Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development

Abstract

Recently, sequence analyses have identified a large number of opposite strands transcripts in the vertebrate genome. Although the transcripts appear to be spliced and polyadenylated, many of them are predicted to represent noncoding RNAs. High levels of noncoding transcripts of the Six3 opposite strand (Six3OS) were recently identified in the embryonic and postnatal retina of the mouse. In this study, we expanded those initial expression analyses, elucidated in detail the developmental expression profile of mouse Six3OS in the brain and visual system, and compared it with that of Six3. Our results show that Six3OS expression overlaps extensively with that of Six3 and is not altered in Six3-null embryos.

New meaning in the message: Noncoding RNAs and their role in retinal development

“…A caveat applies here though, because the isoform of CrxOS selected contains an open reading frame and may be translated into protein, as discussed above, and these experiments did not directly determine whether these effects are mediated by CrxOS-encoded protein or by the CrxOS RNA itself. In the case of Six3 and Six3OS, neither relationship was observed, as mice mutant for Six3 showed no change in Six3OS expression (Geng et al, 2007).…”

“…Overlap in exonic or intronic sequence is sometimes seen between the 5Ј end of the HOSTs and some isoforms of the associated coding mRNA, although this is clearly not the case for all HOSTs or homeodomain transcripts. For instance, though one alternative 5Ј isoform of Six3 is found in an intronic sequence of SixOS, it is clear from fulllength EST and CAGE tag analysis (Geng et al, 2007;Rapicavoli and Blackshaw, unpublished data) that this is a relatively uncommon isoform of Six3 and that the most commonly used transcriptional start site for Six3 lies several kilobases downstream of the common start site for Six3OS. Examination of EST data implied that the HOSTs are usually spliced as well as polyadenylated, and elaborate alternative splicing is sometimes seen; this is particularly pronounced for Six3OS, which shows at least 10 different splice forms (Alfano et al, 2005;Geng et al, 2007).…”

“…Six3OS is essentially coexpressed with Six3 in retinal and diencephalic progenitor cells, while several other regions of the developing brain that express Six3 do not express Six3OS (Geng et al, 2007). In the mature retina, different Six3OS splice forms show differing expression, with some isoforms coexpressed with Six3 in retinal ganglion cells while others are restricted to Muller glia, which do not express Six3 (Blackshaw et al, 2004;Geng et al, 2007). Other HOSTs are expressed in very different cellular patterns from their partnered homeodomain transcription factors.…”

Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function

“…A biochemical function for Sox8OT has not been identified, but it shows concordant expression with its sense partner and may share a promoter (Mercer et al, 2010). The bidirectional lncRNA Six3OS has also been found to work in trans to regulate retinal differentiation (Alfano et al, 2005; Geng et al, 2007; Rapicavoli et al, 2011). Knockdown or overexpression of Six3OS does not affect Six3 expression in the mouse retina, indicating there is not an interaction in cis on the host gene (Rapicavoli et al, 2011).…”

The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity

“…Two of these exons are adjacent to alternatively spliced exons of the human Six3OS orthologue, which lie within intronic regions of the mouse transcript (Figure 1, dark grey bars). This cDNA corresponds to the most abundant isoform in neonatal retina as measured by serial analysis of gene expression (SAGE) tag abundance [32], and also matches the 4.5-kb isoform of Six3OS , previously reported to be the most abundant isoform expressed in embryonic brain [33]. We therefore selected this cDNA for analysis by overexpression.…”