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Research Article

In silico molecular characterization of TGF-β gene family in Bufo bufo: genome-wide analysis

, , , , , , & show all
Received 03 Oct 2023, Accepted 27 Jan 2024, Published online: 12 Feb 2024

References

  • Agrawal, R., Tran, U., & Wessely, O. (2009). The miR-30 miRNA family regulates Xenopus pronephros development and targets the transcription factor Xlim1/Lhx1. Development (Cambridge, England), 136(23), 3927–3936. https://doi.org/10.1242/dev.037432
  • Aguilar, O. A., Hadj-Moussa, H., & Storey, K. B. (2016). Regulation of SMAD transcription factors during freezing in the freeze tolerant wood frog, Rana sylvatica. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology, 201, 64–71. https://doi.org/10.1016/j.cbpb.2016.07.003
  • Aldea, D., Hanna, P., Munoz, D., Espinoza, J., Torrejon, M., Sachs, L., Buisine, N., Oulion, S., Escriva, H., & Marcellini, S. (2013). Evolution of the vertebrate bone matrix: An expression analysis of the network forming collagen paralogues in amphibian osteoblasts. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, 320(6), 375–384. https://doi.org/10.1002/jez.b.22511
  • Asashima, M., Uochi, T., Kinoshita, K., Nishihara, R., Ariizumi, T., & Fukui, A. (2012). Morphogenesis by activins during early amphibian development, Inhibin, Activin and Follistatin: Regulatory Functions in System and Cell Biology. 204.
  • Aykul, S., & Martinez-Hackert, E. (2016). New ligand binding function of human cerberus and role of proteolytic processing in regulating ligand–Receptor interactions and antagonist activity. Journal of Molecular Biology, 428(3), 590–602. https://doi.org/10.1016/j.jmb.2016.01.011
  • Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). MEME Suite: Tools for motif discovery and searching. Nucleic Acids Research, 37(Web Server issue), W202–208. https://doi.org/10.1093/nar/gkp335
  • Bhat, R., Chakraborty, M., Mian, I. S., & Newman, S. A. (2014). Structural divergence in vertebrate phylogeny of a duplicated prototype galectin. Genome Biology and Evolution, 6(10), 2721–2730. https://doi.org/10.1093/gbe/evu215
  • Bo, X., Wu, M., Xiao, H., & Wang, H. (2018). Transcriptome analyses reveal molecular mechanisms that regulate endochondral ossification in amphibian Bufo gargarizans during metamorphosis. Biochimica et Biophysica Acta. General Subjects, 1862(12), 2632–2644. https://doi.org/10.1016/j.bbagen.2018.07.032
  • Bonetti, M. F., & Wiens, J. J. (2014). Evolution of climatic niche specialization: A phylogenetic analysis in amphibians. Proceedings of the Royal Society B: Biological Sciences, 281(1795), 20133229.
  • Buchan, D. W. A., & Jones, D. T. (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research, 47(1), 402–407.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8), 1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
  • Chen, L., Dong, C., Kong, S., Zhang, J., Li, X., & Xu, P. (2017). Genome wide identification, phylogeny, and expression of bone morphogenetic protein genes in tetraploidized common carp (Cyprinus carpio). Gene, 627, 157–163. https://doi.org/10.1016/j.gene.2017.06.020
  • Cheng, C., Yan, K.-K., Hwang, W., Qian, J., Bhardwaj, N., Rozowsky, J., Lu, Z. J., Niu, W., Alves, P., Kato, M., Snyder, M., & Gerstein, M. (2011). Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLOS Computational Biology, 7(11), 1002190.
  • Chen, W., Qian, W., Miao, K., Qian, R., Yuan, S., Liu, W., Dai, J., Hu, C., & Chang, Q. (2022). Comparative mitogenomics of true frogs (Ranidae, Anura), and its implications for the phylogeny and evolutionary history of Rana. Animals, 12(10), 1250. https://doi.org/10.3390/ani12101250
  • Chen, X., Qi, Y., Wu, Z., Wang, X., Li, J., Zhao, D., Hou, H., Li, Y., Yu, Z., Liu, W., Wang, M., Ren, Y., Li, Z., Yang, H., & Xu, Y. (2021). Structural insights into preinitiation complex assembly on core promoters. Science, 372(6541), 8490.
