Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA1111014 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR29007343_1.fastq.gz	Fastqsanger.gz
	SRR29007343_2.fastq.gz	Fastqsanger.gz
	SRR29007345_1.fastq.gz	Fastqsanger.gz
	SRR29007345_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 29

Similar Datasets

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

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

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

2024-12-15 | GSE267299 | GEO

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

2024-12-15 | GSE267298 | GEO

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

Project description:Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [RNA-seq]

| PRJNA1111018 | ENA

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

Project description:Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [ChIP-seq]

| PRJNA1111013 | ENA

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

Project description: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.

| S-EPMC11840125 | biostudies-literature

Multi-scale architecture of archaeal chromosomes

Project description:Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. Here, we reveal that chromosomes of Sulfolobus archaea are organized into CID-like topological domains in addition to the larger A/B compartment-type structures that we described recently. We uncover local rules governing the identity of the topological domains. We also identify long-range loop structures which provide evidence of a hub-like structure that colocalizes genes involved in ribosome biogenesis. In addition to providing high resolution description of archaeal chromosome architectures, our data provide evidence for multiple modes of organization in prokaryotic chromosomes and yield novel insight into the evolution of eukaryotic chromosome conformation.

2020-12-28 | GSE159537 | GEO

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

Project description:In this work, we performed DNA affinity purification of proteins that bind to biotinylated DNA probe, denoted as difL and difR. The enriched proteins were subjected to SDS-PAGE, in-gel tryptic digestion, followed by LC-MSMS.

2024-12-16 | PXD053073 | JPOST Repository

Salmonella sp. 3C strain:3C

Project description:Salmonella sp. 3C strain:3C Genome sequencing

| PRJNA882226 | ENA

Verrucomicrobium sp. 3C strain:3C

Project description:Verrucomicrobium sp. 3C strain:3C Genome sequencing and assembly

| PRJNA165235 | ENA