Methods workshop held at EMBL in March 2017

From March 13.-15. 2017 the FOR2333 team held a three-days methods workshop at the Advanced Training Centre of the EMBL Heidelberg.
Students of participating groups attended training sessions on “bioinformatics”, “professional preparation of scientific figures”, “introduction to structural biology”, and “high-resolution imaging and image processing”. The sessions consisted of lectures and hands-on training, and were
designed to support students and postdocs in their own project.





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Ephrussi lab publishes an unconventional mechanism that loads the kinesin-1 motor onto oskar mRNPs

In this study, the Ephrussi lab shows that an atypical tropomyosin isoform is a direct (m)RNA binding protein that binds preferentially to the dimerizing oskar 3’ UTR and is a component of the transported oskar mRNPs within the female germ-line. In the absence of this tropomyosin isoform, Khc fails to get loaded onto oskar mRNA, which explains the reduced motility and ultimately the failure in oskar localization. This Tm1-I/C dependent recruitment is rather inefficient – only a small fraction of oskar mRNPs acquire Khc – but dynamic, enabling the posterior-ward transport of virtually all oskar mRNPs. Most importantly, however, the Tm1-I/C recruited Khc is inactive. Activation of the motor only commences in the oocyte during mid-oogenesis – possibly to prevent interference with the other transporter of oskar, cytoplasmic dynein – and requires the previously identified exon junction complex (EJC) and associated spliced oskar localization element (SOLE).

Gaspar, I., Sysoev, V., Komissarov, A. and Ephrussi, A. (2016)
An RNA-binding atypical tropomyosin recruits kinesin-1 dynamically to oskar mRNPs.
EMBO J. DOI 10.15252/embj.201696038


Zarnack publishes a meta-analysis of CLIP data in Genome Biology

Haberman et al. Genome Biology (2017) published by Zarnack lab

In collaboration with Jernej Ule’s group at the Francis Crick Institute in London, UK, the Zarnack lab explores how different experimental steps can constrain the identification of RBP binding sites in CLIP experiments. To this end, they analysed publicly available and newly generated data for the RBPs PTBP1, eIF4A3 and U2AF65 that were produced with multiple different CLIP protocols, including iCLIP, eCLIP and irCLIP. Based on these comparisons, they present experimental considerations and computational approaches to enable an accurate identification of RBP crosslink sites.


Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K$, Ule J$
($ shared correspondence)
Insights into the design and interpretation of iCLIP experiments
Genome Biology (2017) 18:7. doi: 10.1186/s13059-016-1130-x

Niessing lab publishes structures of ASH1 mRNP in Nature Struct. Mol. Biol.

In this study the Niessing lab solved three X-ray structures to understand how the E3 localization element of the ASH1 mRNA is folded, how it is recognized in the nucleus by She2p, and how highly specific binding in the cytoplasmic is achieved by the additional joining of the myosin adapter She3p. Quite unexpectedly, the E3 element undergoes major rearrangements upon She2p binding. Furthermore, high RNA specificity in the cytoplasm is achieved through unstructured regions of She3p that introduce steric constraints. This work was performed in close collaboration with the Jansen lab of the FOR2333 team.


Edelmann FT, Schlundt A, Heym RG, Jenner A, Niedner-Boblenz A, Syed MI, Paillart J-C, Stehle R, Janowski R, Sattler M, Jansen R-P, Niessing D
Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex
Nature Structural & Molecular Biology (2017) doi:10.1038/nsmb.3351

Helena Jambor now fellow at “Wissenschaftskolleg zu Berlin”

Dr. Helena Jambor (mentee of the DFG-research unit) has recently been accepted as fellow at the Institute for Advanced Studies (Wissenschaftskolleg zu Berlin), were she researches the history of life science visualization.


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Second FOR2333 meeting from September 5.-7. 2016 in Düsseldorf

Our research network met again, this time at the “Haus der Universität” in Düsseldorf. The focus of this meeting was to foster collaborations and initiate new projects. As local guest speaker we had Prof. Heiner Schaal (Institute of Virology, HHUD) with a very entertaining talk on alternative splicing. Thanks to Michael Feldbrügge and his team for having us…

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Congratulations! Bono and Ephrussi labs publish in Nature Struc Mol Biol and Nature Comm.

Exu-Paper-2016-copyrightThe group of Fulvia Bono published a structure-to-functional analysis of the bicoid mRNA-localization factor Exuperantia (Exu) from Drosophila. Their crystal structure shows that Exu forms a dimer and that each subunit consists of a catalytically inactive 3’-5’ EXO domain and a SAM domain. Both domains are required for binding to a highly structured region in the 3’UTR of the bicoid transcript. Thus, Exu is a non-canonical RNA-binding protein.

Lazzaretti D, Veith K, Kramer K, Basquin C, Urlaub H, Irion U, Bono F.
The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease.
Nat Struct Mol Biol. 2016 Jul 4. doi: 10.1038/nsmb.3254.

Sysoev-etal-RBPThe group of Anne Ephrussi used a very different approach to study mRNA localization in the fruit fly. In this study, all RNA-interacting proteins were mapped before and after maternal-to-zygotic transition of early embryogenesis. From the over 500 detected factors about half of them had not been described before as RNA-binding proteins. Furthermore the comparison of both datasets indicates that the RNA-bound proteome is highly dynamic during early developmental stages.

Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A.
Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila.
Nat Commun. 2016 Jul 5;7:12128. doi: 10.1038/ncomms12128.

First FOR2333 meeting on March 1.- 2. in Blaubeuren

Our first meeting of the DFG Research Unit 2333 (FOR2333) took place on March 1st and 2nd in the guesthouse of the University Tübingen in Blaubeuren. We enjoyed our first get-together with excellent discussions and talks. Looking forward to our next meeting taking place in Düsseldorf on September 5th to 7th, again focusing on ‘macromolecular complexes in mRNA localization’…

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