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.
Most team members are based at the UK Dementia Research Institute at King's College London, with additional members located in satellite teams at Francis Crick Institute in London and the Institute of Chemistry in Ljubljana, Slovenia:
Dementia Research Institute centre at King's
In April 2022, we joined the Dementia Research Institute centre at King's College London, where most team members are based now. The centre is part of the Department of Basic and Clinical Neuroscience.
Institute of Chemistry, Ljubljana, Slovenia
An RNA accelerator team at the institute of Chemisty in Ljubljana.
Recent publication highlight
Griffith L, Capitanchik C et al. (2026) PRMT activity promotes global 3’ UTR shortening in proliferating cells, Mol Cell. 2026 Oct 21
Before a gene can be turned into protein, its messenger RNA must be cut at the end and given a tail. Many genes can be cut at more than one place, and cutting early produces a shorter message that loses much of the regulatory 3’ UTR region controlling when and where the protein is made. Rapidly dividing cells, including many cancers, favour these shortened messages to boost growth-promoting proteins, but what drives the switch has been unclear. This study shows that a chemical modification called arginine methylation is the trigger. Blocking it lengthens the messages across cancer cell lines, patient-derived tumour organoids and activated immune cells, and reduces production of key tumorigenic proteins. The effect works largely through PCF11, a component of the cutting machinery that is itself methylated, which promotes its integration into the cleavage complex. The findings add to our understanding of how PRMT inhibitors, already in clinical trials, put the brakes back on cancer.
A free Nextflow analysis web platform and database
We're collaborating with the London startup Goodwright, who developed the web server flow.bio an end-to-end web platform for biology that allows scientists to run Nextflow omics pre-processing pipelines via a front-end web interface, including our CLIP-seq pipeline. Read more about it here.
Flow lets users share raw data, analyses, and finished results either as part of the public database, or with specified groups of researchers in one click. As it becomes populated with increasing amounts of public data, it will increasingly serve as a database of well-curated raw and processed data. Read more about its manuscript and documentation.
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.
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.
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.
Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.
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 primary 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 2027 to work on the Wellcome Trust project.