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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
MetabolomicsAntioxidant Activity, Phytochemical Profiling by UPLC-QTOF-MS, and In Silico Targeting of the RNA-Binding Protein DRBD18 of Trypanosoma brucei by Bioactive Compounds from Tetradenia riparia and Tetracera poggei
Oxidative stress plays a key role in the pathogenesis of African trypanosomiasis, and plant-derived antioxidants represent a promising source of dual-action compounds capable of both scavenging reactive oxygen species and interfering with parasite survival. The present study investigates the antioxi...
2026-09-10 | MTBLS15597 | MetaboLights
TranscriptomicsQuantitative modeling of transcription factor binding specificities using DNA shape
Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a ...
ORGANISM(S): Homo sapiens 
2014-11-04 | E-GEOD-59845 | biostudies-arrayexpress
MetabolomicsThe Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition

Summary

Primary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS...

2022-02-18 | MTBLS4013 | MetaboLights
ProteomicsProteome analysis of i-motif DNA binding proteins
Non-canonical DNA structures such as G-quadruplex (G4) and i-motif (iM) are formed at the guanine- and cytosine-rich sequences, respectively, and prohibit DNA replication and transcription. The formation and resolution of these non-canonical structures are therefore required to be dynamically regula...
ORGANISM(S): Homo Sapiens (human) 
2024-10-15 | PXD051188 | JPOST Repository
GenomicsMultiplexed identification of the genomic targets of DNA-binding proteins
Transcription factors direct gene expression, and so there is much interest in mapping their genome-wide binding locations. M-BM- Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target g...
ORGANISM(S): Saccharomyces cerevisiae 
2011-02-18 | E-GEOD-27381 | biostudies-arrayexpress
TranscriptomicsVariation in homeodomain DNA-binding revealed by high-resolution analysis of sequence preferences
Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, re...
ORGANISM(S): Mus musculus 
2010-06-26 | E-GEOD-11239 | biostudies-arrayexpress
ProteomicsDNA binding reorganizes the intrinsically disordered C-terminal region of PSC in Drosophila PRC1
Polycomb Group (PcG) proteins regulate gene expression by modifying chromatin. A key PcG complex, PRC1, has two activities: a ubiquitin ligase activity for histone H2A, and a chromatin compacting/nucleosome bridging activity that can inhibit transcription and chromatin remodeling. In Drosophila, the...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2020-05-15 | MSV000085418 | MassIVE
GenomicsProtein/DNA in vitro Binding seq (PB-seq) for Drosophila HSF and genomic Drosophila DNA
DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding and high-throughput sequencing (PB-seq), that allows the binding energy landsca...
ORGANISM(S): Drosophila melanogaster 
2012-02-06 | E-GEOD-32570 | biostudies-arrayexpress
MetabolomicsATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly

The ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary ro...

2022-01-14 | MTBLS3786 | MetaboLights
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