MEA

MEA performs genome-wide allele-specific analysis of DNA methylation (DNAme) and histone modifications to map allelic epigenetic regulation at SNV- and INDEL-resolved loci.

Key Features:

• Allele-Specific Analysis: Incorporates single nucleotide variants (SNVs) and insertions/deletions (INDELs) to analyze allele-specific transcriptional regulation and epigenetic marks.
• INDEL-aware Low Reference Bias: Uses INDEL-aware algorithms to reduce systematic reference bias and improve allelic mapping of DNA methylation.
• Integration of Epigenomic Datasets: Integrates DNAme with RNA-seq and ChIP-seq data to relate transcriptional activity to epigenetic modifications.
• Allele-specific Detection of Histone Marks: Detects allele-specific enrichment of histone modifications including H3K27ac alongside DNAme at imprinted and monoallelically expressed genes.
• Standardized Processing: Provides standardized processing of epigenomic and methylomic datasets to enable high allelic resolution comparisons across samples and species.
• Empirical Validation: Applied to mouse embryonic datasets and human brain epigenomic data to identify dynamically methylated loci and allele-specific enrichment patterns.

Scientific Applications:

• Imprinted Gene Regulation: Enables genome-wide identification and characterization of allele-specific DNAme and histone modification patterns at imprinted loci.
• Developmental Biology: Supports analysis of allelic epigenetic regulation in mammalian development, including mouse embryonic datasets.
• Neuroepigenomics: Facilitates detection of allele-specific H3K27ac and DNAme patterns in human brain epigenomic data.
• Complex Genetic Disease Research: Allows investigation of allele-specific expression and epigenetic variation relevant to genetic and epigenetic disease mechanisms.

Methodology:

The pipeline processes input datasets using INDEL-aware algorithms that incorporate SNVs and INDELs to generate allele-specific DNA methylation maps and integrates these maps with RNA-seq and ChIP-seq epigenomic data.