Post-transcriptional regulatory networks
New!
On 1st of April, the lab will move to University College London, Faculty of Brain Sciences.
We will join the Department of Molecular Neuroscience at the Institute of Neurology.
Messenger RNA (mRNA) carries the genetic information from DNA to the machinery in our cells that makes the proteins. As it travels through the different parts of the cell, an mRNA needs to pass through several regulatory stages. These stages are controlled by RNA-binding proteins (RBPs) and non-coding RNAs, which interact with the mRNA and pre-mRNA. The positioning of RBPs is determined by the sequence and structure of each RNA, therefore each RNA assembles into a unique regulatory ribonucleoprotein complex (RNP). These regulatory RNPs are very dynamic, therefore we study them in intact cells and tissues, employing functional genomics and protein engineering technologies.
Our work aims to:
1) Determine how the regulatory RNPs control pre-mRNA processing and protein translation.
2) Understand how the regulatory RNPs respond to cellular signals, in particular during stress.
3) Define the disease-causing mechanisms of mutations that perturb the regulatory RNPs, with a focus on cancer and neurodegeneration.
As an RNA passes through the cellular regulatory stages, it is like a character from Mozart's Magic Flute, passing through the ordeals of space and time. And here are some of the RNA stories that we have passed through:
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New technologies for studies of protein-RNA interactions.
We developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) to quantify protein-RNA interactions in the whole transcriptome, thereby fully exploiting the power of high-throughput sequencing. We review the progress made in the last years in the technologies for studies of protein-RNA interactions. You can download the manuscript here. We also performed a comparative analysis of iCLIP and CLIP, click here.
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Leading actors
Julian König (iCLIP), Tomaz Curk (iCount), Yoichiro Sugimoto
The latest manuscript describing the iCLIP method and troubleshooting is available from a recent book chapter, the link to the book is here
Press coverage
RNA Analysis Unearths Invaluable Insights
Video protocol
www.jove.com/video/2638/iclip-transcriptome-wide-mapping-protein-rna-interactions-with
Online resources
Question-answer forum on the CLIP method
Question-answer forum on the iCLIP method
In collaboration with the Nick Luscombe lab, we have discovered a major new role for the RNA-binding protein hnRNP C. We have originally shown that hnRNP C specifically recognizes long uridine tracts, and can thereby repress splicing of exons. This was evident by the ultraviolet crosslinking of the hnRNP C1/C2 tetramer, which suggested that the repressed exons are incorporated into the hnRNP particles (see the paper).
Alu elements" > Alu elements" /> We now show (see the Cell manuscript) that hnRNP C represses inclusion of cryptic splice sites in Alu elements by displacing the splicing factor U2AF65 from uridine tracts. Loss of hnRNP C leads to formation of thousands of harmful exons, and mutations disrupting hnRNP C binding cause human diseases. Since the repressive function of hnRNP C prevents the damaging effects of immediate Alu exonization, it enables mutations to gradually create Alu-derived exons. This represents an elegant molecular mechanism that could mediate incremental evolution of new cellular functions.
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Leading actors
Kathi Zarnack (dry lab), Julian König (wet lab), Mojca Tajnik, Iñigo Martincorena
Research Highlight
Nature Reviews Genetics on "Regulating Alu element exonization"
Press Release
LMB news on "The guardian of the transcriptome"
We showed that the activity of most RNA-binding proteins follows defined positional rules, or RNA maps. These maps can be derived by integrating of genome-wide studies of physical and functional protein-RNA integrations. For instance, by integrating TIA iCLIP with splicing analysis upon TIA knockdown, we were able to derive nucleotide-resolution RNA splicing maps of TIA proteins.
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Leading actors
Zhen Wang, Melis Kayikci, Kathi Zarnack, Matteo Cereda
Press coverage
RNA map gives first comprehensive understanding of alternative splicing
Alternative splicing can produce several mRNA isoforms from a gene, and these isoforms can change in the human brain during aging or neurodegeneration (click here). In collaboration with the Chris Shaw lab (KCL), we uncovered the regulatory networks controlled by TDP-43 and FUS. Mutations in these two RBPs can cause amyotrophic lateral sclerosis, therefore it is important to understand their functions in the brain. We showed that TDP-43 binds to long clusters of UG-rich RNA motifs to recognise specific sites on pre-mRNAs and thereby regulate splicing. Moreover, TDP-43 increases its interactions with specific non-coding RNAs in diseased brain, click here. Surprisingly, FUS and TDP-43 rarely regulate splicing the same exons. FUS has little specificity for RNA sequence or structure, and binds across the whole pre-mRNA, with enriched binding to introns flanking the regulated exons. Nevertheless, both proteins regulate a functionally coherent set of transcripts, many of which encode proteins implicated in neurodegenerative disorders (click here).
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Leading actors
James Tollervey, Boris Rogelj, Tomaz Curk, Laura Easton, Josh Witten, Michael Briese
Press coverage
CLIPs of TDP-43 Provide a Glimpse Into Pathology, Alzheimer Research Forum
FUS and Friends: Two Studies Probe FUS’ RNA Partners
New Link Revealed Between Alzheimer's Disease and Healthy Aging, Science Daily