Nakajima K , Tazawa I , Shi YB .

Z01 HD001901-12 Intramural NIH HHS, Z01 HD001901-12 NULL

	Fig. 1. Histological analysis of wild-type and TR-knockout tadpole tails at climax of metamorphosis. (A) Schematic representation of stage-63 tail sampling. A tail was sectioned at one-third of the distance from the tail base as indicated by a red arrow. (B–D) A cross sections of wild-type (B), TRα-knockout (C), and TRβ-knockout (D) stage-63 tadpole tail. Histological images are representative of three individuals examined per panel. (E) A cross section of wild type late stage-62 tadpole tail, which was sectioned about at half of the length. Sections were stained with hematoxylin and eosin. Note that the notochord in TRβ-knockout tail at stage 63 resembles that of the wild type at stage 62, showing the presence of vacuolated cells, i.e., not collapsed, compared to the notochord in the wild type or TRα-knockout tail at stage 63. Abbreviations: M, muscle; NC, notochordal cells; NS, notochord sheath; SC, spinal cord. Scale bars, 0.1 mm.
	Fig. 2. Two methods for isolating notochords. (A) A representative photo of notochord preparation by method-A. The tail skin was cut circumferentially at the junction with the body (the tail base) and the tail was pulled to expose the stretched notochord, which was then isolated by cutting at the two ends of the exposed notochord. Scale bar, 10 mm. (B) A representative photo of notochord preparation by method-B. The skin and muscles of left side were peeled to the end of the tail (white arrow) to expose the notochord (red arrow heads), and notochord was then pulled out. In this case, spinal code was attached to left side that was peeled to the end of the tail (thus not visible in figure). Anterior, left; Dorsal, top. Scale bar, 1 mm.
	Fig. 3. TRβ is highly expressed specifically in the tail notochord at the climax of metamorphosis. The expression levels of TRα (A), TRβ (B) and ratio of TRβ to TRα (C) were determined by RT-PCR in the wild-type stage-60 whole tail (St60), stage-63 whole tail (St63), stage-63 notochord-removed-tail (St63dNC), stage-63 notochord prepared by method-A (noto-A), and method-B (noto-B), respectively. The samples included 5, 5, 8 tails and 38, 15 notochords, respectively. (A, B) The expression levels were shown as the copy number per 100,000 copies of EF1α. Data are expressed as mean ± SE of technical replications (n = 5–6).
	Fig. 4. Preferential high level expression of genes encoding matrix metalloproteinases (MMPs) in the tail notochord at climax of metamorphosis. The expression levels of the ECM-degrading MMP2, MMP9-TH, MMP11, MMP13 and MMP14 were determined by RT-PCR in the stage-60 whole tail (St60), stage-63 whole tail (St63), stage-63 notochord-removed-tail (St63dNC), notochord prepared by method-A (noto-A) and method-B (noto-B), respectively. The fold increase between the samples of St60 and St63, between St63dNC and St63 and between St63dNC and the average of noto-A and noto-B are indicated in the figure. Note all MMPs were upregulated at St63 compared to St60. MMP9-TH and MMP13, and to a lesser extent MMP14, were expressed at much higher levels in the notochord compared to the rest of the tail, leading to significantly lower levels of their mRNAs in St63dNC than that in the whole tail even though notochordal RNA is only a tiny fraction of the total RNA in the tail. The individual sample included 5, 5, 8 tails and 38, 15 notochords, respectively. The expression levels were shown as the copy number relative to EF1α. Data are expressed as mean ± SD of technical replications (n = 3–4).
	Fig. 5. Distinct localizations of MMP9-TH, MMP13 and MMP14 expression in the tail at the climax of metamorphosis. Cross sections of the tail at stage 62 were hybridized with antisense MMP9-TH (A, A′, A″), MMP13 (C, C′, C″) or MMP14 (E, E′, E″) probes or their sense probes (B, B′, D, D′, F, F′). Dark purple deposits indicate the sites of probe binding. Black pigments in some areas, e.g., spinal cord (SC), are melanin (see B, D, F). Note that MMP9-TH mRNA is expressed in the outer sheath cells (OS) and weakly in the connective tissue sheath (CT) surrounding the notochord (NC). MMP13 mRNA is expressed in the outer sheath cells, but not in the connective tissue sheath. MMP14 mRNA is expressed in the connective tissue sheath, fibroblast (FB, E′) and subepidermal fibroblast (SF, E″) but not observed in the outer sheath cells. Boxed areas in the panel A-F are magnified in panel A′-F′, A″, C″ and E″. Scale bars, 0.2 mm (A-F) or 0.05 mm (A′-F′, A″, C″ and F″).