  • Chen, J., Zhang, C.-Y., Chen, J.-Y., Seah, R. W. X., Zhang, L., Ma, L., & Ding, G.-H. (2023). Host defence peptide LEAP2 contributes to antimicrobial activity in a mustache toad (Leptobrachium liui). BMC Veterinary Research, 19(1), 47.
  • Cheon, H., Yang, J., & Stark, G. (2011). The functions of signal transducers and activators of transcriptions 1 and 3 as cytokine-inducible proteins. Journal of Interferon & Cytokine Research: The Official Journal of the International Society for Interferon and Cytokine Research, 31(1), 33–40. https://doi.org/10.1089/jir.2010.0100
  • Dathe, K., Kjaer, K. W., Brehm, A., Meinecke, P., Nürnberg, P., Neto, J. C., Brunoni, D., Tommerup, N., Ott, C. E., Klopocki, E., Seemann, P., & Mundlos, S. (2009). Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. American Journal of Human Genetics, 84(4), 483–492. https://doi.org/10.1016/j.ajhg.2009.03.001
  • Diaz-Garcia, L., Covarrubias-Pazaran, G., Schlautman, B., & Zalapa, J. (2017). SOFIA: An R package for enhancing genetic visualization with circos. Journal of Heredity, 108(4), 443–448. https://doi.org/10.1093/jhered/esx023
  • Edgar, R. C., & Batzoglou, S. (2006). Multiple sequence alignment. Current Opinion in Structural Biology, 16(3), 368–373. https://doi.org/10.1016/j.sbi.2006.04.004
  • Elkasrawy, M., Immel, D., Wen, X., Liu, X., Liang, L.-F., & Hamrick, M. W. (2012). Immunolocalization muscle and bone healing. The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society, 60(1), 22–30. https://doi.org/10.1369/0022155411425389
  • Epstein, B., & Storfer, A. (2016). Comparative genomics of an emerging amphibian virus, G3-Genes Genom. G3 (Bethesda, Md.), 6(1), 15–27. https://doi.org/10.1534/g3.115.023762
  • Ewen‐Campen, B., Schwager, E. E., & Extavour, C. G. (2010). The molecular machinery of germ line specification. Molecular Reproduction and Development, 77(1), 3–18. https://doi.org/10.1002/mrd.21091
  • Ezer, D., Zabet, N. R., & Adryan, B. (2014). Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression. Computational and Structural Biotechnology Journal. 10(17), 63–69. https://doi.org/10.1016/j.csbj.2014.07.005
  • Fan, W., Jiang, Y., Zhang, M., Yang, D., Chen, Z., Sun, H., Lan, X., Yan, F., Xu, J., & Yuan, W. (2017). Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians’ skin. PloS One, 12(12), e0190023. https://doi.org/10.1371/journal.pone.0190023
  • Finn R. D., Clements J., Arndt W., Miller B. L., Wheeler T. J., Schreiber F., Bateman A. & Eddy S.R. (2015). HMMER web server: 2015 update. Nucleic Acids Research, 43, 30–38.
  • Finn R. D., Clements J. & Eddy S. R. (2011). HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 39, 29–37.
  • Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. e., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. Springer.
  • Ghil, J., & Chung, H. (2004). Evidence that platelet derived growth factor (PDGF) action is required for mesoderm patterning in early amphibian (Xenopus laevis) embryogenesis. International Journal of Developmental Biology, 43(4), 329–334.
  • Ghosh, R., Upadhayay, A., & Roy, A. (2017). In silico analysis, structure modeling and phosphorylation site prediction of vitellogenin protein from Gibelion Catla. Journal of Applied Biotechnology and Bioengineering, 3(1), 03–55.
  • Gotea, V., Visel, A., Westlund, J. M., Nobrega, M. A., Pennacchio, L. A., & Ovcharenko, I. (2010). Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Research, 20(5), 565–577. https://doi.org/10.1101/gr.104471.109
  • Gross, M.-L., Piecha, G., Bierhaus, A., Hanke, W., Henle, T., Schirmacher, P., & Ritz, E. (2011). Glycated and carbamylated albumin are more “nephrotoxic” than unmodified albumin in the amphibian kidney. American Journal of Physiology-Renal Physiology , 301(3), 476–485.
