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<p>In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and 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 <i>Thermococcus kodakarensis</i> into TAD-like domains. We find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the <i>T. kodakarensis</i> SMC complex and establishes a boundary at the site-specific recombination site <i>dif</i>. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.</p>

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Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年2月19日

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  • Kodai Yamaura,
  • Naomichi Takemata,
  • Masashi Kariya,
  • Ayami Osaka,
  • Sonoko Ishino,
  • Masataka Yamauchi,
  • Tomonori Tamura,
  • Itaru Hamachi,
  • Shoji Takada,
  • Yoshizumi Ishino,
  • Haruyuki Atomi

摘要

In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and 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 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 structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.