Recent highlights of RNA-polymerase-II-mediated transcription Robert J Sims III, Subhrangsu S Mandal and Danny Reinberg 1 Considerable advances into the basis of RNA-polymerase-II- mediated transcriptional regulation have recently emerged. Biochemical, genetic and structural studies have contributed to novel insights into transcription, as well as the functional significance of covalent histone modifications. New details regarding transcription elongation through chromatin have further defined the mechanism behind this action, and identified how chromatin structure may be maintained after RNAP II traverses a nucleosome. ATP-dependent chromatin remodeling complexes, along with histone chaperone complexes, were recently discovered to facilitate histone exchange. In addition, it has become increasingly clear that transcription by RNA polymerase II extends beyond RNA synthesis, towards a more active role in mRNA maturation, surveillance and export to the cytoplasm. Addresses Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA 1 e-mail: reinbedf@UMDNJ.EDU Current Opinion in Cell Biology 2004, 16:263–271 This review comes from a themed issue on Nucleus and gene expression Edited by Elisa Izaurralde and David Spector 0955-0674/$ – see front matter ß 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.ceb.2004.04.004 Abbreviations DSIF DRB sensitivity inducing factor FACT facilitates chromatin transcription HIRA histone regulatory homolog A HMTase histone methyltransferase NELF negative elongation factor P-TEFb positive transcription elongation factor RNAP II RNA polymerase II RSC remodels the structure of chromatin SAGA Spt-Ada-Gcn5-Acetyltransferase SCP small CTD phosphatases SPT Suppressor of Ty insertion SWR Swi2/Snf2 related TF transcription factor Introduction Over the past few years, the current model of gene regulation has acquired a new degree of sophistication, as advances in our understanding of transcriptional reg- ulation by RNA polymerase II (RNAP II) have developed at a staggering pace. Diverse studies of the transcriptional machinery have provided a detailed view of how the general transcription factors work together to transcribe protein-coding genes efficiently. Importantly, recent advances in the field of gene regulation have more clearly demonstrated that transcription is coupled to mRNA processing, RNA surveillance and export, among other cellular processes. The consequences of DNA accessi- bility represent a major challenge in our attempts to understand how genes are transcriptionally regulated. Great strides have been made regarding the mechanisms behind RNAP II transcription in a chromatin environ- ment. Significant advancements in our understanding of the language of covalent histone modifications have dee- pened our knowledge of the information stored within nucleosomes, the building blocks of chromatin. Here we discuss recent advances in RNAP II transcription, includ- ing structural aspects, mRNA processing and export, elongation through chromatin, histone modifications, and the recent discoveries of histone exchangers. The transcriptional machinery The high-resolution crystal structure of RNAP II has provided detailed insight at the atomic level into how a catalytically active RNAP II is structured and has revealed important aspects of its function [1,2]. Most importantly, significant homology exists between eukar- yotic and bacterial RNA polymerases in their overall structure [3]. The relative positions of the conserved subunits of RNAP II, including Rpb1(b 0 ), Rpb2(b), Rpb3(aI), Rpb11(aII) and Rpb6(o), are consistent in yeast and bacteria, suggesting the existence of an evolu- tionarily conserved mechanism of RNA synthesis during transcription. Notably, the nascent mRNA passes through a positively charged exit channel, and once the RNA is approximately 18 nucleotides long it becomes accessible to the RNA processing machinery. These structural observations are consistent with the coupling of transcript capping to early transcription events. Furthermore, sev- eral additional structural, biochemical and genetic studies conducted over the past few years have yielded important details of RNAP II function [2,4]. Transcription of class II genes requires a coordinated assembly of RNAP II and five factors, TFIID, TFIIB, TFIIF, TFIIE and TFIIH, the so-called general tran- scription factors [5,6]. Transcription initiation begins with the formation of the first phosphodiester bond and phos- phorylation of serine 5 (Ser5) on the C-terminal domain (CTD) of the largest subunit of RNAP II by TFIIH. The CTD of RNAP II, composed of a highly conserved, tandemly repeated heptapeptide motif (YSPTSPS), undergoes extensive phosphorylation and dephosphory- lation during the transcription cycle. The oscillation of www.sciencedirect.com Current Opinion in Cell Biology 2004, 16:263–271