Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1
© Yaklichkin et al; licensee BioMed Central Ltd. 2011
Received: 12 May 2011
Accepted: 15 October 2011
Published: 15 October 2011
The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known.
In this study we identified the avian FOXE1 gene in chicken, turkey and zebra finch, all of which consist of a single exon. Chicken and zebra finch FOXE1 are uniquely located on the sex-determining Z chromosome. In situ hybridization shows that chicken FOXE1 is specifically expressed in the developing thyroid. Its expression is initiated at the placode stage and is maintained during the stages of vesicle formation and follicle primordia. Based on this expression pattern, we propose that avian FOXE1 may be involved in regulating the evagination and morphogenesis of thyroid. Chicken FOXE1 is also expressed in growing feathers. Sequence analysis identified two microdeletions in the avian FOXE1 genes, corresponding to the loss of a transferable repression domain and an engrailed homology motif 1 (Eh1) C-terminal to the forkhead domain. The avian FOXE1 proteins exhibit a significant sequence divergence of the C-terminus compared to those of amphibian and mammalian FOXE1. The codon evolution analysis (dN/dS) of FOXE1 shows a significantly increased dN/dS ratio in the avian lineages, consistent with either a relaxed purifying selection or positive selection on a few residues in avian FOXE1 evolution. Further site specific analysis indicates that while relaxed purifying selection is likely to be a predominant cause of accelerated evolution at the 3'-region of avian FOXE1, a few residues might have evolved under positive selection.
We have identified three avian FOXE1 genes based on synteny and sequence similarity as well as characterized the expression pattern of the chicken FOXE1 gene during development. Our evolutionary analyses suggest that while a relaxed purifying selection is likely to be the dominant force driving accelerated evolution of avian FOXE1 genes, a few residues may have evolved adaptively. This study provides a basis for future genetic and comparative biochemical studies of FOXE1.
FOXE1 is a member of the large and evolutionarily ancient family of forkhead domain-containing transcriptional regulators, which are involved in a variety of developmental and physiological processes in organisms from yeast to mammals . FOXE1, previously termed thyroid transcription factor-2, (TTF-2) was originally isolated by screening a rat cDNA library . The FOXE1 protein was shown to bind specifically to the thyroglobulin promoter and function as a transcriptional repressor [2, 3]. During mouse embryogenesis FoxE1 is expressed in developing thyroid, Rathke's pouch, palate, tongue, epiglottis, pharynx, and oesophagus and in the epithelium of the pharyngeal wall and arches [2, 4]. FOXE1 transcripts are also found in the hair follicle and are regulated by sonic hedgehog signaling in the human and mouse [5, 6]. Consistent with its expression pattern, FOXE1-null mutant mice exhibit either a sublingual or completely absent thyroid gland, cleft palate and abnormal hair structure and growth [7, 6]. Similarly, mutations in the forkhead DNA-binding domain of the human FOXE1 gene cause thyroid agenesis, cleft palate and choanal atresia similar to the phenotype observed in FOXE1-null mutant mice . Taken together, the crucial role of FOXE1 in thyroid formation, palate, and hair development is well established in placental mammals.
Expression of FOXE1 orthologs in other vertebrates is similar to their mammalian counterparts. For example, in the Xenopus embryo, foxe1 is expressed in the developing thyroid, pituitary mesoderm of brachial arches and the pharyngeal endoderm . In the zebrafish embryo foxe1 is expressed in the thyroid, pharynx, and pharyngeal skeleton . In addition, the gene is strongly expressed in the gill and weakly expressed in the brain, eye, and heart in adult zebrafish. However, in contrast to the role of FOXE1 in placental mammals, a loss-of-function study demonstrated that zebrafish foxe1 is not required for the thyroid formation but is necessary for chondrogenesis during pharyngeal skeleton formation . These data suggest that FOXE1 may have acquired the role in the regulation of thyroid development during the evolution of tetrapods, or may have lost this role in the fish lineage. On the other hand, FOXE1 is involved in the regulation of hair morphogenesis, which is a relatively recent skin organ, appearing in the mammalian lineage . This suggests that FOXE1 has acquired a novel regulatory function in the mammalian lineage. Taken together, the data supports substantial functional evolution of FOXE1 during vertebrate evolution.
Despite progress in understanding the function of the mammalian, amphibian and fish FOXE1 genes, nothing is known about FOXE1 gene in birds. The study of FOXE1 of birds can help fill the missing link and provide important insights into the evolution of this gene in vertebrates. Here, we have identified FOXE1 genes in multiple avian species and characterized its expression pattern during chicken development using in situ hybridization. Our data shows that chicken FOXE1 expression is limited to developing thyroid and feathers. We also observe a significant sequence divergence of the N- and C- terminus of the avian FOXE1 proteins and a loss of two repressive domains. Our codon analysis (dN/dS) of avian FOXE1 genes suggests that relaxed purifying selection, or alternatively, positive selection in a subset of residues, might have driven sequence divergence of the avian FOXE1 C-terminus.
