An interactive network of long non-coding RNAs facilitates the Drosophila sex determination decision

Abstract

Genome analysis in several eukaryotes shows a surprising number of transcripts which do not encode conventional messenger RNAs. Once considered noise, these non-coding RNAs (ncRNAs) appear capable of controlling gene expression by various means. We find Drosophila sex determination, specifically the master-switch gene Sex-lethal (Sxl), is regulated by long ncRNAs (>200 nt). The lncRNAs influence the dose sensitive establishment promoter of Sxl, SxlPe, which must be activated to specify female sex. They are primarily from two regions, R1 and R2, upstream of SxlPeand show a dynamic developmental profile. Of the four lncRNA strands only one, R2 antisense, has its peak coincident with SxlPe transcription, suggesting it may promote activation. Indeed, its expression is regulated by the X chromosome counting genes, whose dose determines whether SxlPe is transcribed. Transgenic lines which ectopically express each of the lncRNAs show they can act in trans, impacting the process of sex determination but also altering the levels of the other lncRNAs. Generally, expression of R1 is negative whereas R2 is positive to females. This ectopic expression also results in a change in the local chromatin marks, affecting the timing and strength of SxlPe transcription. The chromatin marks are those deposited by the Polycomb and Trithorax groups of chromatin modifying proteins, which we find bind to the lncRNAs. We suggest the increasing numbers of non-coding transcripts being identified are a harbinger of interacting networks similar to the one we describe.

Trithorax and Polycomb group-dependent regulation: a tale of opposing activities

“…Early reports identified links between specific lncRNAs and PcGdependent silencing, and lncRNAs have thus often been associated with target gene repression (reviewed by Brockdorff, 2013;Mondal and Kanduri, 2013). However, and as we highlight below, a number of recent reports also implicate lncRNAs in activating gene expression (Cabianca et al, 2012;Gomez et al, 2013;Grote et al, 2013;Hamazaki et al, 2015;Herzog et al, 2014;Mulvey et al, 2014;Wang et al, 2011;Yang et al, 2014).…”

“…For instance, in mice the Fendrr lncRNA, which is required for normal heart and body wall development, has been suggested to bind both PRC2 and MLL complexes (Grote et al, 2013). Likewise, in the context of Drosophila sex determination, the R2 antisense lncRNA has been implicated in promoting transcription of the Sex lethal gene via binding interactions with TrxG proteins (Mulvey et al, 2014). Furthermore, the generation of protein-RNA prediction algorithms such as catRAPID has enabled in silico analyses to support potential TrxG protein-lncRNA interaction pairs (Bellucci et al, 2011;Iglesias-Platas et al, 2012).…”

Transcriptome analysis provides insights into differentially expressed genes and long noncoding RNAs involved in sex‐related differences in Amur sturgeon (Acipenser schrenckii)

“…In mouse, 3,996 lncRNAs showed sex‐biased expression that may be associated with germline stem cell acquisition of the sex‐specific properties required for differentiation into gametes (X. Li, Ao, & Wu, ). Drosophila sex determination, specifically the master‐switch gene Sex‐lethal ( Sxl ) was modulated by lncRNAs as the lncRNAs influenced the dose sensitive establishment promoter of Sxl , which must be activated to specify female sex (Mulvey, Olcese, Cabrera, & Horabin, ). Tsx is a lncRNA which performs general functions in the germline, stem cells, and brain in mouse (Anguera et al, ).…”

“…Li, Ao, & Wu, 2017). Drosophila sex determination, specifically the master-switch gene Sex-lethal (Sxl) was modulated by lncRNAs as the lncRNAs influenced the dose sensitive establishment promoter of Sxl, which must be activated to specify female sex (Mulvey, Olcese, Cabrera, & Horabin, 2014). Tsx is a lncRNA which performs general functions in the germline, stem cells, and brain in mouse (Anguera et al, 2011).…”

Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

“…Drosophila the master Sxl gene is regulated by a lncRNA acting in a complex interplay network (Mulvey et al, 2014) and in the crustacean Dhapnia magna a lncRNA regulates the male specific expression of the dsx1 DM domain producing males in response to environmental stimuli (Kato et al, 2018). Moreover, the only diagnostic variant detected between Z and W chromosomes in our study (SNP.3), despite being far from sox2, might be part of a regulatory element, since sox2 enhancers have been identified within a 200 kb region surrounding this gene (Zhou et al, 2014).…”