	Supplemental Fig. 1: Histological alteration of the notochord under in situ hybridization procedures. (A) Schematic representation of notochordal structure as modified from (Corallo et al. 2015). (B-F) Cross sections of the tail at stage 62 with (C-F) or without (B) treatment under the in situ hybridization procedures. Collagen was stained with 0.1% Sirius red (Sigma) in saturated aqueous solution of picric acid (Sigma) for 1 hour. Then the sections were washed in two changes of 0.5%glacial acetic acid (Junqueira et al. 1979). (C): A section hybridized with the control probe. (D): A section hybridized with MMP9-TH anti sense probe. (E): The same section as in (D) showing nuclei stained with hoechst 33342. (F): The merged image of D and E. Note that the hybridization procedure led to the contraction of the inner notochordal cells (NC) and thus the artificial separation of the connective tissue sheath (CT) and the outer sheath cells (OS), giving rise to a thicker collagenous sheath (CS) in C-F compared to B. NS, notochord sheath, which includes CT and CS. Scale bars, 0.1 mm.

Amano, Spatio-temporal regulation and cleavage by matrix metalloproteinase stromelysin-3 implicate a role for laminin receptor in intestinal remodeling during Xenopus laevis metamorphosis. 2005, Pubmed, Xenbase

Amano, Spatio-temporal regulation and cleavage by matrix metalloproteinase stromelysin-3 implicate a role for laminin receptor in intestinal remodeling during Xenopus laevis metamorphosis. 2005, Pubmed , Xenbase
Amano, The matrix metalloproteinase stromelysin-3 cleaves laminin receptor at two distinct sites between the transmembrane domain and laminin binding sequence within the extracellular domain. 2005, Pubmed , Xenbase
Berry, The expression pattern of thyroid hormone response genes in the tadpole tail identifies multiple resorption programs. 1998, Pubmed , Xenbase
Buchholz, Dual function model revised by thyroid hormone receptor alpha knockout frogs. 2018, Pubmed , Xenbase
Cheah, Expression of the mouse alpha 1(II) collagen gene is not restricted to cartilage during development. 1991, Pubmed
Choi, Growth, Development, and Intestinal Remodeling Occurs in the Absence of Thyroid Hormone Receptor α in Tadpoles of Xenopus tropicalis. 2017, Pubmed , Xenbase
Choi, Regulation of thyroid hormone-induced development in vivo by thyroid hormone transporters and cytosolic binding proteins. 2015, Pubmed
Choi, Unliganded thyroid hormone receptor α regulates developmental timing via gene repression in Xenopus tropicalis. 2015, Pubmed , Xenbase
Connors, Characterization of thyroid hormone transporter expression during tissue-specific metamorphic events in Xenopus tropicalis. 2010, Pubmed , Xenbase
Damjanovski, Overexpression of matrix metalloproteinases leads to lethality in transgenic Xenopus laevis: implications for tissue-dependent functions of matrix metalloproteinases during late embryonic development. 2001, Pubmed , Xenbase
Damsky, Signal transduction by integrin receptors for extracellular matrix: cooperative processing of extracellular information. 1992, Pubmed
Eliceiri, Quantitation of endogenous thyroid hormone receptors alpha and beta during embryogenesis and metamorphosis in Xenopus laevis. 1994, Pubmed , Xenbase
Fu, Transcriptional regulation of the Xenopus laevis Stromelysin-3 gene by thyroid hormone is mediated by a DNA element in the first intron. 2006, Pubmed , Xenbase
Fu, Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians. 2009, Pubmed , Xenbase
Fu, A causative role of stromelysin-3 in extracellular matrix remodeling and epithelial apoptosis during intestinal metamorphosis in Xenopus laevis. 2005, Pubmed , Xenbase
Fujimoto, Expression of matrix metalloproteinase genes in regressing or remodeling organs during amphibian metamorphosis. 2007, Pubmed , Xenbase
Fujimoto, One of the duplicated matrix metalloproteinase-9 genes is expressed in regressing tail during anuran metamorphosis. 2006, Pubmed , Xenbase
