However, it is likely that 3′-UTR conservation found in this study could be involved in posttranscriptional regulatory mechanisms as well directing subcellular localization, transcript stability or translatability.
To further characterize the transcription of repetitive elements, we examined binding of Pol III-specific transcription factors, as well as RNA transcript subcellular localization and polyadenylation status.
Sequences in UTRs may control translation, subcellular localization, and transcript stability through a variety of mechanisms (e.g., Mignone et al. 2002).
In particular, 3′UTRs play a central role in translation, stability and subcellular localization of transcripts.
The data can be queried through a web-interface according to various criteria and Boolean combinations ("AND", "OR"), such as developmental stages, tissue types, hybridisation signal intensities, numbers of transcripts, subcellular compartment, or gene identifiers (figure 2).
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).
The levels and subcellular destinations of the transcripts are compared for transcripts expressed using the U6 small nuclear RNA (snRNA), 5S ribosomal RNA (rRNA), and the 7SL RNA component of the signal recognition particle.
For example, Buckley et al. (Neuron 2011) describe the case of some transcripts with retained introns, which drive subcellular location of the transcripts to the dendrites due to the presence of a particular transposable element within their sequence.
The subcellular distribution of the transcript is facilitated by interaction with protein(s) binding to its 3′UTR.
Local splicing in cytoplasmic subcellular compartments to generate transcript variants and regulate gene expression was suggested by Eberwine, and coined the "RNA sentinel hypothesis" (Buckley et al., 2014), which is a tantalizing idea that merits further studies.
