Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CLMS analysis of fission yeast condensin-DNA samples

ABSTRACT: Crosslinking-MS analysis of sulfo-SDA crosslinked fission yeast condensin-DNA samples in the initial binding state (absence of nucleotide) and in the DNA gripping state (in the presence of ADP•BeF3)

ORGANISM(S): Schizosaccharomyces Pombe (fission Yeast)

SUBMITTER: Juri Rappsilber

PROVIDER: PXD041027 | JPOST Repository | Fri Sep 08 00:00:00 BST 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	B221026_08_Lumos_ZC_CO_140_condensin_Bind_SECf6-1.raw	Raw
	B221026_09_Lumos_ZC_CO_140_condensin_Bind_SECf6-2.raw	Raw
	B221026_10_Lumos_ZC_CO_140_condensin_Bind_SECf7-1.raw	Raw
	B221026_11_Lumos_ZC_CO_140_condensin_Bind_SECf7-2.raw	Raw
	B221026_13_Lumos_ZC_CO_140_condensin_Bind_SECf8-1.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Crosslinking/mass spectrometry analysis of Human Separase-Scc1-fusion and cohesin SMC1/SMC3 complexes

Project description:In this study, we employed the photoactivatable crosslinker (sulfo-SDA) to investigate protein-protein interaction between human Separase-Scc1 fusion protein and SMC1/SMC3 cohesin subunits complex in the presence of DNA.

2025-08-28 | PXD061667 | Pride

Genome-wide maps of deaminated CPDs (dCPDs) in yeast genomic DNA in vitro

Project description:Here, we describe a genome-wide map of uracil lesions arising form deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae) genomic DNA that were UV-irradiated and deaminated as naked DNA in vitro. Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method. We used these data to analyze CPD deamination in different trinucleotide sequence contexts.

2025-10-01 | GSE284778 | GEO

Mpe1 senses the polyadenylation signal in pre-mRNA to promote efficient cleavage and control polyadenylation

Project description:Crosslinking mass spectrometry dataset of the Mpe1 and Cft2 bound to the yeast CPF polymerase module. Sulfo-SDA is the crosslinker used.

2023-01-12 | PXD027482 | JPOST Repository

Mapping mitochondrial DNA recombination in yeast

Project description:Mapping mitochondrial DNA recombination in yeast

| PRJEB6084 | ENA

Time-series DNA occupancy during the yeast respiratory cycle

Project description:We use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track the global patterns with respect to the metabolic state of the culture, showing a genome-wide nucleosome focusing in the reductive phase, followed by clearance of the promoter regions

2014-08-06 | GSE60112 | GEO

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses

Project description:crosslinking mass spectrometry results for sulfo-SDA crosslinking of human CUL4-NEDD8/ROC1/DDB1/DCAF1-CtD in complex with SAMHD1 and Vpr protein from simian immunodeficiency virus infecting Cercopithecus cephus (SIVmus Vpr)

2021-07-20 | PXD020453 | Pride

Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution

Project description:Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.

2022-02-23 | PXD025287 | Pride

Nucleotide resolution mapping of Spo11-linked DNA breaks in the yeast genome

Project description:DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes - and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast, and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy enables us to reveal the influence primary DNA sequence has upon Top2 cleavage - distinguishing canonical DNA double-strand breaks (DSBs) from a major population of DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

2019-09-28 | GSE137685 | GEO

Nucleotide resolution mapping of Top2-linked DNA breaks in the yeast genome

Project description:DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo. This data set contains maps of Top2 CCs in the S. cerevisiae genome, generated by CC-seq of BY4741 cells -/+ etoposide (VP16).

2019-09-28 | GSE136675 | GEO

Genomic DNA sequencing of budding yeast strains

Project description:Genomic DNA sequencing of budding yeast strains

| PRJNA470814 | ENA