BACKGROUND Nature has evolved elegant mechanisms to regulate the physical distance
between molecules, or proximity, for a wide variety of purposes. Whether it is activation of …

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 …

Transcription factors canonically bind nucleosome-free DNA, making the positioning of
nucleosomes within regulatory regions crucial to the regulation of gene expression. Using …

Next-generation sequencing (NGS) technologies have been used in diverse ways to
investigate various aspects of chromatin biology by identifying genomic loci that are bound …

The exact positions of nucleosomes along genomic DNA can influence many aspects of
chromosome function. However, existing methods for mapping nucleosomes do not provide …

We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA
polymerase II from the nucleus and performing direct RNA sequencing throughout the decay …

The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II
(Pol II)-mediated transcription, and termination of its activity is necessary to partition the …

We determined genome-wide nucleosome occupancies in mouse embryonic stem cells and
their neural progenitor and embryonic fibroblast counterparts to assess features associated …

The histone variant H2A. Z is a genome-wide signature of nucleosomes proximal to
eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known …

Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but
nucleosome maps are affected by the degree of digestion. It has been proposed that many …