Abstract Eukaryotic RNA polymerase II (Pol II) has been found at both promoters and distal
enhancers, suggesting additional functions beyond mRNA production. To understand this …

As most of the mitochondrial proteome is encoded in the nucleus, mitochondrial functions
critically depend on nuclear gene expression and bidirectional mito-nuclear communication …

R-loops are three-stranded nucleic acid structures that form during transcription, especially
over unmethylated CpG-rich promoters of active genes. In mouse embryonic stem cells …

Regulation of transcription is a tightly choreographed process. The establishment of RNA
polymerase II promoter proximal pausing soon after transcription initiation and the release of …

Delineating how chromosomes fold at length scales beyond one megabase remains
obscure relative to smaller-scale folding into TADs, loops, and nucleosomes. We find that …

At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by
elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other …

Although the locations of promoters and enhancers have been identified in several cell
types, we still have limited information on their connectivity. We developed HiCap, which …

Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene
activation–associated histone modifications. A striking exception is DOT1L-mediated H3K79 …

Transcription elongation has emerged as a regulatory hub in gene expression of
metazoans. A major control point occurs during early elongation before RNA polymerase II …

The heat shock (HS) response involves rapid induction of HS genes, whereas transcriptional
repression is established more slowly at most other genes. Previous data suggested that …