Retrotransposition and Regulatory RNAs

Department 2 - Biochemistry

General interest and approach

Many cellular processes are regulated at the level of RNA. We are interested in understanding the molecular and structural details that govern the fate of RNA molecules in the cell, with a focus on RNA retrotransposition, translational repression and regulated RNA degradation. To achieve this aim we use X-ray crystallography in combination with biochemical approaches and various assays both in vitro and in vivo. Current topics are:

Parasitic RNA - Structural and functional analysis of human LINE-1 and Alu retrotransposons

How dynamic are eukaryotic genomes in evolution and how do they change during cell differentiation, development and disease? These fundamental questions are far from being answered. We are looking at mobile genetic elements in the human genome, the so called retrotransposons, that multiply via an RNA intermediate. The mammalian LINE-1 element is an autonomous retrotransposon and encodes two proteins, ORF1p and ORF2p. The small Alu elements are restricted to primates and rely on the endonuclease and reverse transcriptase functions of the LINE-1 ORF2p protein for retrotransposition. Together, LINE-1 and Alu elements account for at least 25 % of our genomic DNA sequence. In the long term we hope to answer the following questions:

• How do LINE-1 and Alu RNAs get packed into retrotransposition-competent ribonucleoprotein particles (RNPs)?
• How do factors from the ‘host’ cell interact with these RNPs to promote or control retrotransposition?
• How are new genomic integration sites selected and what is the precise mechanism of integration?
• Is it possible to convert these retrotransposons into a genetic tool?
  
  

Decapping the messenger - Structural analysis of the eukaryotic mRNA 5’ decapping complex

The regulation of mRNA turnover is critical for the post-transcriptional control of gene expression, and the removal of the 5’cap from a mRNA is a key step its degradation. In higher eukaryotes decapping requires not only the decapping protein DCP2 and its partner DCP1, but larger assemblies of several proteins that can be localized to cytoplasmic P-bodies. These include the enhancers of decapping EDC3 and EDC4 as well as the DEAD-box protein DDX6. In close collaboration with Elisa Izaurralde our aim is to address the following points:

• What is the connectivity and complex stoichiometry of these partially unstructured multidomain proteins during decapping?
• How dynamic are these interactions, where in the cell and when can we observe them and which ones are mutually exclusive?
• How is the mRNA decapping machinery interlinked with the deadenylation machinery and how are the various mRNA degradation and quality control pathways integrated at the decapping step on a mechanistic level?
  
  

Variations on a theme - Post-transcriptional regulation of RNA in prokaryotes

It has been realized in recent years that post-translational regulation of RNA plays a crucial role in prokaryotes as well as eukaryotes. To complement the insights from our work in eukaryotic systems we are therefore investigating small cis-acting ligand-binding RNAs (riboswitches) and trans-acting small RNAs that interact with the bacterial Sm-like protein Hfq.

Selected publications:

Tritschler F, Braun JE, Eulalio A, Truffault V, Izaurralde E & Weichenrieder O (2009) Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. Mol Cell 33, 661-8. PubMed

Khazina E & Weichenrieder O (2009) Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc Natl Acad Sci U S A 106, 731-6. PubMed

Scientists involved

Elena Khazina, PhD Student

Heiko Keller, PhD Student

Evelyn Sauer, PhD Student

Felix Tritschler (Izaurralde Lab), PhD student

Technicians

Regina Büttner