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ProteomicsMetalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Removal
Cytotoxicity of DNA-protein crosslinks (DPCs) is ascribed largely to their ability to block the progression of DNA replication fork. DPCs are frequently occurring in cells, either as a consequence of metabolism or exogenous agents. The mechanism of DPCs removal is not completely understood. Here, we...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080743 | MassIVE
ProteomicsA quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood
The interaction between transcription factors and genomic DNA forms the basis for spatio-temporal control of gene expression. Therefore, these interactions and their impact on disease and cellular fate are extensively studied on a global level, mainly using techniques based on next-generation sequen...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-03-01 | MSV000079550 | MassIVE
GenomicsAn ancient protein-DNA interaction underlying metazoan sex determination
An ancient protein-DNA interaction underlying metazoan sex determination
PRJNA272406 | ENA
GenomicsGenome-wide protein–DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
Genome-wide protein–DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
PRJNA823803 | ENA
GenomicsGenome-wide protein-DNA interaction analysis of CceR and AkgR transcription factors
To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulat...
ORGANISM(S): Rhodobacter sphaeroides 
2015-02-02 | E-GEOD-63449 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of Bacillus subtilis to identify Noc protein binding sites
Coordination of chromosome segregation and cytokinesis is crucial for efficient cell proliferation. In Bacillus subtilis the nucleoid occlusion protein Noc protects chromosomes by associating with the chromosome and preventing cell division in its vicinity. Using protein localization, ChAP-on-Chip a...
ORGANISM(S): Bacillus subtilis 
2009-07-01 | E-MEXP-2133 | biostudies-arrayexpress
MetabolomicsMetabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community; Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)

Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or syn...

2020-11-04 | MTBLS1830 | MetaboLights
TranscriptomicsA comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation
Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in yeast to probe how histone acetyltransfera...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-11 | E-GEOD-9771 | biostudies-arrayexpress
GenomicsIntrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks
Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks
PRJNA1151020 | ENA
ProteomicsGlobal profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry
Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quan...
ORGANISM(S): Homo sapiens (Human) 
2018-05-02 | PXD007132 | Pride
Transcription Dna-protein interactions Binding affinity Chromatin 
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