Identification and characterization of FoxE1 genes of chicken, zebra finch, and turkey
We further searched for the presence of a zebra finch FOXE1 using a chicken FOXE1 gene as the query against the genomic dataset of zebra finch. The blast search identified a genomic region of 588 bps on the minus strand of Z chromosome with the coordinates 31552116-31551529 bps, (genome version WUGSC 3.2.4/taeGut1) exhibiting 88% similarity to the chicken FOXE1 nucleotide sequence. An ORF was identified in this chromosomal region (Additional File 1, Figure S3), and the corresponding protein sequence exhibited the highest homology to FOXE1 proteins. Thus, this similarity clearly indicated that the indentified region is a zebra finch ortholog of chicken FOXE1 (Additional File 1, Figure S4). However, the zebra finch genomic sequence lacked a 5' - part, encoding an entire N-terminus and a 5' - portion of the forkhead domain because of a gap in the sequence of the Z chromosome. Nevertheless, the region represents a major portion of the gene, encoding a portion of the forkhead domain and an entire C-terminus.
To better characterize FOXE1 in avian lineages, we further searched for FOXE1 gene in the reference genome of turkey. However, despite the recent sequencing of the turkey genome, the FOXE1 gene sequence was not identified. Upon closer inspection, we concluded that the corresponding genomic region is missing from the turkey reference genome. Therefore, we identified the FOXE1 gene from turkey by direct genomic PCR amplification and sequencing. Remarkably, the putative turkey FOXE1 gene exhibited 97% identity to the chicken gene, which is consistent with the reported high similarity of chicken and turkey genomes .
Interestingly, avian FOXE1 genes in both chicken and zebra finch are located on the sex-determining Z chromosome, which is distinct from the chromosomal location of vertebrate orthologs. Fish and mammalian FOXE1 are located on autosomal chromosomes (data not shown). This difference in localization indicates two possibilities: the avian FOXE1 was either part of the ancestral autosomal chromosome which has evolved into the Z chromosome in an ancestral amniote , or FOXE1 genomic locus was translocated onto the Z chromosome. Synteny between the chicken chromosome Z and human Chromosome 9, which includes the sex determining DMRT1, indicates that the chromosome Z evolved from the autosomal chromosome . Human FOXE1 is located on chromosome 9. Therefore, a distinctive chromosomal localization of avian FOXE1 in birds is likely associated with the ancestral autosomal chromosome that subsequently evolved into the Z chromosome.
In summary, by synteny-based analysis of orthology in chicken, and by direct sequencing in turkey, we have identified the avian orthologs of mammalian FOXE1 gene, at least two of which are localized on the sex-determining Z chromosome.
Expression of chicken FoxE1 gene is restricted to the developing thyroid and feathers
Evolution of the avian FoxE1 proteins: a loss of a repressive domain and the Eh1 motif
Additionally, a novel feature in the avian FOXE1 proteins is the presence of an N-terminal polyalanine repeat (Additional File 2, Figure S5), varying from five to nine alanine residues. The polyalanine repeat is also found in FOXE1 of mammals where it is distal to the forkhead domain, but is absent in FOXE1 proteins of amphibians and fish. This suggests that the avian polyalanine repeat arose independently in the avian lineage. The C-terminus of the chicken FOXE1 protein is also enriched with alanine, glycine, and proline residues (Additional File 1, Table S1), as well as short tandem repeats of proline and alanine (Additional File 1, Table S2; ). Proline and alanine-enriched domains are commonly found in transcriptional repressors . This suggests that the avian FOXE1 protein may function as a transcriptional repressor. Thus, while there appears to be an avian-specific loss of two repressive domains in FOXE1 as a result of deletions, we also found an avian specific gain in proline-alanine repeats, which can potentially confer transcriptional repressive activity to avian FOXE1.
Analysis of codon evolution in the avian lineage of FOXE1
Next, we applied the branch-site model to estimate the fraction of codons that are likely to have evolved under positive selection specifically in the five avian branches using the BEB procedure implemented in PAML. We used the five avian branches as the foreground and the other branches as background. The test compares two models: (1) no change in selection was observed in the foreground branches compared to the background branches, and (2) a certain proportion of sites went from being under negative or no selection in the background branches to being under positive selection in the foreground branch. The LRT test statistic (2Δl) of the second model relative to the first model was 13.65 (P = 0.001, df = 2), indicating that a certain fraction of sites did undergo positive selection specifically in the avian lineages. Based on the Bayesian posterior probabilities (BEB) of site class, this analysis detected nineteen sites with BEB ≥ 0.5. Of those, six sites were selected in the branch leading to Galliformes; however, the BEB values for these were less than 0.8. Two of the sites, 196Q and 203L, were detected to be adaptively evolving in bird lineages with probability > 0.95. There were seven additional sites with BEB ≥ 0.8, which are 134R (0.927), 162A (0.858), 164R (0.898), 173P (0.923), 175P (0.884), 211P (0.80) and 249R (0.89). The amino acid coordinates are provided relative to the chicken FOXE1 protein. These results indicate a change in selective pressure on specific amino acids on the branch leading to birds.
