RAMPAGE

RAMPAGE profiles genome-wide polymerase III-transcribed Alu elements and integrates matching RNA-seq and epigenomic datasets to identify, quantify, and characterize their expression and potential regulatory roles.

Key Features:

• High-Resolution Data Generation: Generates high-resolution, long-span RAMPAGE genomic data across multiple biosamples to capture polymerase III transcription at Alu elements.
• Integration with RNA-seq Data: Incorporates matching RNA sequencing (RNA-seq) data from 155 biosamples to improve identification and quantification of expressed Alu elements.
• Comprehensive Atlas Creation: Builds an atlas comprising 17,249 polymerase III-transcribed Alu elements to map expression patterns across cell types.
• Multifaceted Integrative Analysis: Integrates ChIP-seq data for ten histone marks, ChIP-seq for hundreds of transcription factors, whole-genome bisulfite sequencing (WGBS) data, ChIA-PET data, and other functional genomic datasets across multiple biosamples.
• Cell-Type-Specific Enhancer Function Identification: Identifies that older, expressed Alu elements can act as cell-type-specific enhancers for nearby protein-coding genes while human-specific Alu elements remain transcriptionally repressed.

Scientific Applications:

• Expression Profiling: Identification and quantification of polymerase III-transcribed Alu elements across diverse biosamples.
• Regulatory Element Discovery: Detection of Alu-derived sequences that function as cell-type-specific enhancers for nearby protein-coding genes.
• Epigenomic Contextualization: Correlation of Alu transcription with histone modification patterns, transcription factor binding, DNA methylation (WGBS), and chromatin interactions (ChIA-PET).
• Repetitive Element-Gene Interaction Studies: Elucidation of interactions between repetitive Alu elements and gene expression regulation across different cell types.

Methodology:

Uses a pipeline to identify expressed Alu elements from high-resolution RAMPAGE data coupled with matching RNA-seq, and integrates diverse epigenomic datasets for contextual analysis.