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Although originally classified as a non-coding RNA, the male-specific abdominal (MSA) RNA from the Drosophila melanogaster bithorax complex has recently been shown to code for a micropeptide that plays a vital role in determining how mated females use stored sperm after mating. Interestingly, the MSA transcript is a male-specific version of another transcript produced in both sexes within the posterior central nervous system from an alternative promoter, called the iab-8 lncRNA. However, while the MSA transcript produces a small peptide, it seems that the iab-8 transcript does not. Here, we show that the absence of iab-8 translation is due to a repressive mechanism requiring the two unique 5' exons of the iab-8 lncRNA. Through cell culture and transgenic analysis, we show that this mechanism relies on the presence of upstream open reading frames present in these two exons that prevent the production of proteins from downstream open reading frames. Author summary: The study of genome wide transcriptomes has shown that there are a number of non-coding transcripts that play important biological functions. What keeps these transcripts non-coding is generally thought to be the lack of a suitable open reading frame from which a protein can be translated. However, aside from their non-coding functions, the increased use of techniques like ribosome profiling has shown that many predicted non-coding transcripts are, in fact, bound by ribosomes and also make functional peptides. The male-specific abdominal transcript found within the Drosophila bithorax complex is one of them. This transcript codes for a small peptide in the male accessory gland that plays a role in sperm usage. However, an alternative version of this transcript, called the iab-8 lncRNA, is made in the central nervous system, where it does not seem to produce this peptide. Here, we show that the translation of a biologically functional open reading frames can be regulated in different tissues through regulating translation from upstream open reading frames, using the iab-8 transcript as a model. In doing so, this mechanism could limit potentially detrimental protein misexpression through post-transcriptional means. [ABSTRACT FROM AUTHOR]

Hox genes in species across the metazoa encode transcription factors (TFs) containing highly-conserved homeodomains that bind target DNA sequences to regulate batteries of developmental target genes. DNA-bound Hox proteins, together with other TF partners, induce an appropriate transcriptional response by RNA Polymerase II (PolII) and its associated general transcription factors. How the evolutionarily conserved Hox TFs interface with this general machinery to generate finely regulated transcriptional responses remains obscure. One major component of the PolII machinery, the Mediator (MED) transcription complex, is composed of roughly 30 protein subunits organized in modules that bridge the PolII enzyme to DNA-bound TFs. Here, we investigate the physical and functional interplay between Drosophila melanogaster Hox developmental TFs and MED complex proteins. We find that the Med19 subunit directly binds Hox homeodomains, in vitro and in vivo. Loss-of-function Med19 mutations act as dose-sensitive genetic modifiers that synergistically modulate Hox-directed developmental outcomes. Using clonal analysis, we identify a role for Med19 in Hox-dependent target gene activation. We identify a conserved, animal-specific motif that is required for Med19 homeodomain binding, and for activation of a specific Ultrabithorax target. These results provide the first direct molecular link between Hox homeodomain proteins and the general PolII machinery. They support a role for Med19 as a PolII holoenzyme-embedded “co-factor” that acts together with Hox proteins through their homeodomains in regulated developmental transcription. [ABSTRACT FROM AUTHOR]