Hundreds of protein factors participate in transcription and its regulation in eukaryotes. Many
of these proteins regulate specific genes by targeting upstream promoter regions, whereas …

Divergent transcription is common of many promoters in organisms as diverse as mammals
and yeast. Many independent experiments indicate that RNA polymerase II is frequently …

RNA polymerases are highly regulated molecular machines. We present a method (global
run-on sequencing, GRO-seq) that maps the position, amount, and orientation of …

Transcription regulation occurs frequently through promoter-associated pausing of RNA
polymerase II (Pol II). We developed a precision nuclear run-on and sequencing (PRO-seq) …

Despite the conventional distinction between them, promoters and enhancers share many
features in mammals, including divergent transcription and similar modes of transcription …

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic
innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such …

Recent work has shown that the RNA polymerase II enzyme pauses at a promoter-proximal
site of many genes in Drosophila and mammals. This rate-limiting step occurs after …

We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant,
PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start …

DNA sequence variation has been associated with quantitative changes in molecular
phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. …

Transitions between pluripotent stem cells and differentiated cells are executed by key
transcription regulators. Comparative measurements of RNA polymerase distribution over the …