in vitro and in vivo and exert their activity through locus-specific alterations of histone acetylation and associated gene expression. Our multilevel analysis collectively shows how plant-plant interactions interfere with a fundamental cellular process, histone acetylation, by targeting an evolutionarily highly conserved class of enzymes.

Read the Plant Cell Preview Article

New paper connecting GA signaling and ambient-temperature mediated flo...

Posted on October 29, 2015

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana read more

Galvão, V. C., Collani, S, Horrer, D., Schmid, M.

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process. This article is protected by copyright. All rights reserved.

In PNAS: Role of RCF as a HYL1 cofactor in miRNA biogenesis

Posted on October 28, 2015

The KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1 read more

Karlsson, P., Christie, M.D., Seymour, D., Wang, H., Wang, X., Hagmann, J., Kulcheski, F.R. and Manavella, P.A.

The biogenesis of microRNAs (miRNAs), which regulate mRNA abundance through posttranscriptional silencing, comprises multiple well-orchestrated processing steps. We have identified the Arabidopsis thaliana K homology (KH) domain protein REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) as a cofactor affecting miRNA biogenesis in specific plant tissues. MiRNA and miRNA-target levels were reduced in apex-enriched samples of rcf3 mutants, but not in other tissues. Mechanistically, RCF3 affects miRNA biogenesis through nuclear interactions with the phosphatases C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 and 2 (CPL1 and CPL2). These interactions are essential to regulate the phosphorylation status, and thus the activity, of the double-stranded RNA binding protein and DICER-LIKE1 (DCL1) cofactor HYPONASTIC LEAVES1 (HYL1)

Markus officially installed as a professor in Umeå

Posted on October 22, 2015

Formal ceremony and public lecture on the occasion of the university’s 50th birthday. read more

Picture of Markus with Ove Nilsson (left), also former Weigelworld postdoc and now director of the Umeå Plant Science Centre


Upcoming Events


Hilgendorf Lecture Bob Wong

December 7, 4:15 pm
Lecture hall N10, Auf der Morgenstelle 3

Title: Behavioural Responses to a changing world: evolutionary and ecological consequences


Guest Lecture by Claude at SLU Uppsala

Tuesday, December 8
SLU Uppsala, Sweden

"Something to remember? How biotic and abiotic stress affects chromatin in A. thaliana"


International Symposium 'Current Challenges in Next Generation Sequencing'