In this study we report on the identification of the FOXE1 gene of three bird species and the characterization of FOXE1 expression pattern during chicken embryogenesis. Both FOXE1 of chicken and zebra finch are distinctively localized on the sex-determining Z chromosome, in contrast to placental and marsupial FOXE1 genes which are localized on autosomes. In situ hybridization shows that the expression of the chicken FOXE1 gene is restricted to the developing thyroid and feathers. Its thyroid expression is initiated at the stage of placode formation when the thyroid cells evaginate from the pharyngeal floor and migrate, and is also maintained during the stage of thyroid maturation. The process of evagination is characterized by tissue remodeling, which includes modulation of cell adhesiveness and cell mobility. Based on the pattern of FOXE1 expression, we propose that the transcription factor FOXE1 may regulate evagination of thyroid primordia by regulating specific genes required for cell motility and adhesiveness. This observation is supported by previous loss- and gain-of-function studies in the mouse and cell culture, respectively. For example, in FOXE1-null mice the secondary palate remains opened , which indicates inability of the palate shelves to adhere in the mutant mice . Forced expression of mammalian FOXE1 in cell culture resulted in significantly increased expression of an actin-binding protein, tropomyosin isoform 3, and lower expression of integrin beta-1 and collagen type XI alpha-1 . Tropomyosin has been shown to be important for regulating the actin mechanics in the cell cytoskeleton, and can mediate changes in cell morphology, adhesion and migration [27, 28]. Similarly, integrin beta-1 has been shown to mediate cell migration . Moreover, it has been recently shown that human FOXE1 directly regulates the signaling molecule TGF-3β , which in turn, is involved in regulation of cellular adhesion and extracellular matrix . Thus, FOXE1 may be involved in regulation of a set of genes and signaling pathways that are required for controlling cell adhesiveness and motility during migration and morphogenesis of thyroid cells. In the future, it will be important to determine whether chicken FOXE1 directly regulates a similar set of genes during the migration and morphogenesis of the thyroid gland. We also detected expression of FOXE1 in the growing feather, which suggests the acquisition of a novel expression domain by FOXE1 in the bird ancestry; since the feather is a bird specific integumentary appendage.
Two striking features are found in the sequence of avian FOXE1 proteins, which are the sequence divergence of the C-terminus and the loss of two functional domains: a C-terminal aromatic domain and the Eh1 motif as a consequence of two microdeletions. Both domains appear to be involved in mediating transcriptional repression. The aromatic domain of the mammalian FOXE1 protein can inhibit transcription in cell culture when fused to a heterologous DNA-binding domain, thus acting as a transferable repression domain . Nothing is known about direct targets of this repression domain. Interestingly, mammalian FOXE1 represses transcriptional activation mediated by PAX8 in cell culture, which suggests that it may directly interact with transcription factor PAX8, possibly via this repression domain . We noted that the avian genomes lack transcription factor PAX8 (personal communication), which is important for thyroid formation in mammals . This is consistent with an extensive loss of genes in the chicken genome . Thus, it would be interesting to determine whether the loss of the aromatic repressive domain was associated with the loss of the PAX8 locus in birds.
The Eh1 motif is a conserved amino acid sequence , known to mediate physical interaction of other Fox proteins with Groucho/TLE co-repressors. FOXG1, SLP2 (FOXG), FOXD3 and FOXH1 have been shown to interact physically with Groucho/TLE co-repressors via the Eh1 motif ([19, 20, 34] Yaklichkin and Kessler, unpublished data). Strikingly, the Eh1 motif is conserved in all FOXE1 of fish, amphibians, and non-placental mammals, but it was lost in those of birds. Interestingly, a loss of the Eh1 motif is also observed in FOXE1 of placental mammals as an outcome of a microdeletion (Yaklichkin and Kessler, unpublished data). The loss of the Eh1 motif in the avian FOXE1 protein is likely to lead to the loss of Groucho/TLE recruiting activity mediated by the Eh1 motif, and the loss of specific repressive activity dependent on the aromatic domain. Even though the functional implication of both domain losses in avian FOXE1 proteins is not clear, it is likely to affect transcriptional function. It is intriguing that the loss of two putative repressive domains is accompanied by a gain of an N-terminal polyalanine repeat. The avian FOXE1 domain losses may be associated with either functional divergence, loss of co-factor interacting proteins, or even reduction of expression domain. In situ hybridization in the chicken embryo shows that expression of FOXE1 is restricted to the developing thyroid and feathers, and no expression was observed in other internal embryonic tissues. FOXE1 orthologs have additional domain expressions other than in developing thyroid. For instance, frog foxe1 is expressed both in the developing thyroid and pituitary . Foxe1 of zebrafish is expressed in pharyngeal skeleton, gills and thyroid . It is certainly possible that the reduction of expression of FOXE1 in birds has resulted in the loss of these functional sequences. Similarly, a loss of the Eh1 motif in FOXE1 of placental mammals can possibly be associated with a novel functional requirement.
