Additional file 9: Figure S4. of A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis

Time course graphs of the major DE Wnt factors and Wnt pathway members. (XLSX 81 kb

Additional file 6: Figure S3. of A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis

Time course graphs of metalloproteinase (MP) group genes and inhibitors. The FDR-adjusted p-values for the time effect (DESeq GLMs) for all genes are given. (XLSX 23 kb

Additional file 13: Table S9. of A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis

Comparison of polarized gene expression in regeneration between Nematostella and Planaria. The anterior and posterior enriched genes of Planaria are listed with their oral or aboral Nematostella orthologs and homologs when present. The color coding is the same as in Fig. 7. (XLSX 17 kb

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans-5

the ORF (exons 1–3, which contain the Runt domain) were used to characterize the spatial expression of Runx in adult . Similar results were obtained using a longer probe corresponding to the entire transcript (not shown). Labeled anti-sense probes detect expression in the oral region of the anemones, particularly in the ectoderm of the tentacle tips (animal on left). No specific staining was observed using sense-strand probes (animal on right). While expression was always limited to the tentacle and head region there was some background staining that varied between individual animals. Note that the dark color in the mouth of the animal depicted in panel B (arrowhead) does not represent Runx expression, since it is not detected in sections of this region. The arrowhead in Panel C reveals the strong expression at the tentacle tips. These panels show ectodermal expression of in the tentacles as seen in cryostat sections of anemones after whole mount hybridization. Low magnification micrograph of a section through the head and tentacles, revealing general architecture as well as the location of the enlarged micrographs in E and F. Bar = 100 μm Expression of in the ectoderm of the tentacles, Bars in E and F = 50 μm, in G = 20 μm, A thin section of a tentacle from Nematostella, stained with Methylene Blue. Numerous spirocysts (Sp) and several nematocysts (N) can be observed, as can darkly and heterogeneously stained gland cells (G) found towards the apical part of the ectoderm. The elongated cells (S) are probably sensory cells []. The mesoglea (Mes) is schematically marked by a dashed line. Bar = 10 μm. Expression of Nv-Runx in scattered cells in the ectoderm of the body wall (arrowhead). Bar = 20 μm.<p><b>Copyright information:</b></p><p>Taken from "The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans"</p><p>http://www.biomedcentral.com/1471-2148/8/228</p><p>BMC Evolutionary Biology 2008;8():228-228.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527000.</p><p></p

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans-1

Hed structure of their human counterparts (PDB #). The RD is depicted in blue, CBFβ in green and DNA in purple. The interacting residues are depicted as ball and stick models, and colored according to their conservation with their human counterparts (Yellow = identical, Orange = conservative substitution, Red = non-conservative substitution). For clarity, a similar model with the relevant residues numbered according to the Runx RD and CBFβ proteins is provided as Additional file , and detailed tables comparing the residues of all the proteins discussed can be found as Additional files , , . . All of the residues in the RD involved in DNA binding are completely conserved in . The arrow points to compensatory changes in H163 of the RD, which is replaced with C131 in . , showing a second compensatory change which involves the substitution of F153 and M106 in human with K121 and A73 in in the RD and the replacement of Q67 and S65 with H67 and T65 in CBFβ (indicated with arrow). . In the cnidarian proteins, the majority of non-conserved residues which interact with CBFβ are located at the periphery of the interacting surfaces (C, D). and particularly indicate greater sequence divergence within this domain, with non-conservative substituions not being restricted to the periphery. . Most of the functional residues are conserved between all three proteins and the human variant, with most of the non-conservative subsitutions found at the periphery of the binding face.<p><b>Copyright information:</b></p><p>Taken from "The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans"</p><p>http://www.biomedcentral.com/1471-2148/8/228</p><p>BMC Evolutionary Biology 2008;8():228-228.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527000.</p><p></p

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans-3

E available. We then inferred the evolutionary change in Runx (blue) and CBFβ (green) along each branch of this phylogeny by using the JTT matrix to calculate patristic distances. For each node on the tree, the evolutionary change in CBFβ and GAPDH were plotted against the evolutionary change in Runx. The regression reveals a significant and strong correlation between the evolutionary change in Runx and CBFβ (represented by squares and solid line; = 0.83, = 85.11, < 0.0001) but not between Runx and GAPDH (circles and dashed line). The outliers (the circle and square with a Runx branch length of ~0.3) represent the divergence between the protostome ancestor and the common ancestor (see panel A). Both Runx (branch length = ~0.3) and CBFβ (branch length = ~0.44) diverged rapidly within this lineage, while GAPDH continued to evolve more slowly (equivalent branch length in GAPDH tree = ~0.05).<p><b>Copyright information:</b></p><p>Taken from "The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans"</p><p>http://www.biomedcentral.com/1471-2148/8/228</p><p>BMC Evolutionary Biology 2008;8():228-228.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527000.</p><p></p

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans-6

Les and mouth region of adult anemones. No staining could be seen when a control probe from the sense strand was used (right animal). An inset from A, showing strong expression in the tentacle tips (arrow). Expression of in the mouth and extended upper pharynx of the same animal as depicted in A and B. Expression levels in the mouth region differed between different animals. General architecture of the tentacles and mouth region, showing the location of the enlarged micrographs in E and H (panel H is of a different serial section from the same anemone). Ten = tentacle, phx = pharynx. Scale bar = 100 μm. Expression of at the base of the ectoderm of the tentacles (arrowheads) en = endoderm, ec = ectoderm, mes-mesoglea. Bar in E = 100 μm, in F = 20 μm. Expression of in the ectoderm of the mouth (arrows). en = endoderm, ec = ectoderm, mes-mesoglea, gvc = gastrovascular cavity. Bar = 100 μm Enlargement of a region in the mouth, showing the CBFβ expression in cells close to large microbasic mastigophore nematocysts (arrowheads) Bar = 20 μm. Thin (2 μm) epoxy cross section through the mouth region stained with Methylene Blue, revealing the secretory gland cells (gc) and abundance of microbasic mastigophore nematocytes (mbm) of different sizes. Bar = 20 μm.<p><b>Copyright information:</b></p><p>Taken from "The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans"</p><p>http://www.biomedcentral.com/1471-2148/8/228</p><p>BMC Evolutionary Biology 2008;8():228-228.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527000.</p><p></p

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans-4

Ion (including tentacle bases), body column, and physa. Reverse-transcription (RT) PCR was performed on an equal amount of total RNA extracted from each of the four body regions. An equivalent fraction of the amplification reaction was visualized on an agarose gel. Using this assay, expression was detected in the tentacles, and to a lesser extent in the head/pharyngeal region, but not in the column or physa. As a positive control, actin was found to be expressed at high levels in all four body regions.<p><b>Copyright information:</b></p><p>Taken from "The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans"</p><p>http://www.biomedcentral.com/1471-2148/8/228</p><p>BMC Evolutionary Biology 2008;8():228-228.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527000.</p><p></p