To achieve high compaction, most genomic DNA in eukaryotes is incorporated into
nucleosomes; however, regulatory factors and transcriptional machinery must gain access to …

Large-scale cancer genomics, proteomics and RNA-sequencing efforts are currently
mapping in fine detail the genetic and biochemical alterations that occur in cancer. However …

Nucleosome positioning plays a key role in genomic regulation by defining histone–DNA
context and by modulating access to specific sites. Moreover, the histone–DNA register …

Cooperative binding of transcription factors (TFs) to promoters and other regulatory regions
is essential for precise gene expression. The classical model of cooperativity requires direct …

Transcription factors (TFs) recognize specific bases within their DNA-binding motifs, with
each base contributing nearly independently to total binding energy. However, the energetic …

Chromatin organization and composition impart sophisticated regulatory features critical to
eukaryotic genomic function. Although DNA sequence-dependent histone octamer binding …

Transcription of eukaryotic genes by RNA polymerase II (Pol II) is typically accompanied by
nucleosome survival and minimal exchange of histones H3 and H4. The mechanism of …

Genetic regulatory networks enable cells to respond to changes in internal and external
conditions by dynamically coordinating their gene expression profiles. Our ability to make …

Quantitative models of cis-regulatory activity have the potential to improve our mechanistic
understanding of transcriptional regulation. However, the few models available today have …

DNA accessibility to regulatory proteins is substantially influenced by nucleosome structure
and dynamics. The facilitates chromatin transcription (FACT) complex increases the …