Our data on paternal allele-specific transcripts in the first intron of Blcap_v1a may reflect Nnat transcripts extending through the Blcap_v1a promoter region (Fig. 2D).
In myoblasts from one FSHD patient, higher levels of D4Z4 derived RNA could be detected [26], which may reflect stabilized transcripts originating from the most distal edge of the contracted array [27].
This suggests the possibility that these may reflect real transcripts in which a mobile element has been inserted into the genome.
The apparent contrast between the enhancement of digestive activity, which is centered in the midgut, and the decrease in transcripts linked to transcription and translation may reflect changes in transcript abundance occurring at the whole-body level.
The 0.4 mm stage after the three-layered somatic niche is established contains surprisingly few (11) stage-specific transcripts; this may reflect the persistence of transcripts from the previous stage and the absence of cell type specific differentiation transcripts, many of which are likely expressed after this stage.
Furthermore, it has to be considered that transcripts supported by only a small number of aligned reads (≤10) may reflect incompletely assembled transcripts in the reference.
A portion of these polycistronic transcripts may reflect only low-level polycistronic transcription, rather than polycistronic transcripts serving as the dominant isoforms but the rate of polycistronic transcription cannot be readily determined with available data.
Of course low levels of transcript may reflect high levels of expression with considerable spatial or temporal restriction and consequent functional significance.
Biologically, it might be that patterns of gene expression are quite different between these two tissues; the differences in sampled genes therefore may reflect substantial differences in transcript abundances.
These measurements of transcript abundance may reflect both changes in gene-specific transcriptional activity as well as changes in cellular composition.
