Differential gene expression mechanisms ensure cellular differentiation and plasticity to
shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential …

Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA
sequence motifs that are exposed on the surface of a nucleosome and thus access silent …

Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …

The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …

Methods for quantifying gene expression and chromatin accessibility in single cells are well
established, but single-cell analysis of chromatin regions with specific histone modifications …

The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to
be coordinated by transcription factors (TFs), yet demonstrating a specific TF influence has …

Abstract 'Pioneer'transcription factors are required for stem-cell pluripotency, cell
differentiation and cell reprogramming,. Pioneer factors can bind nucleosomal DNA to …

Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes
restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the …

Pioneer transcription factors have the ability to access DNA in compacted chromatin.
Multiple transcription factors can bind together to a regulatory element in a cooperative way …