YAPP

YAPP predicts transcription start sites and promoter regions by integrating CAGE and epigenomic datasets to identify regulatory elements, including promoters and long non-coding RNAs.

Key Features:

• Transcription Start Site Prediction: Utilizes Cap Analysis Gene Expression (CAGE) data to identify putative transcription start sites (TSS) within genomic regions.
• Integration with Epigenomic Data: Incorporates DNase-seq and ChIP-seq datasets to evaluate DNaseI hypersensitivity and the presence of H3K4me3 to predict promoter regions.
• RUNX1 and Hematopoiesis Insights: Identified novel regulatory elements within RUNX1 intron 5, including features at breakpoint regions BCR1, BCR2, and BCR3 associated with DNA double-strand breaks and the t(8;21) translocation.
• Discovery of Novel Long Non-Coding RNAs: Combines CAGE data with expressed sequence tag (EST) evidence to locate a novel long non-coding RNA transcribed from a promoter in the BCR3 region of RUNX1 intron 5.

Scientific Applications:

• Gene Regulation Studies: Maps TSS and promoter locations and identifies associated non-coding RNAs to study gene regulatory mechanisms.
• Cancer Research: Pinpoints regulatory elements within cancer-related genes such as RUNX1 to investigate mechanisms underlying chromosomal translocations (e.g., t(8;21)) and oncogenesis.

Methodology:

Integrates ENCODE and other public DNase-seq, ChIP-seq (including H3K4me3), CAGE, and EST datasets and synthesizes these data to predict promoter regions and identify novel transcriptional elements such as TSS and long non-coding RNAs.