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Accession GMS-65-6 

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TitleCondensed but liquid-like domain organization of active chromatin regions in living human cells
Submit date2023-08-30 13:41:46
Last update date2023-08-30 13:45:54
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
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Total file size22.41 MB
Keywords live-cell imaging  MSD  Brownian dynamics 
 Study
Experiment type
Single-nucleosome imaging
Brownian dynamics simulation of chromatin
next-generation sequencing
Summary In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. ...... [read more: https://pubmed.ncbi.nlm.nih.gov/37018405/ ]
Citation(s) Nozaki T, Shinkai S, Ide S, Higashi K, Tamura S, Shimazoe MA, Nakagawa M, Suzuki Y, Okada Y, Sasai M, Onami S, Kurokawa K, Iida S, Maeshima K. Condensed but liquid-like domain organization of active chromatin regions in living human cells. Sci Adv. 2023 Apr 5;9(14):eadf1488. doi: 10.1126/sciadv.adf1488. Epub 2023 Apr 5. PMID: 37018405; PMCID: PMC10075990.
https://pubmed.ncbi.nlm.nih.gov/37018405/
 Experiment
OrganismHuman
Cell (Tissue) HeLa
Protocol HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (D5796-500ML; Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) (FB-1061/500; Biosera) at 37°C in 5% CO2. For single-nucleosome imaging, cells were plated onto glass-bottomed dishes (3970-035; Iwaki) treated with poly-l-lysine (P1524-500MG; Sigma-Aldrich). Before microscopy imaging, the medium was replaced with DMEM lacking phenol red (21063-029; Thermo Fisher Scientific) and supplemented with 10% FBS.
Data processing
  • mean square displacement (MSD)
  • fluorescence recovery after photobleaching (FRAP)
  • Complementary DNA (cDNA) libraries were synthesized by the DNA SMART ChIP-seq kit
  • paired-end 2 Ã— 100 bp reads on the Illumina HiSeq and NovaSeq
  • Trimmomatic v0.38, with the parameters “HEADCROP:3 LEADING:20 TRAILING:20 MINLEN:50.” Reads were aligned to the hg19 version of the human reference genome with Bowtie2 using the “--very-sensitive” parameter. From mapped reads, PCR duplicates were discarded using the SAMtools rmdup command. To identify broad regions on the chromosomes significantly enriched for the Cy3-dCTP IP sample against the input sample, we used epic2 software, using the parameters “--false-discovery-rate-cutoff 0.05 --bin-size 1000 --gaps-allowed 10”.
 Analysis
[1] Nucleosomes (blue sphares) in active chromatin regions form condensed domains with local nucleosome contacts and cohesin (rings), where nucleosomes fluctuate. Each interphase chromosome (highlighted as different colors) is stably occupied in the nucleus
 Figure8_220129.jpg (435.77 KB)
[2] Dual-color imaging of two neighbor nucleosomes reveals that nucleosomes in euchromatin form condensed domains with ~150 nm diameter. Nucleosomes locally fluctuate in the condensed domain like a liquid
 Final5_copy.mp4 (2.26 MB)
[3] A computational simulation of chromatin Brownian dynamics
 Supplemental_MovieS10.mp4 (6.43 MB)
[4] A computational simulation of chromatin Brownian dynamics
 Supplemental_MovieS11.mp4 (2.99 MB)
[5] A computational simulation of chromatin Brownian dynamics
 Supplemental_MovieS12.mp4 (4.09 MB)
[6] A computational simulation of chromatin Brownian dynamics (cohesin KO)
 Supplemental_MovieS13.mp4 (1.95 MB)
[7] A computational simulation of chromatin Brownian dynamics
 Supplemental_MovieS8.mp4 (3.05 MB)
[8] A computational simulation of chromatin Brownian dynamics
 Supplemental_MovieS9.mp4 (1.20 MB)
 Supplements
[401] Figure8_220129.jpg 
 Nucleosomes (blue sphares) in active chromatin regions form condensed domains with local nucleosome contacts and cohesin (rings), where nucleosomes fluctuate. Each interphase chromosome (highlighted as different colors) is stably occupied in the nucleus
 image/jpeg 435.77 KB MD5: 053b2108e3f9c0adf2a8edf682075323
[402] Final5_copy.mp4 
 Dual-color imaging of two neighbor nucleosomes reveals that nucleosomes in euchromatin form condensed domains with ~150 nm diameter. Nucleosomes locally fluctuate in the condensed domain like a liquid
 video/mp4 2.26 MB MD5: 97bcbdbc78c7c1009eeb2cfbb68abd0b
[405] Supplemental_MovieS10.mp4 
 A computational simulation of chromatin Brownian dynamics
 video/mp4 6.43 MB MD5: 04a6e955a666d6564553a38c1eb16dde
[407] Supplemental_MovieS11.mp4 
 A computational simulation of chromatin Brownian dynamics
 video/mp4 2.99 MB MD5: cf0f53168da452920b7efdf2ab8af1b8
[408] Supplemental_MovieS12.mp4 
 A computational simulation of chromatin Brownian dynamics
 video/mp4 4.09 MB MD5: 001f70a13666768663a890d0b4128b42
[406] Supplemental_MovieS13.mp4 
 A computational simulation of chromatin Brownian dynamics (cohesin KO)
 video/mp4 1.95 MB MD5: 342cca712d5069d359a325c72e7c14bf
[404] Supplemental_MovieS8.mp4 
 A computational simulation of chromatin Brownian dynamics
 video/mp4 3.05 MB MD5: 64bd0cd610f6e5df3ee50dbc84dd18ce
[403] Supplemental_MovieS9.mp4 
 A computational simulation of chromatin Brownian dynamics
 video/mp4 1.20 MB MD5: 16aa057ef3145220c63ccce9a010624f