To investigate the role of selection in the evolution of FOXE1 coding regions in the avian lineages, we used various models of codon evolution dN/dS (ω). Overall, dN/dS (ω) of FOXE1 was estimated to be less than 1, which suggested that FOXE1 were evolving under purifying selection. Significant increase of the dN/dS ratio was estimated between the branches of avian FOXE1 and those of mammals and amphibians, which is indicative of a change in the selection and of the acceleration of evolution of avian 3'FOXE1. The increase of the dN/dS ratio can be a result of either a relaxation of purifying selection or positive selection in specific sites of the C-terminal domain of FOXE1 in the avian lineage. In paralogous regulatory genes, the relaxation of purifying selection was proposed to be a result of paralogous proteins binding to a subset of interacting proteins relative to the ancestral gene copy . By this analogy, relaxation of purifying selection in avian FOXE1 could be a result of loss of ancestral protein interactions and possibly formation of interaction with novel binding proteins. Overall, the C-terminal domain is subjected to fewer functional constraints when compared to the DNA-binding forkhead domain. An increased evolutionary rate of C-terminal regions can be attributed to the capacity of trans-regulatory domains to interact with co-factors and the transcriptional machinery via short interaction motifs. In turn, interaction peptide motifs can evolve quickly due to short size and low affinity of interaction with co-factors .
Our branch-site model identified eighteen C-terminus residues under positive selection in the avian lineage, and two residues, 196Q and 203L, had the highest posterior probability, suggestive of adaptive evolution. Only a single adaptively evolving residue, 134R, was identified in the forkhead DNA-binding domain, which resulted in a non-synonymous substitution in the avian lineage, whereas all other residues lie in the C-terminus. Interestingly, the 196Q and 203L residues are located in a segment (195-207 aa) of avian FOXE1 proteins. This segment shows a strong homology to N-terminal short sequences of the homeobox HOXA13 proteins. The N-terminal portion of the HOXA13 protein contains a trans-regulatory domain, which is likely involved in regulation of transcription. Mouse HOXA13 has been shown to function as a negative regulator . Moreover, HOXA13 can inhibit Smad-mediated activation of transcription by binding directly to Smad co-factors via the N-terminus . However, refined mapping of Smad-interacting sequences have not been conducted. It is likely that the region (195-207 aa) is involved in regulation of transcription based on high homology to the N-terminal segment of homeodomain-containing HOXA13 protein, and adaptively evolving residues may have contributed to avian specific FOXE1 function.
A residue 211P under positive selection was found in the FOXE1 segment (214-225 aa) enriched with proline and alanine residues. This segment shares a high similarity with N-terminal sequences of HOXB3 and HOXA4 proteins of mammals, which are also enriched with proline and alanine residues. Interestingly, the mouse HOXB3 protein can function as a transcriptional repressor , and is expressed in the thyroid primordia and regulates its migration . Minimal repression domains of metazoan transcription factors are known to be often enriched with proline and alanine residues . It is thus predicated that this region may be involved in repression of transcription. It is possible that the avian-specific gain of proline residues has contributed to enhancement of repressive characteristics or the formation of novel avian-specific motifs. Additionally, we cannot exclude the contribution of the N-terminus to transcriptional activity of avian FOXE1, which has gained polyalanine repeats. Thus, relaxed selection in the avian lineage may be the predominant contributor to the accelerated evolution of avian FOXE1 and significant sequence divergence of the C-terminus, whereas a limited positive selection could lead to the formation of novel avian specific transcriptional motifs.
Evolution of gene expression, and thus, the evolution of transcription factors, is likely to play a major role in morphological evolution. Because of the pleiotropic effects of changes in transcription factor sequence, some have argued that changes in gene regulatory networks are predominantly mediated via changes in DNA cis-elements . However, negative pleiotropic effects can be limited by tissue-restricted expression of transcription factors and changes in the transcription factor sequences affecting their interaction with other tissue-specific co-factors . This seems to be the case for FOXE1 evolution in birds. However, directed experiments will be needed to further clarify the functional underpinnings of the evolutionary divergence of avian FOXE1.
Identification of functional FOXE1 orthologs and their codon analysis can provide important insight into their contribution to vertebrate evolution, and offer a foundation for the study of their function across vertebrates. Comparative biochemical studies will be necessary to determine transcriptional function and the effect of the loss of two functional domains in comparison to the other FOXE1 proteins. Building on ongoing functional and structural studies should yield a comprehensive understanding of the evolution of FOXE1 in vertebrates.
