YPA

YPA integrates diverse promoter features for Saccharomyces cerevisiae to enable analysis of transcriptional regulation.

Key Features:

• Promoter Sequences: Detailed sequences of promoters upstream of genes are cataloged.
• Transcription Boundaries and Start Sites (TSSs): Precise transcription start site locations and transcription boundaries are provided.
• Untranslated Regions (UTRs): Both 5'-UTRs and 3'-UTRs are included to capture post-transcriptional regulatory elements.
• TATA Boxes: Core promoter TATA box elements are annotated.
• Transcription Factor Binding Sites (TFBSs): Predicted TFBSs are integrated into promoter annotations.
• Nucleosome Occupancy: Nucleosome positioning information is provided to assess chromatin accessibility.
• DNA Bendability: DNA bendability metrics are included to reflect local DNA flexibility.
• Transcription Factor Binding: Data on actual transcription factor binding events are incorporated.
• TF Knockout Expression: Gene expression changes from transcription factor knockouts are recorded.
• TF-TF Physical Interaction: Information on physical interactions between transcription factors is available.

Scientific Applications:

• Transcriptional regulation analysis: Integrating promoter features supports investigation of mechanisms controlling gene expression.
• Identification of functional TFBSs: Combining TFBS and TF binding data with nucleosome occupancy and DNA bendability reveals sites likely to be accessible and functional.
• Effect of TF knockouts: TF knockout expression data enable assessment of transcription factor contributions to downstream gene expression.
• Regulatory network structure: TF-TF physical interaction data support analysis of combinatorial regulatory complexes and network topology.

Methodology:

YPA integrates diverse promoter features and presents them in a unified manner; specifically, it combines nucleosome occupancy and DNA bendability with TFBS and TF binding data to identify functionally accessible binding sites.