Abstract
The anuran Xenopus laevis has been studied for decades as a model for vertebrate cell and developmental biology. More recently, the highly related species Xenopus tropicalis has offered the opportunity to carry out genetic studies due to its diploid genome as compared to the pseudo-tetraploid Xenopus laevis. Amphibians undergo a biphasic development: embryogenesis to produce a free-living tadpoles and subsequent metamorphosis to transform the tadpole to a frog. This second phase mimics the so-called postembryonic development in mammals when many organs/tissues mature into their adult form in the presence of high levels of plasma thyroid hormone (T3). The total dependence of amphibian metamorphosis on T3 offers a unique opportunity to study postembryonic development in vertebrates, especially with the recent development gene editing technologies that function in amphibians. Here, we first review the basic molecular understanding of the regulation of Xenopus metamorphosis by T3 and T3 receptors (TRs), and then describe a detailed method to use CRISPR to knock out the TR-coactivator SRC3 (steroid receptor coactivator 3), a histone acetyltransferase, in order to study its involvement in gene regulation by T3 in vivo and Xenopus development.
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References
Shi Y-B (1999) Amphibian metamorphosis: from morphology to molecular biology. Wiley, New York
Tata JR (1993) Gene expression during metamorphosis: an ideal model for post-embryonic development. BioEssays 15(4):239–248
Burke LJ, Baniahmad A (2000) Co-repressors 2000. FASEB J 14(13):1876–1888
Jones PL, Shi Y-B (2003) N-CoR-HDAC corepressor complexes: roles in transcriptional regulation by nuclear hormone receptors. In: Workman JL (ed) Current topics in microbiology and immunology: protein complexes that modify chromatin, vol 274. Springer, Berlin, pp 237–268
Glass CK, Rosenfeld MG (2000) The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev 14(2):121–141
Zhang J, Lazar MA (2000) The mechanism of action of thyroid hormones. Annu Rev Physiol 62:439–466
Yoon H-G, Chan DW, Huang ZQ, Li J, Fondell JD, Qin J, Wong J (2003) Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. EMBO J 22:1336–1346
Zhang J, Kalkum M, Chait BT, Roeder RG (2002) The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol Cell 9:611–623
Ishizuka T, Lazar MA (2003) The N-CoR/histone deacetylase 3 complex is required for repression by thyroid hormone receptor. Mol Cell Biol 23:5122–5131
Guenther MG, Lane WS, Fischle W, Verdin E, Lazar MA, Shiekhattar R (2000) A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness. Genes Dev 14:1048–1057
Li J, Wang J, Wang J, Nawaz Z, Liu JM, Qin J, Wong J (2000) Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3. EMBO J 19:4342–4350
Shi YB, Matsuura K, Fujimoto K, Wen L, Fu L (2012) Thyroid hormone receptor actions on transcription in amphibia: the roles of histone modification and chromatin disruption. Cell Biosci 2(1):42. https://doi.org/10.1186/2045-3701-2-42 2045-3701-2-42 [pii]
Jones PL, Sachs LM, Rouse N, Wade PA, Shi YB (2001) Multiple N-CoR complexes contain distinct histone deacetylases. J Biol Chem 276(12):8807–8811
Heimeier RA, Hsia VS-C, Shi Y-B (2008) Participation of BAF57 and BRG1-containing chromatin remodeling complexes in thyroid hormone-dependent gene activation during vertebrate development. Mol Endocrinol 22:1065–1077
Huang Z-Q, Li J, Sachs LM, Cole PA, Wong J (2003) A role for cofactor–cofactor and cofactor–histone interactions in targeting p300, SWI/SNF and Mediator for transcription. EMBO J 22:2146–2155
Demarest SJ, Martinez-Yamout M, Chung J, Chen H, Xu W, Dyson HJ, Evans RM, Wright PE (2002) Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature 415:549–553
Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR (1999) Regulation of transcription by a protein methyltransferase. Science 284:2174–2177
Koh SS, Chen DG, Lee YH, Stallcup MR (2001) Synergistic enhancement of nuclear receptor function by p160 coactivators and two coactivators with protein methyltransferase activities. J Biol Chem 276:1089–1098
Matsuda H, Paul BD, Choi CY, Hasebe T, Shi Y-B (2009) Novel functions of protein arginine methyltransferase 1 in thyroid hormone receptor-mediated transcription and in the regulation of metamorphic rate in Xenopus laevis. Mol Cell Biol 29:745–757
Matsuda H, Paul BD, Choi CY, Shi Y-B (2007) Contrasting effects of two alternative splicing forms of coactivator-associated arginine methyltransferase 1 on thyroid hormone receptor-mediated transcription in Xenopus laevis. Mol Endocrinol 21(5):1082–1094
Matsuura K, Fujimoto K, Das B, Fu L, Lu CD, Shi YB (2012) Histone H3K79 methyltransferase Dot1L is directly activated by thyroid hormone receptor during Xenopus metamorphosis. Cell Biosci 2(1):25. https://doi.org/10.1186/2045-3701-2-25 2045-3701-2-25 [pii]
Yen PM (2001) Physiological and molecular basis of thyroid hormone action. Physiol Rev 81(3):1097–1142
McKenna NJ, O’Malley BW (2001) Nuclear receptors, coregulators, ligands, and selective receptor modulators: making sense of the patchwork quilt. Ann N Y Acad Sci 949:3–5
Li J, O’Malley BW, Wong J (2000) p300 requires its histone acetyltransferase activity and SRC-1 interaction domain to facilitate thyroid hormone receptor activation in chromatin. Mol Cell Biol 20(6):2031–2042
Shi Y-B, Wong J, Puzianowska-Kuznicka M, Stolow M (1996) Tadpole competence and tissue-specific temporal regulation of amphibian metamorphosis: roles of thyroid hormone and its receptors. BioEssays 18:391–399
Sachs LM, Damjanovski S, Jones PL, Li Q, Amano T, Ueda S, Shi YB, Ishizuya-Oka A (2000) Dual functions of thyroid hormone receptors during Xenopus development. Comp Biochem Physiol B Biochem Mol Biol 126(2):199–211
Yaoita Y, Brown DD (1990) A correlation of thyroid hormone receptor gene expression with amphibian metamorphosis. Genes Dev 4(11):1917–1924
Wong J, Shi Y-B (1995) Coordinated regulation of and transcriptional activation by Xenopus thyroid hormone and retinoid X receptors. J Biol Chem 270:18479–18483
Wang X, Matsuda H, Shi Y-B (2008) Developmental regulation and function of thyroid hormone receptors and 9-cis retinoic acid receptors during Xenopus tropicalis metamorphosis. Endocrinology 149:5610–5618
Leloup J, Buscaglia M (1977) La triiodothyronine: hormone de la métamorphose des amphibiens. CR Acad Sci 284:2261–2263
Puzianowska-Kuznicka M, Damjanovski S, Shi Y-B (1997) Both thyroid hormone and 9-cis retinoic acid receptors are required to efficiently mediate the effects of thyroid hormone on embryonic development and specific gene regulation in Xenopus laevis. Mol Cell Biol 17:4738–4749
Nakajima K, Yaoita Y (2003) Dual mechanisms governing muscle cell death in tadpole tail during amphibian metamorphosis. Dev Dyn 227:246–255
Schreiber AM, Brown DD (2003) Tadpole skin dies autonomously in response to thyroid hormone at metamorphosis. Proc Natl Acad Sci U S A 100:1769–1774
Das B, Schreiber AM, Huang H, Brown DD (2002) Multiple thyroid hormone-induced muscle growth and death programs during metamorphosis in Xenopus laevis. Proc Natl Acad Sci U S A 99:12230–12235
Schreiber AM, Das B, Huang H, Marsh-Armstrong N, Brown DD (2001) Diverse developmental programs of Xenopus laevis metamorphosis are inhibited by a dominant negative thyroid hormone receptor. Proc Natl Acad Sci U S A 98:10739–10744
Buchholz DR, Hsia VS-C, Fu L, Shi Y-B (2003) A dominant negative thyroid hormone receptor blocks amphibian metamorphosis by retaining corepressors at target genes. Mol Cell Biol 23:6750–6758
