Genomic views and molecular mechanisms of RNA regulation: RNA modifications and splicing regulation

1 PhD project in the IPP summer call 2021

Scientific background

Posttranscriptional gene regulation plays an important role in development and tissue identity, but also in neurodegenerative diseases and cancer. mRNA fate is regulated by the cooperative action of RNA-binding proteins (RBPs) which recognise specific RNA sequences to form messenger ribonucleoprotein complexes (mRNPs). The information in the RNA sequence and how it is interpreted by RBPs is commonly referred to as the ‘mRNP code’. However, the molecular features that define this code remain poorly understood. Our major goal is to significantly contribute to cracking the mRNP code.

PhD project 1: RNA modifications shape the fate of RNA

The RNA modification N6-methyladenosine (m6A) affects almost every stage of the mRNA metabolism, and its alteration is associated with various physiological defects and diseases. Although a substantial amount of literature describes the function of m6A in various biological processes, the mechanisms by which m6A is deposited on RNA during transcription in the nucleus is still poorly understood.

For this project we will combine our expertise in functional genomics (iCLIP, miCLIP, High-throuput sequencing approaches), molecular biology and computational approaches, to dissect how the m6A machinery is positioned on transcripts. We will characterize the intrinsic specificity of the core enzyme METTL3 and how it is guided by auxiliary RNA binding proteins or modulated by secondary structure. This will help us to understand how these epigenetic marks are placed on the nascent RNAs to determine their fate in the cytoplasm.

PhD project 2: Cracking the splicing code

pre-mRNA splicing constitutes a major step in eukaryotic gene expression. More than 90% of human genes undergo alternative splicing, which contributes to protein diversity and plays a critical role in development and tissue identity. The regulation of splicing is achieved through the coordinated binding of many RNA-binding proteins. It is becoming clear that their recruitment is not solely dependent on the underlying RNA sequence, but is strongly shaped by the interactive environment. Means of interaction include direct competition, cooperative recruitment and the modulation of secondary structure. Knowledge about the acting forces is therefore critical to predict the function of an RNA-binding protein and its impact on the splicing outcome.

This project aims at a global understanding of RBP interactions in the context of splicing regulation. The PhD student will investigate splicing with state-of-the-art techniques such as (nascent RNA sequencing, iCLIP, massive parallel reporter assays). The data will be integrated using network analyses and machine learning strategies to obtain systemic views on the combinatorial action of RBPs in splicing regulation. The project will be based on close collaborations with computational scientists within and outside our group.

Publications relevant to these projects

Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant J-Y, Zarnack K#, König J# and Beli P# (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translationGenome Biol, 20:216 (#indicates joint correspondence) Link

Braun S*, Enculescu M*, Setty ST*, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S#, König J# and Zarnack K# (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesisNat Commun, 9:3315 (*indicates joint contribution, #indicates joint correspondence) Link

Sutandy FXR*, Ebersberger S*, Huang L*, Busch A, Bach M, Kang H-S, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S# and König J# (2018) In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactorsGenome Res, 28:699–713 (*indicates joint contribution, #indicates joint correspondence) Link


Dr Julian König