DNA and protein sequences
DNA sequences of FOXE1 were obtained from the NCBI database http://ncbi.nlm.nih.gov and the Ensembl database (http://ensembl.org, v47). The FOXE1 sequences of chicken, zebra finch and turkey identified in this study were deposited under the accession numbers BK008024, BK008025 and AEE88205, correspondently at the NCBI database. The accession numbers of FOXE1 sequences obtained from the NCBI are following: Homo sapiens (NP_004464), Mus musculus (NP_899121.1), Xenopus laevis (AAS82575.1), Xenopus tropicalis (XP_002936729.1), Macropus eugenii (ADN52078.1), Monodelphis domestica (XP_001372714.1), and FOXE1 of Sus scrofa (ENSSSCT00000005909) was obtained from the Ensembl database v47. The sequence of chicken FOXE1 was obtained from a Z chromosome BAC sequence (AC192757.2) in NCBI. The sequence of zebra finch FOXE1 was obtained from the chromosomal Z region - 31551529-31552116 bp (genome version WUGSC 3.2.4/taeGut1), from UCSC Genome Browser http://genome.ucsc.edu.
Sequence and phylogenetic analysis
Analysis of amino acid composition of deduced FOXE1 protein sequences was performed using the SAPS program (isrec.isb-sib.ch/software/SAPS_form.html; ). A search of FOXE1 in the NCBI chicken genome database was performed using the BLAST server http://blast.ncbi.nlm.nih.gov. Identification of the Eh1 motif in FOXE1 sequences was performed in accordance with the previously described sequence analysis . Multiple sequence alignments were constructed using T-COFFEE, version 7.7.1. (tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi; ). Indels (small insertion or deletion mutations/sequencing errors) in the aligned sequences were removed using the alignment editor BioEdit 188.8.131.52. http://www.mbio.ncsu.edu/bioedit/page2.html. Syntenic alignment was generated by comparing the surrounding genomic region in ensembl and metazome http://www.metazome.net. A phylogenetic tree of FOXE1 genes was constructed by using the software Phylip 3.69 . The phylogenetic tree was converted into a cladogram using MEGA 4 http://www.megasoftware.net/.
The dN/dS (ω) analysis was performed using the program Codeml in the PAML package 3.13  to assess whether FOXE1 evolved under a differential selection in the avian lineage, relative to the rest of the phylogeny. We specifically performed the analysis on the C-terminus of the avian FOXE1 proteins. Positive selection on specific bird lineages were tested using branch models. A model in which ω was fixed across the tree (one-ratio) was compared with models in which ω was allowed to differ in a subset of branches (two- and three-ratio models), and the significance of the difference was assessed using the likelihood ratio tests (LRTs).
To identify the sites under positive selection along the avian FOXE1 genes, we used the branch-site model A. We used the avian branch set as the foreground branches and all other branches as the background. We then tested whether a model which allows a subset of background sites under neutral or purifying selection, to evolve under neutral or positive selection in the foreground. Model significance was tested using the LRTs termed Test 1. In Test 1 branch-site model A is compared with two degrees of freedom to a site model (M1a, "Nearly Neutral") with two site classes: 0 < ω0 < 1 and ω2 = 1. In addition, PAML also computes for each site the posterior probability of belonging to the class that undergoes an increase in dN/dS.
To visualize variation in ω along FOXE1 genes, a slide window analysis was conducted using the software SWAAP 1.0.3. http://asiago.stanford.edu/SWAAP/SwaapPage.htm. A window size was set to 60 bps and the step size to 12 bps. Values of ω were estimated in accordance with the Nei and Gojobori method.
Polymerase Chain Reaction (PCR) Amplification and Sequencing of genomic DNA
Turkey blood was kindly donated by Bolton Turkey Farm, Silverdale, PA. Genomic DNA was isolated from the blood using the QIAamp DNA Blood Midi Kit (cat. number: 51183). For amplification of turkey FOXE1, pairs of primers were designed to regions with 100% identity shared between chicken and zebra finch FOXE1 genes, and upstream and downstream regions of chicken FOXE1. Primer sequences are available by request. PCR fragments covering the single exon FOXE1 were amplified using GC-RICH PCR System (cat. number: 12 140 306 001), Roche Applied Science. PCR mixture was made in accordance with the protocol of the maker. The following conditions in PCR reactions were used: Initial denaturation, 3 min. at 95°C; 1 step - denaturation - 20 sec. at 95°C; 2 step - primer annealing at 60°C, 30 sec.; 3 step - elongation - 1 min. at 68°C, and the final elongation for 7 min. at 68°C. 35 cycles were performed for the amplification of turkey FOXE1. PCR fragments were isolated from 1-1.5% agarose gel using the QIAquick gel Purification Kit (cat. number: 28704) and sequenced by a cycle sequencing reaction by Sanger's dideoxy Terminator Method on a PCR Machine. The sequence of the entire turkey FOXE1 gene and flanking regions was assembled by using the program ApE, a plasmid editor v.1.17.
