Abstract

RNA-binding proteins (RBPs) regulate various mRNA processing steps by binding to cis-regulatory RNA elements (cis elements), such as short RNA sequences or structured RNA elements. RBP function is strongly shaped by the interplay of proteins and RNA in large messenger ribonucleoprotein particles (mRNPs) that control the fate and function of each transcript. These RBPs typically harbour multiple RNA binding domains (RBDs) that mediate combinatorial RNA or protein-protein interactions to dynamically assemble and remodel mRNPs.

We aim to unravel novel principles of the mRNP code by dissecting the molecular mechanisms of 3’ splice site recognition at multiple levels of resolution. We integrate large-scale in vivo and in vitro RBP binding maps with kinetic and high-resolution structural information to address multiple layers of regulation of mRNP assemblies at the 3’ splice site.

We have established a unique approach combining transcript-wide in vivo and in vitro RBP binding maps with functional assays and integrative structural biology. This enabled us to show how the essential splicing factor U2AF2 recognizes RNA sequences and we discovered new trans-acting factors, such as FUBP1 as a novel regulator of the mRNP assembly at the 3’ splice site. In the current project we will decipher the molecular mechanisms of combinatorial 3’ splice-site recognition - from the molecular and structural analysis of protein-RNA and protein-protein interactions to functional consequences of mRNP assembly in living cells.

Project-related publications

Kang HS, Sanchez-Rico C, Ebersberger S, Sutandy FXR, Busch A, Welte T, Stehle R, Hipp C, Schulz L, Buchbender A, Zarnack K, König J, Sattler M. An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2.
(2020) PNAS 117, 7140-7149. doi: 10.1073/pnas.1913483117

Schneider T, Hung LH, Aziz M, Wilmen A, Thaum S, Wagner J, Janowski R, Muller S, Schreiner S, Friedhoff P, Huttelmaier S, Niessing D, Sattler M, Schlundt A, Bindereif. Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.
(2019) Nat Commun 10.   doi: 10.1038/s41467-019-09769-8

Sutandy, F.X.R.*, Ebersberger, S.*, Huang, L.*, Busch, A., Bach, M., Kang, H.S., Fallmann, J., Maticzka, D., Backofen, R., Stadler, P.F., Zarnack, K., Sattler, M., Legewie, S.^#, König, J.^# In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.
(2018). Genome Res 28, 699-713.

Braun, S.*, Setty, S.T.*, Enculescu, M.*, Cortés-López, M., de Almeida, B.P., Sutandy, F.X.R, Schulz, L., Busch, A., Seiler, M., Ebersberger, S., Barbosa-Morais, N.L., Legewie, S.^#, König, J.^#, Zarnack, K.^# Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis.
(2018) Nat Commun doi:10.1038/s41467-018-05748-7.

Kooshapur, H., Choudhury, N.R., Simon, B., Mühlbauer, M., Jussupow, A., Fernandez, N., Jones, A.N., Dallmann, A., Gabel, F., Camilloni, C., Michlewski, G.^#, Caceres, J.F.^#, Sattler, M.^# Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1.
(2018) Nat Commun 9, 2479.

Voith von Voithenberg, L., Sanchez-Rico, C., Kang, H.S., Madl, T., Zanier, K., Barth, A., Warner, L.R., Sattler, M.^#, Lamb, D.C.^# Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift.
(2016) PNAS 113, E7169-E7175.