NuST

NuST analyzes spatial clustering of contiguous genes across scales to link genome organization, nucleoid protein binding (e.g., Fis and H-NS), and transcriptional regulation.

Key Features:

• Multi-Scale Observation: Performs analysis of gene aggregation at multiple scales to identify spatial clusters of contiguous genes influenced by DNA-bridging nucleoid proteins or by nucleoid perturbations.
• Integration of Diverse Data Sources: Integrates gene expression profiles, protein binding data, and genomic information to enable correlation analyses across datasets.
• Internal Database and External Data Support: Supports analyses using an internal aggregated database and publicly available genomic datasets for comparative investigations.

Scientific Applications:

• Nucleoid protein impact analysis: Dissects roles of DNA-bridging nucleoid proteins Fis and H-NS in shaping contiguous gene clusters sensitive to nucleoid perturbations.
• Macrodomain-associated cluster identification: Identifies significant gene clusters at the edges of the Ter macrodomain and associates them with chromosomal macrodomain structure.
• Functional linkage to motility and biofilm regulation: Associates clusters with genes encoding flagellar and chemotaxis machinery and with key regulators of biofilm formation, informing transitions between motility and biofilm lifestyles.
• H-NS binding and gene silencing studies: Relates regions of high H-NS occupancy to transcriptionally silent DNA, pseudo-gene localization, and horizontal gene transfer.

Methodology:

Performs multi-scale gene aggregation analysis and correlation of gene expression profiles, protein-binding data and genomic information using an internal aggregated database and publicly available genomic datasets.