The origin of the transcripts detected at the 2 hpf is uncertain, but the zygote formation in Atlantic cod occurs approximately at 5 hpf [ 31].
However, in breast cancer, TIMP-3 mRNA was found by in situ hybridization to be expressed predominantly in the peritumoral stroma [ 22], whereas its clinicopathological and prognostic value has been evaluated in relation to the expression levels of TIMP-3 mRNA and measured by methods that did not distinguish the cancerous from the stromal origin of the transcripts [ 23, 24].
One of the consequences of the adapter ligation cloning approach used in this study is that strand origin of the expressed transcript is lost.
Neither the role nor the origin of these transcripts in BMSB is clear, but both warrant further investigation.
These results imply significant transcriptional activity of the endosymbiont nucleus in dinotoms, although to reliably pinpoint the origin of these transcripts large-scale phylogenetic analysis will be necessary.
The presence of dinoflagellate-specific SL in five KS transcripts, their similarity (BLASTx) to KS domains from other dinoflagellates (Additional file 1: Tables S5 S7) and the monophyletic clustering of all dinoflagellate KS transcripts within a protistan KS domain cluster in the phylogenies, provides consistent and substantial evidence of the dinoflagellate origin of these transcripts (Fig. 3a).
In support of the mitochondrial origin of these transcripts, a close examination of mitochondrial transcripts in our dataset revealed C → U RNA editing.
The high similarity between the mitochondrial genome and its genomic insertion makes it difficult to define the origin of these transcripts.
This observation prompted us to investigate the origin of the corresponding transcripts.
In both the human [ 16] and the rhesus macaque [ 15], NLRP11 and 13 have been found specifically or preferentially expressed in the oocyte, with a similar expression pattern to other oocyte-specific NLRP genes, i.e., enriched in maturing oocytes and then progressively diminished in embryos, indicating an exclusive maternal origin of these transcripts.
To specifically address the allelic origin of the chromatin-associated transcript, we designed allele-specific primers to an SNP (rs463924) that is located 4 kb downstream of the KCNQ1OT1 transcription start site (Supplementary Material, Figs S2 and S3).
