Inter3d: A ready-to-use pipeline for CTCF-mediated interactome identification with 3D genomics and high-throughput sequencing

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Data required

• samples/cells of two or more conditions.
• RNA-seq, HiC and CTCF ChIP-seq, ATAC-seq or DNase-seq required.
• H3K4me3 and H3K27ac ChIP-seq. (optional)

Inter3d biology mechanism

Inter3d workflow

• Before Inter3d

1. Preprocessing RNA-seq

• Mapping and gene quantification. (not included)
• DEG identification.(not included)

2. Preprocessing ChIP-seq and ATAC-seq

• Mapping to reference genome.(not included)
• Consensus peak calling.(not included)

3. Preprocessing Hi-C.

** We recommend using ENCODE uniform processing pipeline for your raw data preprocessing. https://www.encodeproject.org/pipelines/

• Using Inter3d

4. Identify CTCF-mediated TAD alterations.
5. Identify candidate genes regulated by CTCF binding.
6. Find Enhancer-Promoter pairs regulated by CTCF binding.

Inter3d quick guide

• Input files:

  • DEG list with Log2FoldChange of Case1/Case2
  • ATAC-seq/DNase-seq peaks in Case1 and Case2
  • CTCF ChIP-seq peaks in Case1 and Case2
  • Genome-wide TAD boundary of Case1 and Case2

• Output files:

  • Genome coordinates of candidate enhancers and linked promoters.
    • for etc: ctcf_gain_case1_high_gene_CRE.xls
  • Genome coordinates of candidate CTCF binding sites.
    • for etc: ctcf_gain_case1_high_gene.xls

Run Inter3d with demo dataset used in manuscript

cd demo
bash run_demo.sh

Reference:
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription. Genomics, Proteomics & Bioinformatics. 2024 (online)