Skip to main content

A8: A comparative cellular atlas of environmental plasticity in leaves

Prof. Dr. Uwe Ohler

Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13 (Haus 18), 10115 Berlin

Tel. +49-30-94061752, uwe.ohlerhu-berlinde


Prof. Dr. Kerstin Kaufmann

Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13 (Haus 22), 10115 Berlin

Tel. +49-30-209349740, kerstin.kaufmannhu-berlinde


Prof. Dr. Philip A. Wigge

Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor Echtermeyer Weg 1, 14979 Grossbeeren

Tel 033701 78411, wiggeigzevde


Open positions:

Position DR/004/24 – PhD student Ohler/Kaufmann group



A8 (Kaufmann, Wigge, Ohler) investigates the molecular basis of cell-type specific plastic responses to temperature and nitrogen supply, including cellular differentiation trajectories. In particular, the aim will be to construct a comparative cellular atlas of environmental plasticity in leaves as important environmental sensory organs. The project will map cell-type specific regulatory responses at a genome-wide scale in a comparative manner in A. thaliana and C. bursa-pastoris using tissue-level and single-cell transcriptomics and chromatin accessibility studies. The resulting atlas will facilitate analyses in all other projects of the CRC.


Project-related publications

Silva, C.S., Nayak, A., Lai, X., Hutin, S., Hugouvieux, V., Jung, J.H., López-Vidriero, I., Franco-Zorrilla, J.M., Panigrahi, K.C.S., Nanao, M.H., Wigge, P.A., Zubieta, C. (2020). Molecular mechanisms of Evening Complex activity in Arabidopsis. Proc Natl Acad Sci U S A.; 117:6901-6909

Jung, J.H., Domijan, M., Klose, C., Biswas, S., Ezer, D., Gao, M., Khattak, A.K., Box, M.S., Charoensawan, V., Cortijo, S., Kumar, M., Grant, A., Locke, J.C., Schäfer, E., Jaeger, K.E., Wigge, P.A. (2016). Phytochromes function as thermosensors in Arabidopsis.Science. 354:886-889.

Dickinson, P.J., Kumar, M., Martinho, C., Yoo, S.J., Lan, H., Artavanis, G., Charoensawan, V., Schöttler, M.A., Bock, R., Jaeger, K.E., Wigge, P.A. (2018). Chloroplast Signaling Gates Thermotolerance in Arabidopsis. Cell Rep. 22:1657-1665.

Jung J.H., Barbosa A.D., Hutin S., Kumita J.R., Gao M., Derwort D., Silva C.S., Lai X., Pierre E., Geng F., Kim S.B., Baek S., Zubieta C., Jaeger K.E., Wigge P.A. (2020) A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis. Nature. 585:256-260.

Karabacak Calviello, A., Hirsekorn, A., Wurmus, R., Yusuf, D., Ohler, U. (2019). Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.Genome Biol. 20:42.

Chen, D., Yan, W., Fu, L.Y., Kaufmann, K. (2018). Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nature Communications. doi: 10.1038/s41467-018-06772-3.

Sunaga-Franze D.Y., Muino J.M., Braeuning C., Xu X., Zong M., Smaczniak C., Yan W., Fischer C., Vidal R., Kliem M., Kaufmann K., Sauer S. (2021) Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. Plant J. 108:859-869.

Shahan, R., Hsu C.W., Nolan T.M., Cole B.J., Taylor I.W., Greenstreet L., Zhang S., Afanassiev A., Vlot A.H.C., Schiebinger G., Benfey P.N., Ohler U. (2022) A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.Dev Cell. 57:543-560.e9.

Li, S., Yamada, M., Han, X., Ohler, U., Benfey, P.N. (2016) High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Dev Cell. 39:508-522.