spatzie: An R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions

Abstract

Genomic interactions provide important context to our understanding of the state of the genome. One question is whether specific transcription factor interactions give rise to genome organization. We introduce spatzie, an R package and a website that implements statistical tests for significant transcription factor motif cooperativity between enhancer-promoter interactions. We conducted controlled experiments under realistic simulated data from ChIP-seq to confirm spatzie is capable of discovering co-enriched motif interactions even in noisy conditions. We then use spatzie to investigate cell type specific transcription factor cooperativity within recent human ChIA-PET enhancer-promoter interaction data. The method is available online at https://spatzie.mit.edu.

DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes

“…Some studies have demonstrated that enhancer-promoter interactions regulate target genes in the genome, and specific transcription factor cooperation offers the possibility to understand the cell-type specificity of genome interactions [46], of which Cicero, PEP, and the latest proposed Spatzie attempted to detect the transcription factor motif cooperativity between enhancer-promoter interactions [47][48][49]. To analyze whether the sequence-based features within identified chromatin loops, we first performed experiments using Spatzie where all identified chromatin loops were used in each cell line.…”