  • Haddad, G., Hanington, P. C., Wilson, E. C., Grayfer, L., & Belosevic, M. (2008). Molecular and functional characterization of goldfish (Carassius auratus L.) transforming growth factor beta. Developmental and Comparative Immunology, 32(6), 654–663. https://doi.org/10.1016/j.dci.2007.10.003
  • Hellsten, U., Harland, R. M., Gilchrist, M. J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N. H., Shu, S., Taher, L., Blitz, I. L., Blumberg, B., Dichmann, D. S., Dubchak, I., Amaya, E., Detter, J. C., Fletcher, R., Gerhard, D. S., Goodstein, D., … Rokhsar, D. S. (2010). The genome of the Western clawed frog Xenopus tropicalis. Science (New York, N.Y.), 328(5978), 633–636. https://doi.org/10.1126/science.1183670
  • Huminiecki, L., Goldovsky, L., Freilich, S., Moustakas, A., Ouzounis, C., & Heldin, C.-H. (2009). Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom. BMC Evolutionary Biology. 9, 1–17.
  • Jiang, D., & Liang, J. (2019). A long noncoding RNA links TGF-β signaling in lung fibrosis. American Journal of Respiratory and Critical Care Medicine, 200(2), 123–125. https://doi.org/10.1164/rccm.201812-2313ED
  • Kawasumi, A., Sagawa, N., Hayashi, S., Yokoyama, H., & Tamura, K. (2013). Wound healing in mammals and amphibians: Toward limb regeneration in mammals. In E. Heber-Katz, & D. L. Stocum (Eds.), New perspectives in regeneration (pp. 33–49). Springer Berlin Heidelberg.
  • Klaus, A., Müller, M., Schulz, H., Saga, Y., Martin, J. F., & Birchmeier, W. (2012). Wnt/β-catenin and Bmp signals control distinct sets of transcription factors in cardiac progenitor cells. Proceedings of the National Academy of Sciences of the United States of America, 109(27), 10921–10926. https://doi.org/10.1073/pnas.1121236109
  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054
  • Letunic, I., & Bork, P. (2021). Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Journal of Nucleic Acids, 49(1), 293–296.
  • Lévesque, M., Gatien, S., Finnson, K., Desmeules, S., Villiard, E., Pilote, M., Philip, A., & Roy, S. (2007). Transforming growth factor: β signaling is essential for limb regeneration in axolotls. PloS One, 2(11), e1227. https://doi.org/10.1371/journal.pone.0001227
  • Lienkamp, S. S. (2016). Using Xenopus to study genetic kidney diseases. Seminars in Cell & Developmental Biology, 51, 117–124. https://doi.org/10.1016/j.semcdb.2016.02.002
  • Liu, S., Guo, J., Cheng, X., Li, W., Lyu, S., Chen, X., Li, Q., & Wang, H. (2022). Molecular evolution of transforming growth factor-β (TGF-β) gene family and the functional characterization of lamprey TGF-β2. Frontiers in Immunology, 13, 836226. https://doi.org/10.3389/fimmu.2022.836226
  • Liu, H., Mu, L., Tang, J., Shen, C., Gao, C., Rong, M., Zhang, Z., Liu, J., Wu, X., Yu, H., & Lai, R. (2014). A potential wound healing-promoting peptide from frog skin. The International Journal of Biochemistry & Cell Biology, 49, 32–41. https://doi.org/10.1016/j.biocel.2014.01.010
  • Lochab, A. K., & Extavour, C. G. (2017). Bone Morphogenetic Protein (BMP) signaling in animal reproductive system development and function. Developmental Biology, 427(2), 258–269. https://doi.org/10.1016/j.ydbio.2017.03.002
  • Loh, C.-Y., Arya, A., Naema, A. F., Wong, W. F., Sethi, G., & Looi, C. Y. (2019). Signal transducer and activator of transcription (STATs) proteins in cancer and inflammation: Functions and therapeutic implication. Frontiers in Oncology, 9, 48. https://doi.org/10.3389/fonc.2019.00048
  • Lopez-Hernandez, A., Sberna, S., & Campaner, S. (2021). Emerging principles in the transcriptional control by YAP and TAZ. Cancers, 13(16), 4242. https://doi.org/10.3390/cancers13164242
  • Lu, B., Jiang, J., Wu, H., Chen, X., Song, X., Liao, W., & Fu, J. (2021). A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans). Molecular Ecology Resources, 21(4), 1256–1273. https://doi.org/10.1111/1755-0998.13319
  • Lukas, P. (2018). The influence of bapx1 on amphibian head development and its role for the development of evolutionary novelties. Dissertation.
