Information
Accession GMS-97-2 

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TitleTranscription-coupled changes in genomic region proximities during transcriptional bursting
Submit date2025-05-13 14:56:15
Last update date2025-05-13 15:14:43
Contact Soya SHINKAI
soya.shinkai AT riken.jp
RIKEN BDR
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Total file size11.38 MB
Keywords PHi-C2 Genome DNA Modeling Mesoscale Brownian dynamics 
Nanog 
 Study
Experiment type PHi-C2
seq-DNA-FISH
Live-cell imaging
Summary The orchestration of our genes heavily relies on coordinated communication between enhancers and promoters, yet the mechanisms behind this dynamic interplay during active transcription remain unclear. Here, we investigated enhancer-promoter (E-P) interactions in relation to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence–fluorescence in situ hybridization analyses. Our data reveal that the active state of specific genes is characterized by specific proximities between different genomic regions and the accumulation of transcriptional regulatory factors. Mathematical simulations suggest that an increase in local viscosity could potentially contribute to stabilizing the duration of these E-P proximities. Our study provides insights into the association among E-P proximity, protein accumulation, and transcriptional dynamics, paving the way for a more nuanced understanding of gene-specific regulatory mechanisms.
Citation(s) Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H. (2024) Transcription-coupled changes in genomic region proximities during transcriptional bursting. Science Advances 10, eadn0020
https://doi.org/10.1126/sciadv.adn0020
 Experiment
OrganismMouse
Cell (Tissue) embryonic stem cell
Protocol
Data processing
 Analysis
[981] Genome dynamics in Nanog active state simulated by PHi-C
 adn0020_movie_s2.mp4 (5.37 MB)  

[980] Genome dynamics in Nanog inactive state simulated by PHi-C
 adn0020_movie_s3.mp4 (6.01 MB)  

 Supplements [download all]
[981] adn0020_movie_s2.mp4 
 Genome dynamics in Nanog active state simulated by PHi-C
 video/mp4 5.37 MB MD5: f64a4b23025080847efcacc015d2129a
[980] adn0020_movie_s3.mp4 
 Genome dynamics in Nanog inactive state simulated by PHi-C
 video/mp4 6.01 MB MD5: 5810d5f9cfcf11fa5945fd3deb9201d4