Regulation of Hox Gene Activity by Transcriptional Elongation in Drosophila

Abstract

SUMMARY Hox genes control the anterior-posterior patterning of most metazoan embryos. Their sequential expression is initially established by the segmentation gene cascade in the early Drosophila embryo [1]. The maintenance of these patterns depends on the Polycomb group (PcG) and trithorax group (trxG) complexes during the remainder of the life cycle [2]. We provide both genetic and molecular evidence that the Hox genes are subject to an additional tier of regulation, i.e. at the level of transcription elongation. Both Ultrabithorax (Ubx) and Abdominal-B (Abd-B) genes contain stalled or paused RNA Polymerase II (Pol II) even when silent [3, 4]. The Pol II elongation factors Elongin-A and Cdk9 are essential for optimal Ubx and Abd-B expression. Mitotic recombination assays suggest that these elongation factors are also important for the regulation of Notch, EGF, and Dpp signaling genes. Stalled Pol II persists in tissues where Ubx and Abd-B are silenced by the PcG complex. We propose that stalling fosters both the rapid induction and precise silencing of Hox gene expression during development.

Paused RNA Polymerase II as a Developmental Checkpoint

“…Many Hox genes, tissue determinants (such as tinman , a heart specification gene, and sim , which specifies the ventral midline of the central nervous system), and components of cell signaling pathways (for instance, genes encoding the fibroblast growth factor receptor and bone morphogenetic protein inhibitors) contain Pol II in the early embryo, prior to their activation later in development (Zeitlinger et al, 2007; Muse et al, 2007; Chopra et al, 2009a; see Table 1). Indeed, the first evidence that the release of paused Pol II is a critical mechanism of gene regulation in Drosophila development came from the analysis of three critical segmentation genes, slp1 , engrailed , and wingless (Wang et al, 2007).…”

“…The SEC component AFF4 corresponds to lilliputian ( lilli ), which is essential for embryonic patterning; lilli mutants exhibit a variety of developmental defects, including a severe pair-rule phenotype (Wittwer et al, 2001; Vanderzwan-Butler et al, 2007). Moreover, another component of the SEC, ELL, exhibits a strong genetic interaction with the homeotic gene, Ubx , which contains stalled Pol II in both embryos and wing imaginal disks (Smith et al, 2008; Chopra et al, 2009a). …”

“…Given that paused Pol II is mainly found in promoter-proximal locations within the first 30–50 bp of the transcription unit, it might block the binding of additional Pol II complexes prior to the induction of gene expression. The consequence of such “steric repression” is a lower “background” of expression as compared with genes lacking paused Pol II (see Chopra et al, 2009a). According to this view, paused Pol II might produce a sharp on/off switch in transcription upon induction.…”

“…The Drosophila Antennapedia locus is ~103 Kb in length (Laughon et al, 1986). It contains several promoters, and most of these contain paused Pol II (Chopra et al, 2009a, 2009b). At the established rates of Pol II procession (see Saunders et al, 2006), it should take more than an hour for a single Pol II complex to reach the end of the gene after it is released from the distal-most promoter.…”

Evolution of Insect Dorsoventral Patterning Mechanisms

“…This paradigm of gene expression was seen as a specialized stress response. However, the finding that many developmental control genes contain stalled pol II in the early Drosophila embryo raises the possibility that the control of transcription elongation is an important strategy for differential gene regulation during development (Lis 2007; Zeitlinger et al 2007b; Hendrix et al 2008; Chopra et al 2009). …”