Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

While footprinting analysis of ATAC-seq data can theoretically enable investigation of
transcription factor (TF) binding, the lack of a computational tool able to conduct different …

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation
in all organisms. Genetic variation in regulatory regions has been connected with diseases …

Abstract Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a
simple protocol for detection of open chromatin. Computational footprinting, the search for …

Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …

Gene regulatory networks (GRNs) are key determinants of cell function and identity and are
dynamically rewired during development and disease. Despite decades of advancement …

The mammalian circadian clock, expressed throughout the brain and body, controls daily
metabolic homeostasis. Clock function in peripheral tissues is required, but not sufficient, for …

The transcriptional regulatory structure of plant genomes remains poorly defined relative to
animals. It is unclear how many cis-regulatory elements exist, where these elements lie …

Highlights•Newly identified transcriptional regulators of immunity.•Interactions between
transcriptional regulators and with their target genes.•The effect of phytohormones in …