Advantages and limitations of UV cross‐linking analysis of protein–RNA interactomes in microbes

S Esteban‐Serna, H McCaughan… - Molecular …, 2023 - Wiley Online Library
RNA‐binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles
in adaptive responses in microbes. A robust approach to examine protein–RNA interactions …

Chemical RNA cross-linking: mechanisms, computational analysis, and biological applications

WA Velema, Z Lu - Jacs Au, 2023 - ACS Publications
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually
every function of the cell and is critical for human health. This has led to a substantial …

Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins

CP Sarnowski, M Bikaki, A Leitner - Structure, 2022 - cell.com
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular
technique for low-resolution structural studies of macromolecular complexes. Cross-linking …

Improved analysis of (e) CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

M Katsantoni, E van Nimwegen, M Zavolan - Genome Biology, 2023 - Springer
We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of
binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not …

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

AM Chakrabarti, IA Iosub, FCY Lee, J Ule… - Nucleic Acids …, 2023 - academic.oup.com
The structure of mRNA molecules plays an important role in its interactions with trans-acting
factors, notably RNA binding proteins (RBPs), thus contributing to the functional …

Sensitive detection and structural characterisation of UV-induced cross-links in protein-RNA complexes using CLIR-MS

CP Sarnowski, A Knörlein, T de Vries, M Götze… - bioRxiv, 2022 - biorxiv.org
Cross-linking coupled with mass spectrometry is an increasingly popular methodology for
elucidating structural information from biological complexes. Whilst protein-protein cross …

Computational models to infer regulators of gene expression for high-throughput data

M Katsantoni - 2023 - edoc.unibas.ch
Ever since the formulation of the central dogma of biology, the focus was shifted into how the
various steps up to the protein formation are regulated. RNA-binding proteins (RBPs) have …

[PDF][PDF] Shining light on RNA-protein interactions. How structure guides UV cross-linking in RNA-protein complexes.

A Knörlein - 2022 - research-collection.ethz.ch
To Prof. Dr. Jonathan Hall. I would like to thank you for the opportunity to work in your lab
and your advice, patience, and feedback during my PhD. You always encouraged me to …