Biophysics Seminar- “Effects of DNA sequence on DNA-intrinsically disordered protein coacervation” with Hashini Ekanayake Mudiyanselage (UIC Chemistry) and “Spatial organization of regulatory chromatin at transcription condensates” with Ganesh Pandey (UIC Physics)
Biophysics Seminar
March 14, 2025
2:00 PM - 3:00 PM
Location
SES 2214
Calendar
Download iCal File"Effects of DNA sequence on DNA-intrinsically disordered protein coacervation"
Hashini Ekanayake Mudiyanselage
Zhou Lab, Department of Chemistry
Protein-DNA condensates mediate transcription and regulate gene expression and DNA replication and repair. Previous studies have shown that the coacervation of intrinsically disordered proteins (IDPs) with double-stranded DNA (dsDNA) leads to solid aggregates but that with single-stranded DNA (ssDNA) leads to liquid droplets [1-3]. Moreover, the addition of ssDNA turns IDP-dsDNA aggregates into droplets [3]. The effects of IDP sequences on phase separation have been extensively studied, but the effects of ssDNA sequences are rarely studied. In this work, we study the coacervation of the IDP protamine with ssDNA that have sequences containing self-complementary segments. Self-dimerization of such DNA sequences produces a dsDNA segment with single-stranded overhangs. With increasing lengths of overhangs, protamine-ssDNA coacervates transition from aggregates to droplets. Optical tweezers-directed measurements show that the fusion speed of protamine-ssDNA droplets decreases with increasing lengths of overhangs. Our findings demonstrate that ssDNA sequence controls both the material states and the material properties of IDP-ssDNA coacervates.
1. Vieregg, J. R., et al. J Am Chem Soc 140, 1632-1638 (2018).
2. Shakya, A., King, J. T. Biophys J 115, 1840-1847 (2018).
3. V. Ahlawat, H. E. Mudiyanselage, and H.-X. Zhou (2025). bioRxiv
"Spatial organization of regulatory chromatin at transcription condensates"
Ganesh Pandey
Spille Lab, Department of Physics
Transcription condensates compartmentalize important components of the transcription machinery, such as the Mediator complex, the coactivator Brd4, and RNA Polymerase II (Pol II). Inhibition of Brd4 binding to the active chromatin mark H3K27ac results in the dissolution of condensates. This suggests that active enhancer and promoter regions link transcription condensates to chromatin. But there are thousands of active chromatin regulatory elements in a cell whereas only a few condensates can be detected in a single cell nucleus. It remains unclear what sets apart chromatin structures at condensates and how condensates interact with chromatin structures. We use multicolor single-molecule localization microscopy to uncover how the active chromatin marks H3K27ac, H3K4me1, and H3K4me3 interact with transcription condensates. Our data reveal that active chromatin partitions into transcription condensates. Active promoter marks (H3K27ac, H3K4me3) are enriched towards the core of condensates while enhancer marks (H3K27ac, H3K4me1) are more likely localized to the surface. In contrast, inactive chromatin marks (H3K27me3) are depleted from transcription condensates. Furthermore, we find that several nanoclusters of active chromatin marks are associated with single condensates. This suggests that multiple active regulatory elements interact with condensates simultaneously. An analysis of functional states of Pol II corroborates these chromatin-level results. We find that the initiating phospho-isoform (Ser5p-Pol II) is highly enriched towards the core of condensates where we found the strongest promoter marks. The elongating phospho-isoform (Ser2p-Pol II) is detected in multiple distinct nanoclusters at each condensate, giving additional support for our interpretation that there are multiple simultaneously transcribed elements associated with each condensate. Our results shed new light on the organization of active chromatin at transcription condensates and their functional role in the coexpression of multiple genes.
Date posted
Jan 15, 2025
Date updated
Mar 11, 2025