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| Status |
Public on Dec 15, 2024 |
| Title |
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [3C-seq] |
| Organisms |
Thermoplasma acidophilum; Thermococcus kodakarensis |
| Experiment type |
Other
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| Summary |
Structural maintenance of chromosomes (SMC) complexes fold genomes by extruding DNA loops. In eukaryotes, loop-extruding SMC complexes form topologically associating domains (TADs) by being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We also find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with shape properties of underlying DNA sequences. Our study illuminates not only a eukaryotic-like mechanism of domain formation in archaea, but also an unforeseen role of intrinsic DNA shape in large-scale genome organization.
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| Overall design |
To investigate archaeal 3D genomes, 3C-seq was applied to Thermococcus kodakarensis and Thermoplasma acidophilum.
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| Contributor(s) |
Yamaura K, Takemata N, Kariya M, Osaka A, Ishino S, Yamauchi M, Tamura T, Hamachi I, Takada S, Ishino Y, Atomi H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 13, 2024 |
| Last update date |
Dec 16, 2024 |
| Contact name |
Naomichi Takemata |
| Organization name |
Kyoto University
|
| Department |
Synthetic Chemistry and Biological Chemistry
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| Street address |
Kyoto University, Katsura, Nishikyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
615-8510 |
| Country |
Japan |
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| Platforms (4)
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| GPL28196 |
Illumina NovaSeq 6000 (Thermococcus kodakarensis) |
| GPL34466 |
NextSeq 550 (Thermococcus kodakarensis) |
| GPL34467 |
HiSeq X Ten (Thermoplasma acidophilum) |
| GPL34468 |
NextSeq 550 (Thermoplasma acidophilum) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA1111014 |
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