We predict approximately 1,500 novel structured RNAs in intergenic regions which overlap embryonic transcriptional fragments, as well as 3,000 in 3' and 5' UTRs of protein-coding genes.
Table 2 shows the chromosomal distribution of our predicted ncRNAs and Figure 5 gives the length distributions of our predictions in intergenic sequence which overlap embryonic transcriptional data before and after filtering criteria are applied.
The second gene set with highly significant overlap (EMBRYONIC STEM CELL UP; p < 5.53E-09) was derived from a study of gene expression profiles in mouse embryonic stem cells compared to differentiated brain and bone marrow cells [ 73].
We have taken the advantage of this genetic system to visualize mesodermal derivatives (in this case, lateral plate) and have demonstrated that this population, unlike Nestin-creER T2 -traced cells, overlaps with embryonic skeletal precursors expressing osterix protein (an accepted marker of osteoprogenitor cells).
While the nub-46 and pdm2-34 enhancers drove overlapping but nonidentical expression during embryonic and larval NB lineage development (Fig. 5d, h, Fig. 8a, c), nub-49b and pdm2-37a regulated similar expression patterns during postembryonic NB lineage development (Fig. 8b, d).
Gene set enrichment analysis (GSEA; http://www.broad.mit.edu/gsea/index.jsp) of over 200 direct Myc up-regulated target genes in P493-6 cells reveals a significant overlap with embryonic (p = 3.2e−16) or neural (p = 9.4e−19) stem cell gene sets.
Overlap between embryonic liver development and liver cancer is not only in cell cycle or apoptosis, but also in metabolic pathways associated with carbohydrate and lipid metabolism [ 30].
To further investigate Isl1 as a putative target gene of Shox2, we compared the spatial expression of both genes and found that Shox2 and Isl1 expression overlap in embryonic mouse hearts.
This conclusion was subsequently challenged when it was suggested that the overlap with embryonic stem cell transcriptional programs was the reflection for a shared dependence on c-MYC activity rather than related to the stemness phenotype of ES cells [43].
Snail1 and Snail2 display overlapping roles in EMT in normal embryonic and breast development and are upregulated to varying degrees in invasive carcinogenesis [ 41, 43, 51].