Molecular cloning and in situ hybridization with FoxE1 GC-rich probe
To clone a chicken FOXE1 cDNA, mRNA was isolated from day 5 chicken embryos using the Qiagen RNeasy Mini Kit (cat. number: 74104). cDNA was synthesized using 1 μg of RNA per a reverse Transcription (RT) reaction with the Tetro cDNA Synthesis Kit (cat. number: Bio-65042). PCR was used for template generation with the GC-rich PCR System Kit (cat. number: 12 140 306 001), Roche Applied Science; 34 cycles of annealing at 50°C were performed. PCR products were isolated and purified with the QIAquick Purification Kit (cat. number: 28106). All protocols were performed in accordance with kit instructions The cDNA template for generating the chicken FOXE1 antisense RNA in situ hybridization probe was produced by RT-PCR using the following primers: forward primer, 5'TTATAAAAGCTTGCGGCCGCAGAATATCGGCAAGGGCAACTACTGGAC3'; reverse primer, 5'GCTCTAGAAATTAACCCTCACTAAAGG gcggggacgaacctGTCG3'. Chicken FOXE1 sequences are bolded, the T3 RNA polymerase binding site is italicized, remaining sequence contains restriction sites (PsiI, HindIII, NotI, XbaI). The PCR generated cDNA template was sequenced to confirm identity. A standard 504 bps RNA probe of FOXE1 was produced using T3 polymerase and in situ hybridizations were performed in according to the GEISHA mRNA Detection Protocol http://geisha.arizona.edu/geisha/protocols.jsp.
We would like to thank Bolton Turkey Farm for kindly providing us turkey blood. We are grateful to Klaus Kaestner for the opportunity of working in the laboratory and sequencing turkey FoxE1, and to Jia Zhang for her excellent technical assistance. We are thankful to Tatiana Yatskievych and Terry Sesepasara for additional in situ hybridization. We would also like to thank Andrea Wahlberg for reading the manuscript and technical assistance. This work is supported by NIH grant GM085226 to SH.
- Hannenhalli S, Kaestner KH: The evolution of Fox genes and their role in development and disease. Nat Rev Genet. 2009, 10 (4): 233-40. 10.1038/nrg2523.View ArticlePubMedPubMed Central
- Zannini M, Avantaggiato V, Biffali E, Arnone MI, Sato K, Pischetola M, Taylor BA, Phillips SJ, Simeone A, Di Lauro R: TTF-2, a new forkhead protein, shows a temporal expression in the developing thyroid which is consistent with a role in controlling the onset of differentiation. EMBO J. 1997, 16 (11): 3185-97. 10.1093/emboj/16.11.3185.View ArticlePubMedPubMed Central
- Perrone L, Pasca di Magliano M, Zannini M, Di Lauro R: The thyroid transcription factor 2 (TTF-2) is a promoter-specific DNA-binding independent transcriptional repressor. Biochem Biophys Res Commun. 2000, 275 (1): 203-8. 10.1006/bbrc.2000.3232.View ArticlePubMed
- Dathan N, Parlato R, Rosica A, De Felice M, Di Lauro R: Distribution of the titf2/foxe1 gene product is consistent with an important role in the development of foregut endoderm, palate, and hair. Dev Dyn. 2002, 224 (4): 450-6. 10.1002/dvdy.10118.View ArticlePubMed
- Eichberger T, Regl G, Ikram MS, Neill GW, Philpott MP, Aberger F, Frischauf AM: FOXE1, a new transcriptional target of GLI2 is expressed in human epidermis and basal cell carcinoma. 2004. J Invest Dermatol. 2004, 122 (5): 1180-7. 10.1111/j.0022-202X.2004.22505.x.View ArticlePubMed
- Brancaccio A, Minichiello A Grachtchouk M, Antonini D, Sheng H, Parlato R, Dathan N, Dlugosz AA, Missero C: Requirement of the forkhead gene Foxe1, a target of sonic hedgehog signaling, in hair follicle morphogenesis. Hum Mol Genet. 2004, 13 (21): 2595-606. 10.1093/hmg/ddh292.View ArticlePubMed
- De Felice M, Ovitt C, Biffali E, Rodriguez-Mallon A, Arra C, Anastassiadis K, Macchia PE, Mattei MG, Mariano A, Schöler H, Macchia V, Di Lauro R: A mouse model for hereditary thyroid dysgenesis and cleft palate. Nat Genet. 1998, 19 (4): 395-8. 10.1038/1289.View ArticlePubMed
- Clifton-Bligh RJ, Wentworth JM, Heinz P, Crisp MS, John R, Lazarus JH, Ludgate M, Chatterjee VK: Mutation of the gene encoding human TTF-2 associated with thyroid agenesis, cleft palate and choanal atresia. Nat Genet. 1998, 19 (4): 399-401. 10.1038/1294.View ArticlePubMed
- El-Hodiri HM, Seufert DW, Nekkalapudi S, Prescott NL, Kelly LE, Jamrich M: Xenopus laevis FoxE1 is primarily expressed in the developing pituitary and thyroid. Int J Dev Biol. 2005, 49 (7): 881-4. 10.1387/ijdb.052011he.View ArticlePubMed
