DNA-loop extruding SMC complexes can traverse one another in vivo
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA649231 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12339409_1.fastq.gz | Fastqsanger.gz | |||
| SRR12339409_2.fastq.gz | Fastqsanger.gz | |||
| SRR12339410_1.fastq.gz | Fastqsanger.gz | |||
| SRR12339410_2.fastq.gz | Fastqsanger.gz | |||
| SRR12339411_1.fastq.gz | Fastqsanger.gz |
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Project description:Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.
2021-06-10 | GSE155279 | GEO
Project description:Chromosome organization mediated by structural maintenance of chromosomes (SMC) complexes is vital in many organisms. SMC complexes act as motors that extrude DNA loops, but it remains unclear what happens when multiple complexes encounter one another on the same DNA in living cells and how these interactions may help to organize an active genome. We therefore created a crash-course track system to study SMC complex encounters in vivo by engineering defined SMC loading sites in the Bacillus subtilis chromosome. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of chromosome folding patterns. Through three-dimensional polymer simulations and theory, we determine that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to avoid traffic jams while spatially organizing the genome.
| S-EPMC8878250 | biostudies-literature
Project description:Mammalian genomes are folded by the distinct actions of SMC complexes which include the chromatin loop-extruding cohesin, the sister-chromatid cohesive cohesin, and the mitotic chromosome-associated condensins 1-3. While these complexes function at different stages of the cell cycle, they co-exist on chromatin during the G2/M-phase transition, when genome structure undergoes a dramatic reorganization 1,2. Yet, how distinct SMC complexes affect each other and how their mutual interplay orchestrates the dynamic folding of 3D genome remains elusive. Here, we engineered all possible cohesin/condensin configurations on mitotic chromosomes to delineate the concerted, mutually influential action of SMC complexes. We find that: (i) Condensin disrupts extrusive-cohesin binding at CTCF sites, thereby promoting the disassembly of interphase TADs and loops during mitotic progression. Conversely, extrusive-cohesin impedes condensin mediated mitotic chromosome spiralization. (ii) Condensin diminishes cohesive-cohesin peaks and, conversely, cohesive-cohesin antagonizes condensin-mediated mitotic chromosome longitudinal shortening. Co-presence of extrusive- and cohesive-cohesin synergizes these effects and dramatically inhibits mitotic chromosome condensation. (iii) Extrusive-cohesin positions cohesive-cohesin at CTCF binding sites. However, cohesive-cohesin by itself cannot be arrested by CTCF molecules, is insufficient to establish TADs or loops and lacks loop extrusion capacity, implying non-overlapping function with extrusive-cohesin. (iv) Cohesive-cohesin restricts extrusive-cohesin mediated chromatin loop expansion. Collectively, our data describe a comprehensive three-way interplay among major SMC complexes that dynamically sculpts chromatin architecture during cell cycle progression.
2024-12-21 | GSE269952 | GEO
Project description:Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops. How collisions between SMC complexes and DNA polymerases are resolved in vivo remains poorly understood. Taking advantage of the ability to load SMC complexes at defined sites in the Bacillus subtilis genome, we investigated this problem. We engineered head-on and head-to-tail collisions between SMC complexes and the replisome, and monitored SMC translocation by time-resolved ChIP-seq and Hi-C and replisome progression by marker frequency analysis. We report that SMC complexes do not affect replication progression. By contrast, the replisome blocks SMC translocation regardless of collision orientation. Combining experimental data with simulations, we determined that SMC is first blocked by the replisome and then released from the chromosome. However, occasionally SMC can bypass the replisome and continue translocating. Our findings establish that the replisome is a barrier to SMC-mediated DNA-loop extrusion, with implications for chromosome organization in all organisms.
2025-07-07 | GSE282455 | GEO
Project description: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.
2024-12-15 | GSE267297 | GEO
Project description: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.
2024-12-15 | GSE267299 | GEO
Project description: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.
2024-12-15 | GSE267298 | GEO
Project description:DNA loop-extruding SMC complexes play vital roles in genome maintenance and DNA immunity. However, the ability of these ring-shaped DNA motors to navigate large DNA-bound obstacles, such as DNA/RNA polymerases and ribosomes in prokaryotes, has remained unclear. Here, we demonstrate that a bacterial SMC Wadjet complex can efficiently bypass obstacles larger than the SMC coiled coil lumen if they are linked to the extruded DNA by single-stranded DNA (ssDNA). This process is mediated by the selective entrapment of the ssDNA linker within the SMC hinge channel, which acts as an obligate gate—permitting ssDNA passage while excluding double-stranded DNA (dsDNA). By threading the linker through the hinge gate as dsDNA is translocated through the SMC motor, the obstacle can follow a trajectory distinct from its associated dsDNA, remaining outside the SMC ring. This mechanism enables continuous dsDNA entrapment while successfully bypassing obstacles. We show that hinges of diverse SMC complexes including eukaryotic condensin and Smc5/6 also selectively accommodate ssDNA, suggesting that hinge bypass is a conserved feature across SMC proteins. We demonstrate that while the hinge domain is essential for obstacle bypass, it is dispensable for loop extrusion, showing that these functions are independent, provided by separate SMC modules. These findings uncover the long-sought function of the SMC hinge toroid and provide the first mechanistic explanation for how DNA-entrapping SMC complexes can extrude loops on chromosomal DNA densely populated with obstacles. Integrating hinge bypass into the DNA loop extrusion model, we propose that the hinge may also facilitate the passage of RNA and peptide, enabling bypass of transcription-associated ribonucleoprotein complexes and other SMC complexes.
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Project description:Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large family of proteins, nucleoid-associated proteins (NAPs) and the SMC complexes, play important roles organizing the genome. NAPs are abundant DNA-binding proteins that can bend, wrap, bridge and compact DNA, while SMC complexes load on the chromosome, translocate on the DNA, and extrude DNA loops. How SMC loop extrusion is influenced by various NAPs remains unknown. In this study, we expressed a collection of representative prokaryotic chromosome-associated proteins in Bacillus subtilis, which introduce distinct DNA structures and pose different challenges for SMC loop extrusion. By fluorescence microscopy and chromatin immunoprecipitation experiments, we observed that these proteins bound to the genome in characteristic manners. Through genome-wide chromosome conformation capture assays, we found that the SMC complex can traverse these DNA-binding proteins without slowing down. Our findings reveal that the DNA loop extrusion activity of the SMC complex is unaffected by the chromosome-associated proteins and highlight the robustness of SMC motors on the busy chromatin.
2025-01-17 | GSE269767 | GEO
Project description:Bacillus subtilis SMC complexes are topologically loaded at centromeric sites adjacent to the replication origin by the partitioning protein ParB. These ring-shaped ATPases then translocate down the left and right chromosome arms while tethering them together. Here we show that the site-specific recombinase XerD that resolves chromosome dimers is required to unload SMC tethers when they reach the terminus. We identify XerD-specific binding sites in the terminus region and show that they dictate the site of unloading in a manner that depends on XerD but not its catalytic residue, its partner protein XerC, or the recombination site dif. Finally, we provide evidence that ParB and XerD homologs perform similar functions in Staphylococcus aureus. Thus, loading and unloading of SMC complexes are mediated by two broadly conserved factors: one involved in origin segregation, the other in terminus resolution. Similar site-specific unloading activities could modulate eukaryotic SMC complexes during interphase and mitosis.
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