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

Author:

Yamaura Kodai,Takemata NaomichiORCID,Kariya Masashi,Ishino Sonoko,Yamauchi Masataka,Takada Shoji,Ishino Yoshizumi,Atomi Haruyuki

Abstract

SUMMARYStructural 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 ofThermococcus kodakarensisinto TAD-like domains. We also find that TrmBL2, a nucleoid- associated protein that forms a stiff nucleoprotein filament, stalls theT. kodakarensisSMC complex and establishes a boundary at the site-specific recombination sitedif. 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 not only a eukaryotic-like mechanism of domain formation in archaea, but also an unforeseen role of intrinsic DNA structure in large-scale genome organization.

Publisher

Cold Spring Harbor Laboratory

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