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SPP1935 -- Deciphering the mRNP code :
RNA-bound Determinants of Post-transcriptional Gene Regulation

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laboratoriesProf. Dr. Heissmeyer

Vigo Heissmeyer Center
Institute for Immunology, Ludwig-Maximilians-Universität München, Biomedical Center (BMC)

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Grosshaderner Str. 9, 82152 Planegg-Martinsried

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0049089218075629


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Deciphering the combinatorial activity of cis-elements and trans-acting factors in Icos mRNA regulation

Colaboration with Prof. Dr. Dierk Niessing



Lab InfoPROJECT INFORMATION :

The inducible costimulator of T cells (Icos) is critical for humoral immune responses since its loss- or gain-of-function is linked to immunodeficiency or autoimmunity, respectively. Icos has been shown to be under extensive post-transcriptional control. The published information so far demonstrates the regulation of Icos mRNA by the RNA-binding protein Roquin, the endonuclease Regnase-1 as well as several miRNAs. Furthermore, our preliminary data identified a novel cofactor in Roquin-mediated Icos repression.

The current knowledge typically relates the identification of one cis-element within an mRNA 3’ UTR to the regulation by one trans-acting factor. However, these noncoding sequences can be very long and often contain many different binding sites for trans-acting factors that either work independently, cooperatively or even interfere with each other’s function. In addition, there is little information how distant sequences or secondary structures influence the folding or accessibility of each other and jointly contribute to the post-transcriptional regulation of an entire mRNA.

Here, we focus on the long 3’ UTR of the mouse Icos mRNA for which we propose to acquire complementary information from several unbiased approaches leading to in depth structure-function studies that will then elucidate its combinatorial regulation. First, we will identify the proteome that is associated with this mRNA after cross-linking and sequence-specific pull-down of the mRNA from cell extracts. We will then analyze the secondary structure of the encoded sequence of the Icos 3’ UTR by chemical probing. Third we will systematically address the functional importance of sequences in this 3’ UTR by comprehensive random mutagenesis with about 11,000 sequence alterations. This, to our knowledge unprecedented approach, will systematically test individual mutations in the physiologic molecular context in primary T cell cultures to identify all regulatory elements of this long 3’ UTR. Finally, we shall bring together all the information and ask whether the individual trans-acting factors bind their cis-elements independently or in cooperation, how they interact with their cofactors, the translation machinery and factors of mRNA decay.

Overall, this work shall establish the functional and structural landscape of the Icos mRNA cis-elements that is then accessed by combinations of trans-acting factors, which engage in different physical and functional co-operations to realize regulation of the Icos mRNA in a context-dependent, differential or dynamic manner.

Focus of the group:
immunology and post-transcriptional gene regulation




Lab techsKEY TECHNOLOGIES :

- Inducible gene ablation
- Immune cell phenotyping
- SELEX
- PAR-CLIP
- Ribosome footprinting



PublicationsPUBLICATIONS :

Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.
Janowski R, Heinz GA, Schlundt A, Wommelsdorf N, Brenner S, Gruber AR, Blank M, Buch T, Buhmann R, Zavolan M, Niessing D#, Heissmeyer V#, Sattler M#.
Nat Commun. 2016 Mar 24;7:11032. doi: 10.1038/ncomms11032. #Co-corresponding authors.

Cleavage of roquin and regnase-1 by the paracaspase MALT1 releases their cooperatively repressed targets to promote T(H)17 differentiation.
Jeltsch KM, Hu D, Brenner S, Zöller J, Heinz GA, Nagel D, Vogel KU, Rehage N, Warth SC, Edelmann SL, Gloury R, Martin N, Lohs C, Lech M, Stehklein JE, Geerlof A, Kremmer E, Weber A, Anders HJ, Schmitz I, Schmidt-Supprian M, Fu M, Holtmann H, Krappmann D, Ruland J, Kallies A, Heikenwalder M, Heissmeyer V.
Nat Immunol. 2014 Nov;15(11):1079-89. doi: 10.1038/ni.3008.

Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.
Schlundt A, Heinz GA, Janowski R, Geerlof A, Stehle R, Heissmeyer V#, Niessing D#, Sattler M#.
Nat Struct Mol Biol. 2014 Aug;21(8):671-8. doi: 10.1038/nsmb.2855. #Co-corresponding authors.

Roquin paralogs 1 and 2 redundantly repress the Icos and Ox40 costimulator mRNAs and control follicular helper T cell differentiation.
Vogel KU, Edelmann SL, Jeltsch KM, Bertossi A, Heger K, Heinz GA, Zöller J, Warth SC, Hoefig KP, Lohs C, Neff F, Kremmer E, Schick J, Repsilber D, Geerlof A, Blum H, Wurst W, Heikenwälder M, Schmidt-Supprian M, Heissmeyer V.
Immunity. 2013 Apr 18;38(4):655-68. doi: 10.1016/j.immuni.2012.12.004.

Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay.
Hoefig KP, Rath N, Heinz GA, Wolf C, Dameris J, Schepers A, Kremmer E, Ansel KM, Heissmeyer V.
Nat Struct Mol Biol. 2013 Jan;20(1):73-81. doi: 10.1038/nsmb.2450.