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Localization of the transcripts of the six Cav α1 subunits of Nematostella by ISH demonstrated complex spatiotemporal expression patterns.
FISH experiments also confirmed this result because no change in the localization of the transcripts and no labeling in the oocytes were observed.
The DIG-labeled probes were detected as previously described [ 105], and the resulting dark blue to purple color indicated localization of the transcripts.
Following G418 selection, stable clones were expanded and analyzed by immunofluorescence to confirm subcellular localization of the transcripts via the C-terminal encoded V5 tag, as described previously (O'Flaherty et al., 2010 ).
The staining obtained using the RNAscope method appeared to be more distinct and to reflect more accurately the subcellular localization of the transcripts, compared to the staining in the standard and the optimized whole-mount FISH, which appears more aggregated and more diffuse.
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The full-length transcript of MIAT was also localized in the nucleus when overexpressed in HeLa cells (Fig. 1H), suggesting that nuclear localization of the transcript is a common feature of Gomafu homologues in different vertebrate species.
We further investigated the subcellular localization of the transcript by fluorescent in situ hybridization (FISH) and found that the transcript was diffusely localized in the nuclei of spinal neurons (Fig. 1G), yielding a spotted pattern similar to that observed for the mouse Gomafu RNA (Sone et al. 2007).
DNA sequences for the target genes were identified based on their GC content, which ranged from 35 60%, the localization of the transcript within 300 to 800 bases of the 3' end, and the minimal homology with other genes to reduce the cross-hybridization potential.
This revealed the absolute numbers and intra-cellular localizations of the transcripts of interest, clearly demonstrating that transcripts of Gck, Gcgr, Nlrp6, and Mlxipl were indeed substantially more numerous in the nucleus compared to the cytoplasm.
The differential localization of these transcripts and proteins could be a species-specific signature stressing their more or less functional importance in one species versus the other.
Hybridization histochemical localization of the different transcripts was performed on every 6th or 12th section of the entire rostrocaudal extent of each brain.
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