The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …

Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion,
which is characterized by reduced effector function and proliferation, and the expression of …

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 …

Physical access to DNA is a highly dynamic property of chromatin that plays an essential
role in establishing and maintaining cellular identity. The organization of accessible …

Understanding complex tissues requires single-cell deconstruction of gene regulation with
precision and scale. Here, we assess the performance of a massively parallel droplet-based …

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 …

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

Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA
(cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo …

Advances in genomics technology have provided the means to probe myriad chromatin
interactions at unprecedented spatial and temporal resolution. This has led to a profound …

Background Cytosine DNA methylation is widely described as a transcriptional repressive
mark with the capacity to silence promoters. Epigenome engineering techniques enable …