Methods in molecular biology, Год журнала: 2024, Номер unknown, С. 157 - 176
Опубликована: Сен. 16, 2024
Язык: Английский
Cell, Год журнала: 2024, Номер 187(23), С. 6424 - 6450
Опубликована: Ноя. 1, 2024
Every cell must solve the problem of how to fold its genome. We describe folded state chromosomes is result combined activity multiple conserved mechanisms. Homotypic affinity-driven interactions lead spatial partitioning active and inactive loci. Molecular motors through loop extrusion. Topological features such as supercoiling entanglements contribute chromosome folding dynamics, tethering loci sub-nuclear structures adds additional constraints. Dramatically diverse conformations observed throughout cycle across tree life can be explained differential regulation implementation these basic propose that first functions are mediate genome replication, compaction, segregation mechanisms have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, types, species.
Язык: Английский
Процитировано
10
Molecular Microbiology, Год журнала: 2025, Номер 123(2), С. 89 - 100
Опубликована: Фев. 1, 2025
In September 2023, the Biology and Physics of Prokaryotic Chromosomes meeting ran at Lorentz Center in Leiden, The Netherlands. As part workshop, those attendance developed a series discussion points centered around current challenges for field, how these might be addressed, field is likely to develop over next 10 years. staff facilitated discussions via tools aimed optimizing productive interactions. This Perspective article summary reflects state-of-the-art field. It expected help colleagues advancing their own research related prokaryotic chromosomes inspiring novel interdisciplinary collaborations. forward-looking perspective highlights open questions driving builds on impressive recent progress areas as represented by accompanying reviews, perspectives, articles this issue. These underline multi-disciplinary nature multiple length scales which chromatin studied vitro highlight differences similarities bacterial archaeal chromatin-associated processes.
Язык: Английский
Процитировано
1
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Фев. 19, 2025
In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled roadblock proteins. It remains unclear whether a similar mechanism domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog the bacterial Smc-ScpAB complex organizes genome Thermococcus kodakarensis into TAD-like domains. We find TrmBL2, nucleoid-associated protein forms stiff nucleoprotein filament, stalls T. SMC establishes boundary at site-specific recombination site dif. TrmBL2 tens additional non-boundary loci with lower efficiency. Intriguingly, stalling efficiency is correlated properties underlying sequences. Our study illuminates eukaryotic-like archaea role intrinsic structure large-scale organization. Eukaryotic are organized arrays compact structures called TADs. Here authors member Archaea, prokaryotic closest to Eukarya, uses chromosomal formation.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Май 14, 2024
SUMMARY Structural maintenance of chromosomes (SMC) complexes fold genomes by extruding DNA loops. In eukaryotes, loop-extruding SMC form topologically associating domains (TADs) being stalled roadblock proteins. It remains unclear whether a similar mechanism domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog the bacterial Smc-ScpAB complex organizes genome Thermococcus kodakarensis into TAD-like domains. We also find TrmBL2, nucleoid- associated protein forms stiff nucleoprotein filament, stalls T. and establishes boundary at site-specific recombination site dif . TrmBL2 tens additional non-boundary loci with lower efficiency. Intriguingly, stalling efficiency is correlated structural properties underlying sequences. Our study illuminates not only eukaryotic-like archaea, but unforeseen role intrinsic structure large-scale organization.
Язык: Английский
Процитировано
1
Methods in molecular biology, Год журнала: 2024, Номер unknown, С. 157 - 176
Опубликована: Сен. 16, 2024
Язык: Английский
Процитировано
0