Paused RNA polymerase II as a developmental checkpoint

Abstract

The textbook view of gene activation is that the rate-limiting step is the interaction of RNA polymerase II (Pol II) with the gene's promoter. However, studies in a variety of systems, including human embryonic stem cells and the early Drosophila embryo, have begun to challenge this view. There is increasing evidence that differential gene expression often depends on the regulation of transcription elongation via the release of Pol II from the proximal promoter. I review the implications of this mechanism of gene activation with respect to the orderly unfolding of complex gene networks governing animal development.

Figure 1. The First Steps in Transcription Activation

A transcription factor, such as TBP/TFIID, binds to specific promoter elements, including TATA. This leads to the recruitment of additional general transcription factors, including TFIIA, TFIIB, TFIIF, and ultimately, RNA polymerase II (Pol II). The initial binding is unstable, given that the promoter complex is in a closed conformation. Recruitment of TFIIH leads to the formation of an open complex and the onset of transcription. Stable transcription depends on the phosphorylation of the Pol II C-terminal region (CTD), which fosters promoter escape. Adapted from Gilmour (2009).

Figure 2. RNA Polymerase II Binding at Developmental Patterning Genes

RNA polymerase II (Pol II) binding at the proximal promoter regions of developmental patterning genes, including sog (A), which encodes a bone morphogenetic protein inhibitor, and sim (B), which specifies the ventral midline of the central nervous system. (A) Pol II chromatin immunoprecipitation (ChIP)-chip, genome-wide run on assays (Gro-Seq) and ChIP-Seq assays using extracts from 2–4 hr mutant embryos that lack a dorsal nuclear gradient and contain only dorsal ectoderm (Zeitlinger et al., 2007). Although sog is silent in these embryos, Pol II is clearly bound to the promoter region of the gene. (B) An ~10 kb region of the Drosophila genome, which contains the linked sim and timeout genes. ChIP-chip assays identified Pol II binding in the promoter region of sim, but not timeout, in early, 2–4 hr embryos. Pol II binding is seen at the sim promoter in pipe and rm⁹/rm¹⁰ mutants, which produce only dorsal ectoderm and neurogenic ectoderm, respectively. No binding is observed in Toll^10b mutants, which produce only mesoderm (Zeitlinger et al., 2007).

Figure 3. Paused Pol II and Its Release from the Proximal Promoter

The top panel shows a promoter DNA template with paused RNA polymerse II (Pol II). The promoter region contains sequence elements that foster binding and activation of Pol II, including GAGA, TATA, initiator, and downstream promoter element/pause button (DPE/PB) motifs. Pol II is typically paused just downstream of the DPE region. It has undergone promoter escape and contains phosphorylation of serine 5 (Ser5) in the C-terminal domain (CTD). DSIF (5,6-dichloro-1-β-D-ribofuranoxylbenzimidazole sensivitiy-inducing factor) and NELF (negative elongation factor) help to arrest Pol II by binding to the nascent transcript (typically 30–50 nucleotides in length). Recruitment of P-TEFb (positive transcription elongation factor b) causes the release of NELF and the phosphorylation of Ser2 in the CTD, resulting in Pol II procession into the main body of the gene.

Figure 4. Activation of Paused and Nonpaused Genes

(Left) The Drosophila thisbe gene lacks binding of RNA polymerase II (Pol II), based on both chromatin immunoprecipitation assays (not shown) and Gro-Seq assays (shown). The gene exhibits a stochastic pattern of activation in the early embryo, with nascent transcripts detected in only about half of all nuclei that will ultimately express the gene. (Right) In contrast, the sog gene contains paused Pol II and exhibits a synchronous pattern of activation.