  • Mable, B., Alexandrou, M., & Taylor, M. (2011). Genome duplication in amphibians and fish: An extended synthesis. Journal of Zoology, 284(3), 151–182. https://doi.org/10.1111/j.1469-7998.2011.00829.x
  • Makanae, A., Mitogawa, K., & Satoh, A. (2016). Cooperative inputs of Bmp and Fgf signaling induce tail regeneration in urodele amphibians. Developmental Biology, 410(1), 45–55. https://doi.org/10.1016/j.ydbio.2015.12.012
  • McLennan, I. S., & Pankhurst, M. W. (2015). Anti-Müllerian hormone is a gonadal cytokine with two circulating forms and cryptic actions. Journal of Endocrinology, 226(3), 45–57.
  • Mehta, A. S., & Singh, A. (2019). Insights into regeneration tool box: An animal model approach. Developmental Biology, 453(2), 111–129. https://doi.org/10.1016/j.ydbio.2019.04.006
  • Menger, B., Vogt, P. M., Kuhbier, J. W., & Reimers, K. (2010). Applying amphibian limb regeneration to human wound healing: A review. Annals of Plastic Surgery, 65(5), 504–510. https://doi.org/10.1097/SAP.0b013e3181d376f9
  • Miura, S., Hanaoka, K., & Togashi, S. (2008). Skeletogenesis in Xenopus tropicalis: Characteristic bone development in an anuran amphibian. Bone, 43(5), 901–909. https://doi.org/10.1016/j.bone.2008.07.005
  • Montagner, M., Martello, G., & Piccolo, S. (2016). Monitoring Smad activity in vivo using the Xenopus model system. Methods in molecular biology, 1344, 245–259.
  • Morikawa, M., Derynck, R., & Miyazono, K. (2016). TGF-β and the TGF-β family: Context-dependent roles in cell and tissue physiology. Cold Spring Harbor Perspectives in Biology, 8(5), 21873.
  • Neff, A. W., King, M. W., & Mescher, A. L. (2011). Dedifferentiation and the role of sall4 in reprogramming and patterning during amphibian limb regeneration. Developmental Dynamics: An Official Publication of the American Association of Anatomists, 240(5), 979–989. https://doi.org/10.1002/dvdy.22554
  • Olivieri, D. N., Mirete-Bachiller, S., & Gambón-Deza, F. (2021). Insights into the evolution of IG genes in Amphibians and reptiles. Developmental and Comparative Immunology, 114, 103868. https://doi.org/10.1016/j.dci.2020.103868
  • Opazo, J. C., Kuraku, S., Zavala, K., Toloza‐Villalobos, J., & Hoffmann, F. G. (2019). Evolution of nodal and nodal‐related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates. Evolution & Development, 21(4), 205–217. https://doi.org/10.1111/ede.12292
  • Opazo, J. C., & Zavala, K. (2018). Phylogenetic evidence for independent origins of GDF1 and GDF3 genes in amphibians and mammals. BioRxiv, 293522.
