FOCUS | editorial Corrected: Publisher Correction Five decades of eukaryotic The biochemical identifcation of three nuclear RNA polymerases fundamentally altered our understanding of regulation.

ifty years ago, our understanding only eukaryotic transcriptional regulation promoters, a novel function at the time, and of transcription was informed by but also other DNA-dependent processes ultimately paved the way to show how post- Fpioneering studies of bacteriophage and (Nature 224, 234–237 (1969); Fed. Proc. 28, transcriptional modifications of bacterial RNA polymerases, which revealed 599 (1969); Science 170, 447–449 (1970); permit or preclude transcriptional activity. that a polymerase engages single or bipartite Biochem. Biophys. Res. Commun. 38, Transcription elongation is facilitated DNA elements either directly or via 165–171 (1970)). by factors that modify or remodel a polymerase-associated σ subunit to initiate As an independent investigator, or that directly target the Pol II gene-specific RNA synthesis. Coordinate Bob Roeder and his group went on to elongation complex to regulate its activity. was largely achieved either define the DNA-binding factors that direct A Perspective by Joan and Ron Conaway by the linear arrangement of within specific initiation from Pol II and Pol III (https://doi.org/10.1038/s41594-019-0283-1) or by the association of bacterial promoters in vitro, to identify the first describes the biochemical identification σ factors to direct the core RNA polymerase gene-specific regulatory factor, TFIIIA, and characterization of the latter class to sequence-specific promoter elements. required for 5S rDNA gene transcription of accessory factors, including TFIIS, In this context, the biochemical (the first reported zinc-finger DNA-binding the first described elongation factor that purification and identification of factor), and to describe the ordered assembly reactivates arrested Pol II complexes on three nuclear RNA polymerases was of general transcription factors at promoters DNA templates. The subsequent discovery unprecedented. Each RNA polymerase had to create a pre-initiation complex that of Elongin and ELL—factors that suppress a dedicated function in the synthesis of the directs gene-specific transcription Pol II pausing at sites where it is prone to precursor of large ribosomal subunit rRNAs initiation by Pol II or Pol III. arrest—led to the identification of the ‘super (Pol I), 5S rRNA and tRNAs required for The unanticipated complexity of these elongation complex’ (SEC) that includes synthesis (Pol III) and protein- initiation factors was augmented by the the p-TEFb kinase that phosphorylates the encoding mRNAs (Pol II). The subsequent observed complexity of DNA elements Pol II CTD. Several genes encoding SEC demonstration that, despite their subunit and DNA-binding that mediate subunits are translocation partners for complexity, these enzymes were incapable gene- or cell-type-specific transcription by the methyltransferease MLL in leukemia, of initiating RNA synthesis at their cognate Pol II and led to the definition of establishing a link between misregulated Pol promoters within DNA templates in vitro and elements that coordinate II elongation and leukemogenesis. launched an entire field of investigation to expression of genes in distant locations The foundational biochemical studies identify their accessory transcription factors within the genome via interactions that defined key factors and cofactors that that has uncovered an ever-expanding with sequence-specific activator- or mediate eukaryotic transcriptional regulation complexity of regulatory mechanisms. enhancer-binding factors. The subsequent have been augmented by technological To celebrate the anniversary of identification of cofactors, such as Mediator, advances that allowed their functions to this landmark discovery, we present a that bridge enhancer-bound regulatory be examined both at gene-specific loci and special Focus on 50 years of eukaryotic factors and promoter-bound transcription genome-wide within cells. A Perspective transcription, with commissioned historical factors, provided additional insights by John Lis (https://doi.org/10.1038/ Perspectives and a Review highlighting key into gene- and cell-specific regulatory s41594-019-0288-9) traces the contributions advances in the biochemical elucidation mechanisms that we now know contribute to of emerging technologies to elucidating and characterization of the nuclear RNA three-dimensional genome architecture. transcriptional mechanisms by targeted polymerases and the protein factors and DNA As the central role of chromatin in disruption of factor activities, tracking elements that control their activities. The gene expression is now well established, interactions, nucleosomal authors of these historical pieces narrate the it is difficult to imagine a time when its configuration and RNA polymerase activity remarkable progress in our understanding of functional significance was questioned. A at base-pair resolution and monitoring these topics from a personal perspective. Perspective by Jim Kadonaga (https://doi. enhancer–promoter interactions on a A Review by Robert (“Bob”) Roeder org/10.1038/s41594-019-0278-y) relates genomic scale. Combined with current provides a central narrative of the Focus, the initial resistance of the transcription super-resolution microscopy and cryo-EM as it describes discoveries spanning a field, which at the time was focused on visualization of transcription intermediates, research career that has provided seminal purified, reconstituted systems using we anticipate that the molecular interactions contributions to the field over five decades naked DNA templates, to the potential underlying transcriptional regulation in vivo (https://doi.org/10.1038/s41594-019- benefits of assessing RNA polymerase will continue to be illuminated. 0287-x). His initial 1969 discovery, as a activity on chromatin-assembled DNA We hope that each piece conveys the graduate student, of three nuclear RNA substrates. Although this approach was excitement of the contemporaneous polymerase activities from multiple seen as ‘throwing a wrench into the works’ discoveries and reinforces their contributions , distinguished by their metal of a biochemically defined system, it to our understanding of the mechanisms and DNA template preferences, and shown ultimately proved that chromatin was a underlying RNA polymerase function by Pierre Chambon to be differentially spoke in the wheel of the transcription cycle. and how coordinate or differential gene sensitive to the fungal toxin, α-amanitin, Transcriptional activators were shown to expression is achieved in eukaryotic cells. ❐ marks both the dateline of our anniversary counteract repressive chromatin structures Focus and the beginning of a field of through activities Published online: 26 August 2019 scientific investigation that has informed not that favor ‘open’ chromatin configurations at https://doi.org/10.1038/s41594-019-0303-1

Nature Structural & | VOL 26 | SEPTEMBER 2019 | 757 | www.nature.com/nsmb 757