RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression
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MINI-REVIEW
RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression Olga Calvo1 Received: 10 May 2020 / Revised: 26 May 2020 / Accepted: 28 May 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract In eukaryotes, cellular RNAs are produced by three nuclear RNA polymerases (RNAPI, II, and III), which are multisubunit complexes. They share structural and functional features, although they are specialized in the synthesis of specific RNAs. RNAPII transcribes the vast majority of cellular RNAs, including mRNAs and a large number of noncoding RNAs. The structure of RNAPII is highly conserved in all eukaryotes, consisting of 12 subunits (Rpb1-12) organized into five structural modules, among which the Rpb4 and Rpb7 subunits form the stalk. Early studies suggested an accessory role for Rpb4, because is required for specific gene transcription pathways. Far from this initial hypothesis, it is now well established that the Rpb4/7 heterodimer plays much wider roles in gene expression regulation. It participates in nuclear and cytosolic processes ranging from transcription to translation and mRNA degradation in a cyclical process. For this reason, Rpb4/7 is considered a coordinator of gene expression. New functions have been added to the list of stalk functions during transcription, which will be reviewed herein: first, a role in the maintenance of proper RNAPII phosphorylation levels, and second, a role in the establishment of a looped gene architecture in actively transcribed genes. Keywords RNAPII · Rpb4/7 · Transcription · Rpb1-CTD phosphorylation · Gene looping
Introduction RNA polymerases (RNAPs) are nuclear multisubunit complexes responsible for the transcription of all cellular RNAs. They are present in all kingdoms of life and exhibit remarkable structural and functional similarities (Table 1). Only one RNAP is present in Bacteria and Archaea, while most eukaryotic organisms exhibit three RNAPs (I, II, and III) (Cramer et al. 2008; Werner and Grohmann 2011). Plants are an exception among eukaryotes in that they harbor two additional polymerases, RNAPIV and V (Haag and Pikaard 2011). The functions of RNAPI, II, and III are conserved across eukaryotes, producing rRNAs, mRNAs, and tRNAs, respectively, though RNAPII and III can transcribe some other type of small RNAs, whose specific synthesis may
Communicated by M. Kupiec. * Olga Calvo [email protected] 1
Instituto de Biología Funcional y Genómica (IBFG), CSICUSAL, C/ Zacarías González 2, Salamanca 37007, España
differ depending on the species (Cramer 2002; Dieci et al. 2007; Huet et al. 1985; Ling and Yuen 2019). The RNAPII structure is highly conserved in eukaryotes from yeast to humans. It contains 12 subunits (Rpb112; Fig. 1a) organized into five structural modules (core, jaw-lobe, shelf, clamp, and stalk), with relative mobility among them, that mediate the activity and processivity of the polymerase (Armache et al. 2003, 2005; Cramer et al. 2000, 2001). The two largest subu
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