  • Oshima, Y., Naruse, K., Nakamura, Y., & Nakamura, M. (2009). Sox3: A transcription factor for Cyp19 expression in the frog Rana rugosa. Gene, 445(1-2), 38–48. https://doi.org/10.1016/j.gene.2009.05.011
  • Pabijan, M., Palomar, G., Antunes, B., Antoł, W., Zieliński, P., & Babik, W. (2020). Evolutionary principles guiding amphibian conservation. Evolutionary Applications, 13(5), 857–878. https://doi.org/10.1111/eva.12940
  • Pan, Q., Kay, T., Depincé, A., Adolfi, M., Schartl, M., Guiguen, Y., & Herpin, A. (2021). Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 376(1832), 20200091. https://doi.org/10.1098/rstb.2020.0091
  • Pantic, J. M., Jovanovic, I. P., Radosavljevic, G. D., Arsenijevic, N. N., Conlon, J. M., & Lukic, M. L. (2017). The potential of frog skin-derived peptides for development into therapeutically-valuable immunomodulatory agents. Molecules (Basel, Switzerland), 22(12), 2071. https://doi.org/10.3390/molecules22122071
  • Predes, D., Cruz, J. V. R., Abreu, J. G., & Mendes, F. A. (2019). CUB domain-containing protein 1 (CDCP1) binds transforming growth factor beta family members and increase TGF-β1 signaling pathway. Experimental Cell Research, 383(1), 111499. https://doi.org/10.1016/j.yexcr.2019.111499
  • Qi, Z., Nie, P., Secombes, C. J., & Zou, J. (2010). Intron-containing type I and type III IFN coexist in amphibians: Refuting the concept that a retroposition event gave rise to type I IFNs. Journal of Immunology (Baltimore, Md.: 1950), 184(9), 5038–5046. https://doi.org/10.4049/jimmunol.0903374
  • Rasche, H., & Hiltemann, S. (2020). Galactic Circos: User-friendly Circos plots within the Galaxy platform. GigaScience, 9(6), 1-6. https://doi.org/10.1093/gigascience/giaa065
  • Rashmi, R., Nandi, C., & Majumdar, S. (2021). Evolutionarily conserved regions of THAP9 transposase reveal new motifs for subcellular localization and post-translational modification. BioRxiv, 454642.
  • Ricci, L., Cabrera, F., Lotito, S., & Tiozzo, S. (2016). Redeployment of germ layers related TFs shows regionalized expression during two non-embryonic developments. Developmental Biology, 416(1), 235–248. https://doi.org/10.1016/j.ydbio.2016.05.016
  • Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L. B., Hood, L., & Galas, D. J. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (New York, N.Y.), 328(5978), 636–639. https://doi.org/10.1126/science.1186802
  • Roelants, K., Fry, B. G., Norman, J. A., Clynen, E., Schoofs, L., & Bossuyt, F. (2010). Identical skin toxins by convergent molecular adaptation in frogs. Current Biology: CB, 20(2), 125–130. https://doi.org/10.1016/j.cub.2009.11.015
  • Roelants, K., Fry, B. G., Ye, L., Stijlemans, B., Brys, L., Kok, P., Clynen, E., Schoofs, L., Cornelis, P., & Bossuyt, F. (2013). Origin and functional diversification of an amphibian defense peptide arsenal. PLoS Genetics, 9(8), e1003662. https://doi.org/10.1371/journal.pgen.1003662
  • Rogers, C., Jayasena, C., Nie, S., & Bronner, M. E. (2012). Neural crest specification: Tissues, signals, and transcription factors. Wiley Interdisciplinary Reviews. Developmental Biology, 1(1), 52–68. https://doi.org/10.1002/wdev.8
  • Sánchez‐Montes, G., Wang, J., Ariño, A. H., & Martínez‐Solano, Í. (2018). Mountains as barriers to gene flow in amphibians: Quantifying the differential effect of a major mountain ridge on the genetic structure of four sympatric species with different life history traits. Journal of Biogeography. 45(2), 318–331. https://doi.org/10.1111/jbi.13132
  • Sarvagalla, S., Kolapalli, S. P., & Vallabhapurapu, S. (2019). The two sides of YY1 in cancer: A friend and a foe. Frontiers in Oncology, 9, 1230. https://doi.org/10.3389/fonc.2019.01230
  • Schubert, F. R., Sobreira, D. R., Janousek, R. G., Alvares, L. E., & Dietrich, S. (2014). Dact genes are chordate specific regulators at the intersection of Wnt and Tgf-β signaling pathways. BMC Evolutionary Biology, 14, 1–20.
  • Sghaier, H., Ghedira, K., Benkahla, A., & Barkallah, I. (2008). Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria. BMC Genomics, 9(1), 297. https://doi.org/10.1186/1471-2164-9-297
  • Sigrist, C. J. A., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., & Hulo, N. (2009). PROSITE, a protein domain database for functional characterization and annotation. Journal of Nucleic Acids, 38(1), 161–166.
