Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …

Cell states result from the ordered activation of gene expression by transcription factors.
Transcription factors face opposing design constraints: they need to be dynamic to trigger …

Regulatory DNA sequences within enhancers and promoters bind transcription factors to
encode cell type-specific patterns of gene expression. However, the regulatory effects and …

Highlights•3D genome organization undergoes dramatic changes in cancer.•Oncogenes
can be ectopically activated by SV-induced enhancer hijacking.•Tumor suppressor genes …

The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene
expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI …

Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown
great promise in linking regulatory elements to genes. However, existing methods differ in …

Objective An increased risk of primary biliary cholangitis (PBC) has been reported in
patients with systemic sclerosis (SSc). Our study aims to investigate the shared genetic …

Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with
the promoters of their target genes. However, genome-wide depletions of architectural …

Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide
range of biological processes in both health and disease. High-throughput screens using …

In vertebrates, gene transcription is performed by generic eukaryotic molecular machinery
under influence of sequence-specific DNA-binding transcription factors that control gene …