Buchholz DR, Tomita A, Fu L, Paul BD, Shi Y-B (2004) Transgenic analysis reveals that thyroid hormone receptor is sufficient to mediate the thyroid hormone signal in frog metamorphosis. Mol Cell Biol 24:9026–9037
Hasebe T, Buchholz DR, Shi YB, Ishizuya-Oka A (2011) Epithelial-connective tissue interactions induced by thyroid hormone receptor are essential for adult stem cell development in the Xenopus laevis intestine. Stem Cells 29(1):154–161. https://doi.org/10.1002/stem.560
Wen L, Fu L, Guo X, Chen Y, Shi YB (2015) Histone methyltransferase Dot1L plays a role in postembryonic development in Xenopus tropicalis. FASEB J 29:385–393. https://doi.org/10.1096/fj.14-252171
Guo X, Zhang T, Hu Z, Zhang Y, Shi Z, Wang Q, Cui Y, Wang F, Zhao H, Chen Y (2014) Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis. Development 141(3):707–714. https://doi.org/10.1242/dev.099853
Lei Y, Guo X, Deng Y, Chen Y, Zhao H (2013) Generation of gene disruptions by transcription activator-like effector nucleases (TALENs) in Xenopus tropicalis embryos. Cell Biosci 3(1):21. https://doi.org/10.1186/2045-3701-3-21 2045-3701-3-21 [pii]
Lei Y, Guo X, Liu Y, Cao Y, Deng Y, Chen X, Cheng CH, Dawid IB, Chen Y, Zhao H (2012) Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs). Proc Natl Acad Sci U S A 109:17484–17489. https://doi.org/10.1073/pnas.1215421109 1215421109 [pii]
Nakayama T, Fish MB, Fisher M, Oomen-Hajagos J, Thomsen GH, Grainger RM (2013) Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis 51(12):835–843. https://doi.org/10.1002/dvg.22720
Blitz IL, Biesinger J, Xie X, Cho KW (2013) Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis 51(12):827–834. https://doi.org/10.1002/dvg.22719
Wang F, Shi Z, Cui Y, Guo X, Shi YB, Chen Y (2015) Targeted gene disruption in Xenopus laevis using CRISPR/Cas9. Cell Biosci 5:15. https://doi.org/10.1186/s13578-015-0006-1
Yen PM (2015) Unliganded TRs regulate growth and developmental timing during early embryogenesis: evidence for a dual function mechanism of TR action. Cell Biosci 5:8. https://doi.org/10.1186/2045-3701-5-8
Wen L, Shi YB (2015) Unliganded thyroid hormone receptor alpha controls developmental timing in Xenopus tropicalis. Endocrinology 156:721–734. https://doi.org/10.1210/en.2014-1439
Choi J, Suzuki KI, Sakuma T, Shewade L, Yamamoto T, Buchholz DR (2015) Unliganded thyroid hormone receptor alpha regulates developmental timing via gene repression as revealed by gene disruption in Xenopus tropicalis. Endocrinology 156:735–744. https://doi.org/10.1210/en.2014-1554
Sachs LM (2015) Unliganded thyroid hormone receptor function: amphibian metamorphosis got TALENs. Endocrinology 156(2):409–410. https://doi.org/10.1210/en.2014-2016
Choi J, Ishizuya-Oka A, Buchholz DR (2017) Growth, development, and intestinal remodeling occurs in the absence of thyroid hormone receptor alpha in tadpoles of Xenopus tropicalis. Endocrinology 158(6):1623–1633
Wen L, Shibata Y, Su D, Fu L, Luu N, Shi Y-B (2017) Thyroid hormone receptor α controls developmental timing and regulates the rate and coordination of tissue specific metamorphosis in Xenopus tropicalis. Endocrinology 158(6):1985–1998
Paul BD, Buchholz DR, Fu L, Shi Y-B (2005) Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development. J Biol Chem 280:27165–27172
Paul BD, Fu L, Buchholz DR, Shi Y-B (2005) Coactivator recruitment is essential for liganded thyroid hormone receptor to initiate amphibian metamorphosis. Mol Cell Biol 25:5712–5724
Paul BD, Buchholz DR, Fu L, Shi Y-B (2007) SRC-p300 coactivator complex is required for thyroid hormone induced amphibian metamorphosis. J Biol Chem 282:7472–7481
Havis E, Sachs LM, Demeneix BA (2003) Metamorphic T3-response genes have specific co-regulator requirements. EMBO Rep 4:883–888
Paul BD, Shi Y-B (2003) Distinct expression profiles of transcriptional coactivators for thyroid hormone receptors during Xenopus laevis metamorphosis. Cell Res 13:459–464
