BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transcription factor (TF) footprinting identifies protein-DNA binding sites using chromatin accessibility and TF sequence motifs.
• Standard enrichment tests for TF footprints are biased by chromatin accessibility and GC content, leading to false positives.
• Accurate identification of regulatory TF binding is crucial for understanding cell-specific gene regulation.

Purpose of the Study:

• To develop a novel post-processing method, BiFET, to correct for biases in TF footprint enrichment analyses.
• To improve the accuracy and reduce false positive rates in identifying cell/condition-specific TF regulatory activities.
• To demonstrate the utility of BiFET in analyzing TF footprints from various ATAC-seq datasets.

Main Methods:

• Developed the Bias-free Footprint Enrichment Test (BiFET) to account for chromatin accessibility and GC content biases.
• Applied BiFET to TF footprint data from EndoC-βH1 ATAC-seq samples analyzed with CENTIPEDE, HINT-BC, and PIQ algorithms.
• Compared BiFET's performance against the traditional hypergeometric test for power and false positive rate.

Main Results:

• BiFET effectively corrects for biases related to chromatin accessibility and GC content in TF footprint enrichment.
• BiFET demonstrated increased statistical power and a reduced false positive rate compared to the hypergeometric test.
• Application of BiFET to human PBMC and pancreatic islet ATAC-seq data successfully identified putative TFs associated with cell-type-specific loci.

Conclusions:

• BiFET is a robust method for unbiased TF footprint enrichment analysis.
• The developed method enhances the reliability of identifying regulatory transcription factors in cell-specific genomic regions.
• BiFET offers a valuable tool for advancing the study of gene regulation through TF binding analysis.