HiC-TE

HiC-TE analyzes Hi-C sequencing data to quantify and visualize contacts among repetitive DNA families such as ribosomal DNA, centromeric satellites, and LTR retrotransposons and to assess their contributions to three-dimensional genome organization.

Key Features:

• Binning by Repeat Families: Bins Hi-C read pairs by repeat family instead of by chromosomal location to focus analysis on interactions among repetitive elements.
• Integration with Reference Genome and Repeat Analysis Tools: Integrates Hi-C data with reference genome annotations and repeat annotations using Nextflow for workflow orchestration.
• Contact Quantification: Identifies and quantifies contacts between specific repeat families from Hi-C data.
• Output Visualizations: Produces heatmaps showing contact frequencies between repeat families and circular diagrams depicting spatial distributions of repeat family contacts.
• Repeat Annotation Compatibility: Accepts repeat annotations from TE-greedy-nester (tandem repeats and LTR retrotransposons) or user-supplied GFF3 files for other repeat types.

Scientific Applications:

• Understanding Genome Architecture: Reveals preferential homotypic and heterotypic interactions among repeat families to inform 3D genome structure analyses.
• Comparative Genomics: Enables cross-species comparisons of repeat-mediated chromatin interactions across eukaryotic genomes, including plant genomes.
• Functional Genomics: Provides data on repeat interactions that can inform studies of gene regulation and chromosomal stability.

Methodology:

Bins Hi-C read pairs by repeat family, integrates Hi-C data with reference genome annotations, uses Nextflow for workflow management, accepts TE-greedy-nester outputs or GFF3 repeat annotations, quantifies contacts between repeat families, and generates heatmaps and circular diagrams.