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Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor
(BioMed Central, 2014-01)
Background: Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread ...
Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group a streptococcus
(Wiley, 2020)
Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram-positive bacteria. Most functional assessments of CcpA, including ...
ChIP-seq reveals a role for CrzA in the Aspergillus fumigatus high-osmolarity glycerol response (HOG) signalling pathway
(Wiley-Blackwell, 2014-11-01)
Aspergillus fumigatus is an opportunistic pathogen and allergen of mammals. Calcium signalling is essential for A. fumigatus pathogenicity and is regulated by the CrzA transcription factor. We used ChIP-seq (Chromatin ...
Creating 2D occupancy plots using plot2DO
(Springer, 2020)
Chromatin organization and epigenetic marks play a critical role in stem cell pluripotency and differentiation. Chromatin digestion by micrococcal nuclease (MNase) followed by high-throughput sequencing (MNase-seq) is the ...
ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network
(Oxford University Press, 2017-03)
LuxR-type transcription factors control diverse physiological functions necessary for bacterial adaptation to environmental changes. In the intracellular pathogen Brucella, the LuxR homolog VjbR has been shown to regulate ...
The SEB-1 transcription factor binds to the STRE motif in Neurospora crassa and regulates a variety of cellular processes including the stress response and reserve carbohydrate metabolism
(2016-05-01)
When exposed to stress conditions, all cells induce mechanisms resulting in an attempt to adapt to stress that involve proteins which, once activated, trigger cell responses by modulating specific signaling pathways. In ...
A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and PremRNA Processing
(Public Library Of Science, 2015-07)
High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory ...