Ule Lab
Welcome to the RNA networks lab
RNA is a multitalented molecule: it can store genetic information as well as catalyse chemical reactions. According to the RNA world hypothesis, these talents stem from the central role of RNA at the origin of life. In ‘modern’ cells, RNA molecules carry genetic information from DNA to proteins, and in addition they form wonderfully intricate networks of interactions with proteins and other molecules.
We study how RNA networks direct the workings of a cell by regulating gene expression and protein homeostasis. RNAs are coated by proteins to form ribonucleoprotein complexes (RNPs). These proteins guide the RNA on its journey through the cell to regulate gene expression, while the RNAs also regulate the functions of bound proteins and thereby affect their homeostasis. To understand these RNA networks, we develop new techniques that reveal protein-RNA and RNA-RNA interactions within cells and interrogate their functions.
In particular, we investigate how RNPs contribute to the functions of nerve cells in development, how they help us understand brain evolution, and how faulty RNPs lead to conditions affecting the nervous system, particularly neurodegenerative diseases such as amyotrophic lateral sclerosis. We hope our discoveries will open opportunities for new therapies for these diseases.
Institute of Chemistry Ljubljana Slovenia
An ERC grant, co-hosted at the Ljubljana Chemistry Institute, funds a satellite lab at the institute since 2020.
Recent publication highlights
Kuret K, Amalietti AG, Jones DM, Capitanchik C, Ule J. (2022) Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. Genome Biol. Sep 9;23(1):191.
We previously developed iCLIP, a method to efficiently identify sites of protein-RNA crosslinking across the transcriptome. However, these crosslink sites don't necessarily align with all the RNA sequence motifs that are recognised by proteins to drive their binding specificity. We therefore developed new software, positionally-enriched k-mer analysis (PEKA, available here), which enables user-friendly detection of enriched RNA motifs from individual CLIP datasets and visualizes their positional profiles around crosslink sites. We also showed how CLIP meta-analyses can yield insights into the extent and specificity of motif enrichment in each dataset, and provide such analysis of ENCODE eCLIP for exploratory analysis in an RBP-centric and motif-centric manner. This is the first manuscript fully done by the Ljubljana satellite, led by the PhD student Klara.
Hallegger et al, TDP-43 condensation properties specify its RNA-binding and regulatory repertoire Cell. 2021 Sep 2;184(18).
Many neurodegenerative diseases are associated with formation of toxic aggregates of TDP-43, which result from the strong propensity of TDP-43 for molecular condensation. We addressed the long-standing question of whether such condensation propensity affects its RNA binding specificity and function. We created variants of TDP-43 with a gradient of condensation properties and used comparative iCLIP to find its roles in binding to long RNA regions that contain widely dispersed binding motifs, a phenomenon we refer to as ‘binding region condensates’. Thereby, TDP-43 regulates a select subset of 3’UTR isoforms, including autoregulation of TDP-43 itself. Our study thus shows that changes in TDP-43 condensation can deregulate a selective subset of RNAs, which could contribute to the early stages of neurodegenerative diseases. More from Martina on the paper here.
A free CLIP analysis pipeline and web platform
Together with the London startup Goodwright, we developed a web server iMaps for streamlined analysis of CLIP data, which is freely available for general use. Read more about it here.
iMaps can be used to analyse unpublished data in a secure manner, and to share your data publicly upon publication. Read more about its documentation. It is based on the open access Nextflow pipelines co-developed by the Nick Luscombe team. As it becomes populated with increasing amounts of public data, it will increasingly also serve as a database of well-curated raw and processed data.
Recently published methods
iiCLIP: An improved iCLIP protocol that is technically convenient and efficient, enables quality control via non-radioactive analysis of protein-RNA complexes, and produces data of high specificity.
Ribocutter: A streamlined Cas9-based protocol for removing abundant rRNA/ncRNA contaminants from Ribo-seq, CLIP or other RNA-seq libraries and a software tool for designing ready-to-order sgRNA templates.
CLIP data analysis pipeline: nf-core/clipseq - a robust Nextflow pipeline for quality control and analysis of CLIP sequencing data.
Ultraplex: Software for user friendly, streamlined and robust demultiplexing of complex sequencing libraries, such as those produced by various CLIP and ribosome profiling protocols.
clipplotr: A command-line tool for visual comparative and integrative analyses with normalisation and smoothing options for data to be shown alongside reference annotation tracks and functional genomic data.
PEKA: Positionally-enriched k-mer analysis, a computational tool for analysis of enriched motifs from CLIP datasets, which minimises the impact of technical and regional genomic biases by internal data normalisation.
Tosca: a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data.
13C-dynamods: A 13C labeling approach to quantify the turnover of base modifications in newly transcribed RNA, which enables studies of the origin of modified RNAs and its dynamics under nonstationary conditions.
SPACE: Silica Particle Assisted Chromatin Enrichment to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins.
We moved south of the River Thames
On 1/4/22, the team moved from the Crick institute to KCL, where Jernej took the position of UK DRI Centre Director at King's. The London lab is now based at the King's Denmark Hill campus (within the Maurice Wohl institute), while a satellite lab of 3 people remains at the Francis Crick institute till end of 2024, which is required to complete the Wellcome Trust project.