"Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions

Abstract

Much of the complex process of RNP biogenesis takes place at the gene cotranscriptionally. The target for RNA binding and processing factors is, therefore, not a solitary RNA molecule but, rather, a transcription elongation complex (TEC) comprising the growing nascent RNA and RNA polymerase traversing a chromatin template with associated passenger proteins. RNA maturation factors are not the only nuclear machines whose work is organized cotranscriptionally around the TEC scaffold. Additionally, DNA repair, covalent chromatin modification, "gene gating" at the nuclear pore, Ig gene hypermutation, and sister chromosome cohesion have all been demonstrated or suggested to involve a cotranscriptional component. From this perspective, TECs can be viewed as potent "community organizers" within the nucleus.

Figure 1. Processing and elongation factors associated with the human pol II TEC

The conserved heptad repeat sequence with Serines 2, 5 and 7 that are differentially phosphorylated during the transcription cycle highlighted. The 5′-3′ distributions of CTD phosphorylations, processing factors and elongation factors are derived from ChIP studies (eg (Glover-Cutter et al., 2008) (Yoh et al., 2007)). Human capping enzyme (HCE), cap methyltransferase (MT) and the cleavage polyadenylation factors, CPSF, and CstF are shown. Elongation factors Spt5 that binds HCE and Spt6 that binds phospho-Ser2 are shown. Scissors depict RNA cleavage at the poly (A) site. B). 5′-3′ distribution of RNA pol II density on a typical human gene showing pausing at the start site and downstream of the poly (A) site.

Figure 2. A) CTD phosphorylation and processing factor recruitment at the budding yeast pol II TEC

5′-3′ distributions of factors are based on ChIP studies as in Fig. 1A. Four factors that bind directly to the CTD are depicted: the cap methyltransferase (MT) and guanylyltransferase (GT), the termination factor Nrd1 and the cleavage/polyadenylation factor Pcf11. “ Gene gating” by putative interaction between the nuclear pore and the TEC is depicted by a yellow arrow. B). ChlP-Chip analysis of the 5′-3′ distribution of total pol II density (left) and Ser2 and Ser5 phosphorylated pol II (right) on a typical highly transcribed yeast gene, (RPL3). Results are from (P. Megee and D.B. unpublished).

Figure 3. The rate of elongation affects splice site selection and folding of the nascent RNA

A) Differential histone H3 K36 trimethylation (H3K36me3) of worm and mouse exons and introns (Kolasinska-Zwierz et al., 2009) by Setd2 which binds the CTD (Yoh et al., 2008) is indicated. H3K36me3 increases 5′-3′ on most genes. B) A fast elongation rate and short “window of opportunity” favors exon skipping whereas slow elongation favors exon 2 (E2) inclusion (after (de la Mata et al., 2003). Elongation rate can also affect co-transcriptional RNA folding and potentially also binding of different RNA binding proteins (RBP).

Figure 4. The RNA polymerase II TEC as a locator of chromatin proteins

A) Possible mechanism of cohesin (pink rings) localization by convergent transcription in yeast (after (Lengronne et al., 2004)). B) Mutually exclusive protein:protein and protein:RNA interactions and handoff reactions facilitate assembly of export-competent mRNP’s. In reaction 1 the yeast export adaptor Yra1 is handed off from Pcf11 to the RNA helicase Sub2. In reaction 2, Yra1 is handed off to the export receptor Mex67/Mtr2. C) Mobilization of histones during pol II transcription elongation. FACT and Swi/Snf travel with the TEC to facilitate disassembly and reassembly of nucleosomes. Displaced histones could be handed off to the nascent RNA before they are re-deposited behind the polymerase.