Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt

Project description

The project aims to address the evolutionary dynamics of the different sub-compartments of the nucleus of eukaryotic cells and reveal how they relate to genome function. The compartmentalization of the nucleus into functional condensates, so-called membraneless organelles (MLOs), contributes to transcriptional regulation. Some MLOs form by liquid-liquid phase separation in the cytoplasm and nucleoplasm of eukaryotic cells and have been tightly linked to different aspects of RNA biogenesis and metabolism. Homeostatic changes in MLOs occur during differentiation, and are also associated with diseases, including cancers and viral infections. In the nucleus, the most prominent MLOs are nucleoli, which are sites dedicated to the transcription of ribosomal RNA. Other nuclear MLOs include: 1) Cajal bodies (CBs) that are small compartments forming on active loci of small nuclear (sn)RNA transcription, typically observed in cells with high transcriptional and splicing demands, 2) nuclear speckles (NSs), which interact with active genes and represent hubs for pre-mRNA synthesis and metabolism, 3) paraspeckles, compartments involved in the regulation of gene expression, and 4) PML (promyelocytic leukemia) nuclear bodies (PML-NBs), which play a role in SUMOylation and interact with chromatin, transcriptional regulators, and proteins involved in DNA damage response and apoptosis. PML-NBs are also thought to function as hubs for protein modification in the nucleus, and to control the rate of cell cycle progression. Recent evidence suggests that different MLOs share homeostatic regulators, however their functional and evolutionary links remain poorly understood. This project comprises of three parts: P1) to reconstruct the shared evolutionary history of the core protein and non-coding RNA components of the different nuclear MLOs, using phylogenetic, structural bioinformatics and molecular evolution tools (Marsh lab). P2) to reveal how MLO evolution relates to changes in functional aspects of the genome (Battich lab). For example, to compare the evolution of the core components with 1) the evolution of non-coding RNA gene families, 2) properties of gene expression regulation, such as the distance between transcription starts sites and enhancers, 3) the signatures of 3D architecture derived from published Hi-C contact maps from different metazoan and related unicellular species, and 4) gene expression complexity in single cells from different metazoan species. P3) to test various hypotheses derived from P1 and P2,e.g., by reconstructing of ancestral proteins sequences (Marsh lab) and experimentally testing their impact on genomic functions using state-of-the-art -omics measurements, such as time-resolved single-cell RNA-seq and Hi-C or SPRITE (Battich lab).

Relevant literature

Berchtold D, Battich N, Pelkmans L, 2018, A systems-level study reveals regulators of membrane-less organelles in human cells, Molecular Cell, 72, 6, 1035-1049.e5

Battich N, Beumer J, de Barbanson B, Krenning L, Chloé B, Tanenbaum M, Clevers H, van Oudenaarden A, 2020, Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies, Science, 367, 6482, 1151-1156

Ilik İA, Malszycki M, Lübke AK, Schade C, Meierhofer D, Aktaş T, 2020, ON and SRRM2 are essential for nuclear speckle formation, eLife, 9, e60579

Hirose T, Ninomiya K, Nakagawa S, Yamazaki T, 2022, A guide to membraneless organelles and their various roles in gene regulation, Nat Rev Mol Cell Biol, online ahead of print.

Badonyi M, Marsh JA, 2022, Large protein complex interfaces have evolved to promote cotranslational assembly, eLife, 10, e79602