Reporter-ChIP-nexus captures paused Pol II on transfected plasmids and shows that pausing stability is influenced by core promoter sequences, especially by the initiator with a G at +2 position.

The first zygotic genes are transcribed without RNA polymerase II pausing from a TATA-enriched promoter.

The transcriptional control system of a sea urchin gene reveals the deep evolutionary conservation of a gene regulatory network underlying morphogenesis.

Gene expression timing during Drosophila development is specified by multiple classes of RNA polymerase II core promoters, and the embryonic transcriptome includes thousands of evolutionarily conserved long noncoding RNAs.

In a synthetic system, spreading of chromatin-mediated silencing to nearby genes depends on distance and can bypass genetic insulators, while reactivation after release of gene targeting is coordinated by insulators and promoters.

The seemingly simple, constitutive response of the patched/Ptch1 gene to Hedgehog signaling is in fact regulated by large batteries of context-specific Hedgehog-responsive enhancers in both fly and mouse, allowing tissue-specific tuning of the Hedgehog pathway in animal development and evolution.

An orphan TBP-associated factor, TAF9B, works in conjunction with the histone acetyl-transferase PCAF as transcriptional co-regulators of neuronal differentiation.

Variability in bacterial transcription start site selection involves DNA “scrunching” and “anti-scrunching,” which may represent a general mechanism for start site selection in all organisms.

A new multistep hierarchical cascade controls activation of an integrative and conjugative element in a small subpopulation of cells in its bacterial host, yielding proficient DNA transferring cells.

The elongation rate of RNA Polymerase II varies greatly between and along genes, as this enzyme accelerates from stable pausing to rapid elongation within genes, and is influenced by CG-content, exons and chromatin.