We also analyzed the promoters of 15 genes with a documented function in meiosis (Additional file 7, Table S3) with Pscan.
Finally, the pooled rare variant in BAS1 was associated with LD, JIC2W, and short days without vernalization at USC (SD), agreeing with its documented function in photomorphogenesis, hypocotyl elongation, and flowering time (Turk et al. 2005).
Interestingly, the adenine-rich motifs were also found in promoter regions of 15 selected genes with a documented function in meiosis (Additional file 7, Table S3 and Additional file 8, Figure S5).
The multiple talents of SNEV, however, include a well documented function in DNA repair [ 23- 25, 40], but also in pre-mRNA splicing, ubiquitination and proteasomal breakdown as well as adipogenic and neurogenic differentiation, where another phosphorylation sites plays a crucial role [ 28, 29].
Among the 13 candidate promoters that have no documented function in meiosis, ten have shown meiotic activity (≈77%) by driving the expression of GFP signal in meiocytes, thus revealing that our preliminary data has a high reliability for isolating meiotically-active promoters (Table 1).
tra is crucial for normal female somatic sex determination and behavior, again with no documented functions in males.
Of the 12 genes differentially expressed in the combined ZLL-dependent versus ZLL-independent accessions, none were tightly linked to the Ler/Col FHE loci or had documented functions in meristem development or RNAi.
This cluster included a number of genes with well documented functions in myelination, like the myelin genes Mbp, Mpz and Mag, lipid synthesis enzymes such as Hmgcr, and components of other pro-myelination signalling pathways such as Fzd3, a Wnt receptor (Tawk et al., 2011), and GPR126 (Monk et al., 2011) (Fig. 8D).
Indeed, the yeast, human and Drosophila orthologs of Arabidopsis PCFS4 have been documented to function in transcription termination and RNA Polymerase II proccessivity by interacting with the C-terminal domain of Pol II [57] [59].
Several regulatory molecules of unassigned or poorly documented function were also implicated in some of these processes, and they became candidates for future gene function validation efforts.
