Developmental RNA processing of 3′UTRs in Hox mRNAs as a context-dependent mechanism modulating visibility to microRNAs

Abstract

SUMMARYThe Drosophila Hox gene Ultrabithorax (Ubx) controls the development of thoracic and abdominal segments, allocating segmentspecific features to different cell lineages. Recent studies have shown that Ubx expression is post-transcriptionally regulated by two microRNAs (miRNAs), miR-iab4 and miR-iab8, acting on target sites located in the 3Ј untranslated regions (UTRs) of Ubx mRNAs. Here, we show that during embryonic development Ubx produces mRNAs with variable 3ЈUTRs in different regions of the embryo. Analysis of the resulting remodelled 3ЈUTRs shows that each species harbours different sets of miRNA target sites, converting each class of Ubx mRNA into a considerably different substrate for miRNA regulation. Furthermore, we show that the distinct developmental distributions of Ubx 3ЈUTRs are established by a mechanism that is independent of miRNA regulation and therefore are not the consequence of miR-iab4/8-mediated RNA degradation acting on those sensitive mRNA species; instead, we propose that this is a hard-wired 3ЈUTR processing system that is able to regulate target mRNA visibility to miRNAs according to developmental context. We show that reporter constructs that include Ubx short and long 3ЈUTR sequences display differential expression within the embryonic central nervous system, and also demonstrate that mRNAs of three other Hox genes suffer similar and synchronous developmental 3ЈUTR processing events during embryogenesis. Our work thus reveals that developmental RNA processing of 3ЈUTR sequences is a general molecular strategy used by a key family of developmental regulators so that their transcripts can display different levels of visibility to miRNA regulation according to developmental cues.

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

“…In addition, HOX loci are known to host at least three miRNA genes (Lagos-Quintana et al 2001;Bender 2008;Stark et al 2008;Tyler et al 2008), one of which was previously shown to be regulated by Polycomb (Ronshaugen et al 2005). Among the suspected targets are the HOX genes themselves (Stark et al 2008;Tyler et al 2008;Thomsen et al 2010), thus providing an opportunity for direct regulatory feedback. Another interesting aspect is the novel connection to important growth-regulating miRNAs such as bantam and mir-8, in line with known PcG targets in cell cycle control (Martinez et al 2006;Oktaba et al 2008).…”

Integrating transcription kinetics with alternative polyadenylation and cell cycle control

“…36 Like polo, ubx mRNAs contain target sites for miRNAs, however the differential expression of the two ubx mRNAs is not due to miRNA silencing but to alternative polyadenylation. Additionally, the longer ubx isoform is not upregulated in proliferation deficient string mutants, suggesting that proliferation is not the driving-force behind ubx alternative polyadenylation.…”

MicroRNA-encoded behavior in Drosophila

“…Previous work in our laboratory focused on the mechanisms and impact of RNA regulation on the expression and neural function of the Drosophila Hox genes (3)(4)(5)(6). These genes encode a family of evolutionarily conserved transcription factors that control specific programs of neural differentiation along the body axis (7)(8)(9) offering an opportunity to investigate how RNA regulation relates to the formation of complex tissues such as the nervous system.…”

“…Here we use the Hox gene system to investigate the roles played by a single miRNA locus (miR-iab4/8) (3,(10)(11)(12)(13)(14)30) on the specification of the nervous system during early Drosophila development. This miRNA locus controls the embryonic expression of posterior Hox genes (3,(10)(11)(12)(13)(14).…”

“…This miRNA locus controls the embryonic expression of posterior Hox genes (3,(10)(11)(12)(13)(14). Given that we found no detectable differences in the morphological layout of the main components of the nervous system in late Drosophila embryos of wild type and miR-iab4/8 null mutants (herein ∆miR, (13)) (Fig S3B-F) we analysed early larval behaviour as a stratagem to probe the functional integrity of the late embryonic nervous system.…”