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
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
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.
Read more ›
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…
Read more ›
The 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.
The 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.
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’…
Read more ›
Our DFG Research Unit 2333 on „mRNA localization“ just received a positive funding decision from the DFG. We are excited and look forward to start our network. More details will follow soon… (October 15th 2015)
Press releases: Tuebingen University / Duesseldorf University / LMU Munich