Tomita A, Buchholz DR, Shi Y-B (2004) Recruitment of N-CoR/SMRT-TBLR1 corepressor complex by unliganded thyroid hormone receptor for gene repression during frog development. Mol Cell Biol 24:3337–3346
Sachs LM, Jones PL, Havis E, Rouse N, Demeneix BA, Shi Y-B (2002) N-CoR recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development. Mol Cell Biol 22:8527–8538
Sato Y, Buchholz DR, Paul BD, Shi Y-B (2007) A role of unliganded thyroid hormone receptor in postembryonic development in Xenopus laevis. Mech Dev 124:476–488
Matsuura K, Fujimoto K, Fu L, Shi Y-B (2012) Liganded thyroid hormone receptor induces nucleosome removal and histone modifications to activate transcription during larval intestinal cell death and adult stem cell development. Endocrinology 153:961–972
Wong J, Shi Y-B, Wolffe AP (1997) Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: hormone-regulated chromatin disruption is not sufficient for transcriptinal activation. EMBO J 16:3158–3171
Wong J, Shi YB, Wolffe AP (1995) A role for nucleosome assembly in both silencing and activation of the Xenopus TR beta A gene by the thyroid hormone receptor. Genes Dev 9(21):2696–2711
Bilesimo P, Jolivet P, Alfama G, Buisine N, Le Mevel S, Havis E, Demeneix BA, Sachs LM (2011) Specific histone lysine 4 methylation patterns define TR-binding capacity and differentiate direct T3 responses. Mol Endocrinol 25:225–237
Grimaldi A, Buisine N, Miller T, Shi YB, Sachs LM (2013) Mechanisms of thyroid hormone receptor action during development: lessons from amphibian studies. Biochim Biophys Acta 1830(7):3882–3892. https://doi.org/10.1016/j.bbagen.2012.04.020 S0304-4165(12)00125-0 [pii]
Sachs LM, Amano T, Shi YB (2001) An essential role of histone deacetylases in postembryonic organ transformations in Xenopus laevis. Int J Mol Med 8(6):595–601
Sachs LM, Amano T, Rouse N, Shi YB (2001) Involvement of histone deacetylase at two distinct steps in gene regulation during intestinal development in Xenopus laevis. Dev Dyn 222(2):280–291
Nakayama T, Blitz IL, Fish MB, Odeleye AO, Manohar S, Cho KW, Grainger RM (2014) Cas9-based genome editing in Xenopus tropicalis. Methods Enzymol 546:355–375
Montague TG, Cruz JM, Gagnon JA, Church GM, Eivind Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42:W401–W407
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One 10(4):e0124633. https://doi.org/10.1371/journal.pone.0124633
Naito Y, Hino K, Bono H, Ui-Tei K (2015) CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31(7):1120–1123. https://doi.org/10.1093/bioinformatics/btu743
Nieuwkoop PD, Faber J (1965) Normal table of Xenopus laevis. North Holland Publishing, Amsterdam
Fu L, Wen L, Luu N, Shi YB (2016) A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing. Sci Rep 6:35488. https://doi.org/10.1038/srep35488
Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32(6):569–576. https://doi.org/10.1038/nbt.2908
Wu M, Gerhart J (1991) Raising Xenopus in the laboratory. Methods Cell Biol 36:3–18
Acknowledgments
This work in the laboratory was supported by the Intramural Research Program of National Institute of Child Health and Human Development, National Institutes of Health. Y. Shibata was supported in part by a Japan Society for the Promotion of Science Research Fellowship for Japanese Biomedical and Behavioral Researchers at the National Institutes of Health.
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Shibata, Y., Bao, L., Fu, L., Shi, B., Shi, YB. (2019). Functional Studies of Transcriptional Cofactors via Microinjection-Mediated Gene Editing in Xenopus. In: Liu, C., Du, Y. (eds) Microinjection. Methods in Molecular Biology, vol 1874. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8831-0_29
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