RNA-Protein Complexes and Cell Proliferation

  • Functional and Structural Genomics
Employee image

Priv. Doz. Dr. Maiwen Caudron-Herger

Once per cell cycle, cells face the challenging task of accurately segregating their chromosomes into two identical sets. Although cell division is highly regulated, errors may occur, leading to either cell death or the genome instability that underlies many human diseases such as cancer. RNA-protein complexes are critical regulatory elements in important cellular processes, including cell division, which we are investigating.

Microscope image showing the cell division stage with spindle fibers radiating from two centrosomes at opposite ends. The background is dark, highlighting the intricate network of fibers critical for chromosome alignment and separation during mitosis.
“Cells have the wonderful ability to assemble a great variety of dynamic structures performing very complex and specific tasks. Our goal is to improve our understanding of the underlying regulatory mechanisms and to answer the question of how dysfunction can lead to disease.”

PD Dr. Maïwen Caudron-Herger

Our Research

A microscopic image shows a cell during division, featuring a vibrant purple mitotic spindle structure with surrounding blue and green dots representing proteins. A scale bar indicates a size of 5 micrometers, highlighting cellular details essential for understanding cell proliferation.

Despite significant advances in cell biology, the complex processes that regulate and drive cell division are still not fully understood, creating opportunities for discoveries related to the causes and vulnerabilities of highly proliferative diseases such as cancer. 

RNA-protein complexes have emerged as critical regulatory elements in multiple key cellular processes with significant relevance to health and disease, making them attractive targets for research. Our current projects address the pivotal role of RNA and RNA-protein complexes in orchestrating the functional assembly of critical mitotic structures for the error-free completion of cell division. By integrating the RNA component, our approach adds a new level of complexity to the analysis of key events in this fundamental phase of the cell cycle. 

Our approach is characterized by its interdisciplinary and collaborative nature, encompassing a diverse spectrum of methodologies. These include immunoprecipitation to probe protein-protein interactions, UV crosslinking and immunoprecipitation (iCLIP)-based approaches to investigate protein-RNA interactions, high-throughput sequencing and bioinformatic analyses to identify interacting RNA transcripts, and confocal microscopy imaging to localize proteins, RNAs and their interactions. 

In addition to the impact on our basic understanding of cell division, the newly acquired knowledge has great potential to be translated into innovative cancer therapy strategies by targeting yet unexplored cellular functions associated with specific RNA-protein interactions.

Important Concepts

R-DeeP is a database for RNA-dependent proteins. It illustrates a sucrose density gradient analysis showing shifts in control versus RNase samples, including mass spectrometry data. The image highlights the identification of over 500 new RNA-dependent proteins and their experimental validation.

We recently developed the concept of RNA dependence, where we defined a protein as RNA dependent when its interactome depends on the presence of RNA. This concept has been translated into a comprehensive proteome-wide, unbiased and quantitative screening method called R-DeeP.
R-DeeP is based on the fractionation of cellular lysate – with and without prior RNase treatment – by sucrose density gradient ultracentrifugation and subsequent analysis by proteome-wide mass spectrometry or Western blotting of individual proteins.
R-DeeP determines the ability of a protein to form protein complexes exclusively in the presence of RNA by direct or indirect interaction with the RNA molecules. In the R-DeeP screen, we identified a significant enrichment for microtubule-related proteins. This indicates previously unknown potential functional implications of RNA-protein interactions, particularly in the context of cell division.

Check our updated database at R-DeeP3.dkfz.de.

Related publications:

 

Our Projects

Microscopic image showing a densely packed arrangement of cells, with distinct green and blue hues. The green filaments likely represent cellular structures, while the blue areas indicate nuclei. A scale bar shows a measurement of 10 micrometers, providing context for the size of the cells.

RNA-dependent proteins during cell division

We have created an atlas of RNA-dependent proteins (see concept above) which highlights a great number of mitotic factors as unconventional RNA-binding proteins: they seem to bind to RNA in absence of known RNA-binding domains. This suggests an important role for RNA during cell division in multiple parts of the cell division machinery (microtubules, condensed chromosomes, kinetochores, centrosomes etc ...), which we aim to understand. In particular, our projects investigate the role of mitotic unconventional proteins in the context of breast and ovarian cancers using a multidisciplinary approach.

Funding and support:

Related publications:

Our Team

  • Employee image

    Priv. Doz. Dr. Maiwen Caudron-Herger

    Group Leader

  • Employee image

    Dr. Simona Cantarella

    Postdoc

  • Employee image

    Jeanette Simone Seiler

    Technical Assistant

  • Employee image

    Jana Theiß

    Technical Assistant

  • Praarthanaa Jaisankar

    Praarthanaa Jaisankar

    Master Student

  • Employee image

    Jinxin Wang

    Erasmus Student

  • Employee image

    Jamie Kleer

    Student - Molecular Biotechnology - Bachelor Thesis

Team and Picture Gallery

Selected Publications

2025 - Nature Communications 16, 2325
2024 - Nucleic Acids Res. gkae536
2021 - Nucleic Acids Res. 49:D425-436.
2020 - Nature Protocols. 15:1338-1370.
2019 - Mol Cell. 75:184-199.

Our Databases

The image presents data from RBP2GO, highlighting 13 species and 105 RBP datasets. It lists 22,552 RBP candidates and includes sections on Gene Ontology, detailing biological processes, molecular functions, and cellular components. The overall theme relates to research in gene function and interactions.

RBP2GO provides a comprehensive database of RNA-binding or RNA-dependent proteins from all available proteome-wide studies in 13 different species. It includes the annotation of their functions as well as interaction partners - and allows also reverse searches for RNA-binding proteins with specific molecular functions, biological processes, cellular compartments or a known link to cancer. RBP2GO is published in Nucleic Acids Research 2021. A new version of RBP2GO is now available online (RBP2GO-2-beta), which offers information on domains of the proteins and more specifically RNA-binding domains, as published in Nucleic Acids Research 2024.

Further Information

Research and Team Posters

Teaching at Heidelberg University

Three young women stand together, smiling and engaging with a sketch or presentation on a whiteboard. They appear to be collaborating or discussing educational content in a bright, modern classroom environment. One woman wears a sweater with the text “Professional Overthinker.”

Get in touch with us

Employee image

Priv. Doz. Dr. Maiwen Caudron-Herger

Form

Form data is loaded ...