Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [3C-seq]

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. To investigate archaeal 3D genomes, 3C-seq was applied to Thermococcus kodakarensis and Thermoplasma acidophilum.

染色体结构维持（Structural maintenance of chromosomes, SMC）复合物通过挤压DNA环来折叠基因组。在真核生物中，环挤压型SMC复合物可被阻滞蛋白（roadblock proteins）停滞，从而形成拓扑关联结构域（topologically associating domains, TADs）。目前尚不明确原核生物中是否存在类似的结构域形成机制。
本研究借助高分辨率染色体构象捕获测序（3C-seq）证实，细菌Smc-ScpAB复合物的古菌同源物可将柯达热球菌（Thermococcus kodakarensis）的基因组组装为类TAD结构域。研究同时发现，类核结合蛋白（nucleoid-associated protein）TrmBL2可形成刚性核蛋白丝，能够停滞柯达热球菌的SMC复合物，并在位点特异性重组位点dif处建立边界。此外，TrmBL2还可在数十个其他非边界位点以较低效率阻滞SMC复合物。有趣的是，这种阻滞效率与对应DNA序列的固有形状特性存在相关性。本研究不仅揭示了古菌中类似真核生物的结构域形成机制，还发现了DNA固有形状在大规模基因组组织中此前未被预见的作用。
为研究古菌三维基因组，本研究对柯达热球菌（Thermococcus kodakarensis）和嗜酸热原体（Thermoplasma acidophilum）应用了3C-seq技术。