Nucleosome positioning is critical for gene expression and most DNA-related processes.
Here we review the dominant patterns of nucleosome positioning that have been observed …

In individual cells, transcription is a random process obeying single-molecule kinetics. Often,
it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the …

Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to
mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that …

We systematically generated large-scale data sets to improve genome annotation for the
nematode Caenorhabditis elegans, a key model organism. These data sets include …

The recognition of specific DNA sequences by proteins is thought to depend on two types of
mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily …

Mechanical deformations of DNA such as bending are ubiquitous and have been implicated
in diverse cellular functions. However, the lack of high-throughput tools to measure the …

Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …

Knowing the precise locations of nucleosomes in a genome is key to understanding how
genes are regulated. Recent'next generation'ChIP–chip and ChIP–Seq technologies have …

R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a
DNA: RNA hybrid and a displaced DNA single strand. R loops impact the genome of many …

Nucleosome organization is critical for gene regulation. In living cells this organization is
determined by multiple factors, including the action of chromatin remodellers, competition …