- Nakada C, Iida A, Tabata Y, Watanabe S: Forkhead transcription factor foxe1 regulates chondrogenesis in zebrafish. Zool B Mol Dev Evol. 2009, 312 (8): 827-40.View Article
- Dodgson JB, Delany ME, Cheng HH: Poultry Genome Sequences: Progress and Outstanding Challenges. Cytogenet Genome Res. 2011, 134 (1): 19-26. 10.1159/000324413.View ArticlePubMed
- Graves JA: Sex determination: Birds do it with a Z gene. Nature. 2009, 461 (7261): 177-8. 10.1038/461177a.View ArticlePubMed
- Nanda I, Zend-Ajusch E, Shan Z, Grützner F, Schartl M, Burt DW, Koehler M, Fowler VM, Goodwin G, Schneider WJ, Mizuno S, Dechant G, Haaf T, Schmid M: Conserved synteny between the chicken Z sex chromosome and human chromosome 9 includes the male regulatory gene DMRT1: a comparative (re)view on avian sex determination. Cytogenetics and Cell Genetics. 2000, 89 (1-2): 67-78. 10.1159/000015567.View ArticlePubMed
- Hamburger V, Hamilton HL: A series of normal stages in the development of the chick embryo. 1951. Dev Dyn. 1992, 195 (4): 231-72. 10.1002/aja.1001950404.View ArticlePubMed
- Smuts MS, Hilfer SR, Searls RL: Patterns of cellular proliferation during thyroid organogenesis. J Embryol Exp Morphol. 1978, 48: 269-86.PubMed
- Yatskievych TA, Pascoe S, Antin PB: Expression of the homebox gene Hex during early stages of chick embryo development. Mech Dev. 1999, 80 (1): 107-9. 10.1016/S0925-4773(98)00204-4.View ArticlePubMed
- Parlato R, Rosica A, Rodriguez-Mallon A, Affuso A, Postiglione MP, Arra C, Mansouri A, Kimura S, Di Lauro R, De Felice M: An integrated regulatory network controlling survival and migration in thyroid organogenesis. Dev Biol. 2004, 276 (2): 464-75. 10.1016/j.ydbio.2004.08.048.View ArticlePubMed
- Yaklichkin S, Vekker A, Stayrook S, Lewis M, Kessler DS: Prevalence of the EH1 Groucho interaction motif in the metazoan Fox family of transcriptional regulators. BMC Genomics. 2007, 8: 201-10.1186/1471-2164-8-201.View ArticlePubMedPubMed Central
- Yaklichkin S, Steiner AB, Lu Q, Kessler DS: FoxD3 and Grg4 physically interact to repress transcription and induce mesoderm in Xenopus. J Biol Chem. 2007, 282 (4): 2548-57.View ArticlePubMedPubMed Central
- Roth M, Bonev B, Lindsay J, Lea R, Panagiotaki N, Houart C, Papalopulu NN: FoxG1 and TLE2 act cooperatively to regulate ventral telencephalon formation. Development. 2010, 137 (9): 1553-62. 10.1242/dev.044909.View ArticlePubMedPubMed Central
- Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S: Methods and algorithms for statistical analysis of protein sequences. Proc Natl Acad Sci USA. 1992, 89 (6): 2002-6. 10.1073/pnas.89.6.2002.View ArticlePubMedPubMed Central
- Hanna-Rose W, Hansen U: Active repression mechanisms of eukaryotic transcription repressors. Trends Genet. 1996, 12 (6): 229-34. 10.1016/0168-9525(96)10022-6.View ArticlePubMed
- Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13 (5): 555-6.PubMed
- Yang Z: Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998, 15 (5): 568-73.View ArticlePubMed
- Taya Y, O'Kane S, Ferguson MW: Pathogenesis of cleft palate in TGF-beta3 knockout mice. Development. 1999, 126 (17): 3869-79.PubMed
- Hishinuma A, Ohmika N, Namatame T, Ieiri T: TTF-2 stimulates expression of 17 genes, including one novel thyroid-specific gene which might be involved in thyroid development. Mol Cell Endocrinol. 2004, 221 (1-2): 33-46. 10.1016/j.mce.2004.04.003.View ArticlePubMed
- Gupton SL, Anderson KL, Kole TP, Fischer RS, Ponti A, Hitchcock-DeGregori SE, Danuser G, Fowler VM, Wirtz D, Hanein D, Waterman-Storer CM: Cell migration without a lamellipodium: translation of actin dynamics into cell movement mediated by tropomyosin. J Cell Biol. 2005, 168 (4): 619-31. 10.1083/jcb.200406063.View ArticlePubMedPubMed Central
- Bach CT, Creed S, Zhong J, Mahmassani M, Schevzov G, Stehn J, Cowell LN, Naumanen P, Lappalainen P, Gunning PW, O'Neill GM: Tropomyosin isoform expression regulates the transition of adhesions to determine cell speed and direction. Mol Cell Biol. 2009, 29 (6): 1506-14. 10.1128/MCB.00857-08.View ArticlePubMedPubMed Central
- Leavesley DI, Schwartz MA, Rosenfeld M, Cheresh DA: Integrin beta 1- and beta 3-mediated endothelial cell migration is triggered through distinct signaling mechanisms. J Cell Biol. 1993, 121 (1): 163-70. 10.1083/jcb.121.1.163.View ArticlePubMed
- Venza I, Visalli M, Parrillo L, De Felice M, Teti D, Venza M: MSX1 and TGF-beta3 are novel target genes functionally regulated by FOXE1. Mol Genet. 2011, 20 (5): 1016-25.
