Ubiquitination condensates sculpt genome architecture via non-enzymatic chromatin mechanics

Laura D. Gallego^1*, Frane Miljkovic^1,4*, Maren Schneider^1*, Emma Rusch^2,4*, Justin S. Cha³, Edvinas Stankunas^1,4, Anete Romanauska¹, Yap Shing Nim¹, Anne M. Gardner³, B. Franklin Pugh³, Anton Goloborodko² & Alwin Köhler^1#

¹ Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna and Medical University of Vienna, Austria
² Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
³ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
⁴ Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
^* These authors contributed equally to this work
^# Correspondence: alwin.koehler@maxperutzlabs.ac.at

PMID: XXXXXXXX

GEO ID : GSE305782

Abstract

Biomolecular condensates are emerging as regulators of genome organization, but how their physical properties shape 3D chromatin architecture remains unclear. Non-enzymatic condensates may bridge distal loci, while enzymatic ones modulate histone modifications by locally concentrating reactants. The scaffold protein Lge1 and the E3 ligase Bre1 form layered condensates that promote histone H2B ubiquitination. Here we show that these ubiquitination condensates generate mechanical forces, reshaping gene body topology in relation to promoter and terminator regions, independently of histone H2B ubiquitination. Single-molecule biophysics reveals that the CoRE (Condensate Regulatory Element) of Lge1 governs DNA entry into condensates and mechanical force generation in vitro. Micro-C shows that CoRE residues are required to maintain gene body architecture in vivo, coupling condensate mechanics to specific transcriptional outcomes and cellular fitness. Our findings define a mechanical role for enzymatic condensates that is separable yet synergistic with their catalytic function, leaving a fine-scaled mechanical imprint on the genome.

Table of Contents

data

Stores BAM, BigWig, Fastq, BED, and Occupancy composite files.

bin

Stores scripts and executables that are not run directly but called by other scripts. In order to run other scripts, you must download the scriptmanager container to this folder.

00_Download_and_Preprocessing

To download data and calculate normalization factors:

cd 00_Download_and_Preprocessing
./1_download_data.sh
sbatch 3_calculate_scaling_factors.slurm

01_Bulk_Processing

To process data:

cd 01_Bulk_Processing
sbatch bulk_tagpileup.slurm
sbatch igg_tagpileup.slurm

create_supplementary_data_table.ipynb contains the code for creating Supplementary_table_1.xlsx