  • Stephens, A. D., Banigan, E. J., & Marko, J. F. (2019). Chromatin’s physical properties shape the nucleus and its functions. Current Opinion in Cell Biology, 58, 76–84. https://doi.org/10.1016/j.ceb.2019.02.006
  • Sun, Y.-B., Xiong, Z.-J., Xiang, X.-Y., Liu, S.-P., Zhou, W.-W., Tu, X.-L., Zhong, L., Wang, L., Wu, D.-D., Zhang, B.-L., Zhu, C.-L., Yang, M. M., Chen, H.-M., & Li, F. (2015). Whole-genome sequence of the Tibetan frog and the comparative evolution of tetrapod genomes. Proceedings of the National Academy of Sciences of the United States of America, 112(11), 1257–1262.
  • Suzuki, A., Uno, Y., Takahashi, S., Grimwood, J., Schmutz, J., Mawaribuchi, S., Yoshida, H., Takebayashi-Suzuki, K., Ito, M., Matsuda, Y., Rokhsar, D., & Taira, M. (2017). Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Developmental Biology, 426(2), 236–244. https://doi.org/10.1016/j.ydbio.2016.04.014
  • Suzuki, A., Yoshida, H., van Heeringen, S. J., Takebayashi-Suzuki, K., Veenstra, G. J. C., & Taira, M. (2017). Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Developmental Biology, 426(2), 336–359. https://doi.org/10.1016/j.ydbio.2016.09.016
  • Tantin, D. (2013). Oct transcription factors in development and stem cells: Insights and mechanisms. Development (Cambridge, England), 140(14), 2857–2866. https://doi.org/10.1242/dev.095927
  • Tsutsumi, R., Yamada, S., & Agata, K. (2016). Functional joint regeneration is achieved using reintegration mechanism in Xenopus laevis. Regeneration (Oxford, England), 3(1), 26–38. https://doi.org/10.1002/reg2.49
  • Wang, Y., Tang, H., DeBarry, J. D., Tan, X., Li, J., Wang, X., Lee, T-h., Jin, H., Marler, B., Guo, H., Kissinger, J. C., & Paterson, A. H. (2012). MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Journal of Nucleic Acids, 40(7), 49–49.
  • Weiss, A., & Attisano, L. (2013). The TGFbeta superfamily signaling pathway. Wiley Interdisciplinary Reviews. Developmental Biology, 2(1), 47–63. https://doi.org/10.1002/wdev.86
  • Whitfield, T. W., Wang, J., Collins, P. J., Partridge, E. C., Aldred, S. F., Trinklein, N. D., Myers, R. M., & Weng, Z. (2012). Functional analysis of transcription factor binding sites in human promoters. Genome Biology, 13(9), R50. https://doi.org/10.1186/gb-2012-13-9-r50
  • Wu, M. Y., & Hill, C. S. (2009). TGF-β superfamily signaling in embryonic development and homeostasis. Developmental Cell, 16(3), 329–343. https://doi.org/10.1016/j.devcel.2009.02.012
  • Xu, S., Zhang, S., Zhang, W., Liu, H., Wang, M., Zhong, L., Bian, W., & Chen, X. (2022). Genome-wide identification, phylogeny, and expression profile of the Dmrt (Doublesex and Mab-3 Related Transcription Factor) gene family in channel catfish (Ictalurus punctatus). Frontiers in Genetics, 13, 891204. https://doi.org/10.3389/fgene.2022.891204
  • Yang, S., Zhang, X., Li, X., Yin, X., Teng, L., Ji, G., & Li, H. (2022). Evolutionary and expression analysis of mov10 and mov10l1 reveals their origin, duplication and divergence. International Journal of Molecular Sciences, 23(14), 7523. https://doi.org/10.3390/ijms23147523
  • Young, J. J., Kjolby, R. A., Wu, G., Wong, D., Hsu, S-W., & Harland, R. M. (2017). Noggin is required for first pharyngeal arch differentiation in the frog Xenopus tropicalis. Developmental Biology, 426(2), 245–254. https://doi.org/10.1016/j.ydbio.2016.06.034
  • Zeng, Y., Gong, M., Lin, M., Gao, D., & Zhang, Y. (2020). A review about transcription factor binding sites prediction based on deep learning. IEEE Access, 8, 219256–219274. https://doi.org/10.1109/ACCESS.2020.3042903

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