- Gato A, Martinez ML, Tudela C, Alonso I, Moro JA, Formoso MA, Ferguson MW, Martínez-Alvarez C: TGF-beta(3)-induced chondroitin sulphate proteoglycan mediates palatal shelf adhesion. Dev Biol. 2002, 250 (2): 393-405. 10.1006/dbio.2002.0792.View ArticlePubMed
- Mansouri A, Chowdhury K, Gruss P: Follicular cells of the thyroid gland require Pax8 gene function. Nat Genet. 1998, 19: 87-90. 10.1038/ng0598-87.View ArticlePubMed
- Hughes AL, Friedman R: Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Mol Biol Evol. 2008, 25 (12): 2681-8. 10.1093/molbev/msn207.View ArticlePubMedPubMed Central
- Andrioli LP, Oberstein AL, Corado MS, Yu D, Small S: Groucho-dependent repression by sloppy-paired 1 differentially positions anterior pair-rule stripes in the Drosophila embryo. Dev Biol. 2004, 276: 541-551. 10.1016/j.ydbio.2004.09.025.View ArticlePubMed
- Dermitzakis ET, Clark AG: Differential selection after duplication in mammalian developmental genes. Mol Biol Evol. 2001, 18 (4): 557-62.View ArticlePubMed
- Neduva V, Russell RB: Linear motifs: evolutionary interaction switches. FEBS Lett. 2005, 579 (15): 3342-5. 10.1016/j.febslet.2005.04.005.View ArticlePubMed
- Yamamoto M, Kuroiwa A: Hoxa-11 and Hoxa-13 are involved in repression of MyoD during limb muscle development. Dev Growth Differ. 2003, 45 (5-6): 485-98. 10.1111/j.1440-169X.2003.00715.x.View ArticlePubMed
- Williams TM, Williams ME, Heaton JH, Gelehrter TD, Innis JW: Group 13 HOX proteins interact with the MH2 domain of R-Smads and modulate Smad transcriptional activation functions independent of HOX DNA-binding capability. Nucleic Acids Res. 2005, 33 (14): 4475-84. 10.1093/nar/gki761.View ArticlePubMedPubMed Central
- Wong EY, Wang XA, Mak SS, Sae-Pang JJ, Ling KW, Fritzsch B, Sham MH: Hoxb3 negatively regulates Hoxb1 expression in mouse hindbrain patterning. Dev Biol. 2011, 352 (2): 382-92. 10.1016/j.ydbio.2011.02.003.View ArticlePubMed
- Manley NR, Capecchi MR: Hox group 3 paralogs regulate the development and migration of the thymus, thyroid, and parathyroid glands. Dev Biol. 1998, 195 (1): 1-15. 10.1006/dbio.1997.8827.View ArticlePubMed
- Carroll SB: Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell. 2008, 134 (1): 25-36. 10.1016/j.cell.2008.06.030.View ArticlePubMed
- Wagner GP, Lynch VJ: The gene regulatory logic of transcription factor evolution. Trends Ecol Evol. 2008, 23 (7): 377-85. 10.1016/j.tree.2008.03.006.View ArticlePubMed
- Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000, 302 (1): 205-17. 10.1006/jmbi.2000.4042.View ArticlePubMed
- Felsenstein J: Mathematics vs. Evolution: Mathematical Evolutionary Theory. Science. 1989, 246 (4932): 941-2. 10.1126/science.246.4932.941.View ArticlePubMed
- Darnell DK, Kaur S, Stanislaw S, Davey S, Konieczka JH, Yatskievych TA, Antin PB, GEISHA: An In situ hybridization gene expression resource for the chicken embryo. Cytogenet Genome Res. 2007, 117 (1-4): 30-5. 10.1159/000103162.View ArticlePubMed
- Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res. 2004, 14 (6): 1188-90. 10.1101/gr.849004.View ArticlePubMedPubMed Central
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.