Gregorieff, In Situ Hybridization to Identify Gut Stem Cells. 2015, Pubmed
Grimaldi, Mechanisms of thyroid hormone receptor action during development: lessons from amphibian studies. 2013, Pubmed , Xenbase
Hasebe, Spatial and temporal expression profiles suggest the involvement of gelatinase A and membrane type 1 matrix metalloproteinase in amphibian metamorphosis. 2006, Pubmed , Xenbase
Hasebe, Expression profiles of the duplicated matrix metalloproteinase-9 genes suggest their different roles in apoptosis of larval intestinal epithelial cells during Xenopus laevis metamorphosis. 2007, Pubmed , Xenbase
Hasebe, Evidence for a cooperative role of gelatinase A and membrane type-1 matrix metalloproteinase during Xenopus laevis development. 2007, Pubmed , Xenbase
Ishizuya-Oka, Transient expression of stromelysin-3 mRNA in the amphibian small intestine during metamorphosis. 1996, Pubmed , Xenbase
Ishizuya-Oka, Requirement for matrix metalloproteinase stromelysin-3 in cell migration and apoptosis during tissue remodeling in Xenopus laevis. 2000, Pubmed , Xenbase
Kenney, Ultrastructural identification of collagen and glycosaminoglycans in notochordal extracellular matrix in vivo and in vitro. 1978, Pubmed
Lazar, Thyroid hormone receptors: multiple forms, multiple possibilities. 1993, Pubmed
Mangelsdorf, The nuclear receptor superfamily: the second decade. 1995, Pubmed
Mathew, Differential regulation of cell type-specific apoptosis by stromelysin-3: a potential mechanism via the cleavage of the laminin receptor during tail resorption in Xenopus laevis. 2009, Pubmed , Xenbase
Matsuda, Novel functions of protein arginine methyltransferase 1 in thyroid hormone receptor-mediated transcription and in the regulation of metamorphic rate in Xenopus laevis. 2009, Pubmed , Xenbase
Nakajima, Regulation of thyroid hormone sensitivity by differential expression of the thyroid hormone receptor during Xenopus metamorphosis. 2012, Pubmed , Xenbase
Nakajima, Programmed cell death during amphibian metamorphosis. 2005, Pubmed , Xenbase
Nakajima, Thyroid Hormone Receptor α- and β-Knockout Xenopus tropicalis Tadpoles Reveal Subtype-Specific Roles During Development. 2018, Pubmed , Xenbase
Nakajima, Dual mechanisms governing muscle cell death in tadpole tail during amphibian metamorphosis. 2003, Pubmed , Xenbase
Nelson, Matrix metalloproteinases: biologic activity and clinical implications. 2000, Pubmed
Okada, Translational regulation by the 5'-UTR of thyroid hormone receptor α mRNA. 2012, Pubmed , Xenbase
Patterton, Transcriptional activation of the matrix metalloproteinase gene stromelysin-3 coincides with thyroid hormone-induced cell death during frog metamorphosis. 1995, Pubmed , Xenbase
Paul, SRC-p300 coactivator complex is required for thyroid hormone-induced amphibian metamorphosis. 2007, Pubmed , Xenbase
Paul, Coactivator recruitment is essential for liganded thyroid hormone receptor to initiate amphibian metamorphosis. 2005, Pubmed , Xenbase
Paul, Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development. 2005, Pubmed , Xenbase
Sachs, Nuclear receptor corepressor recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development. 2002, Pubmed , Xenbase
Sachs, Unliganded thyroid hormone receptor function: amphibian metamorphosis got TALENs. 2015, Pubmed , Xenbase
Sakane, Functional analysis of thyroid hormone receptor beta in Xenopus tropicalis founders using CRISPR-Cas. 2018, Pubmed , Xenbase
Sato, A role of unliganded thyroid hormone receptor in postembryonic development in Xenopus laevis. 2007, Pubmed , Xenbase
Schmidt, Modulation of epithelial morphogenesis and cell fate by cell-to-cell signals and regulated cell adhesion. 1993, Pubmed
Shi, Dual functions of thyroid hormone receptors in vertebrate development: the roles of histone-modifying cofactor complexes. 2009, Pubmed , Xenbase
Shi, Tadpole competence and tissue-specific temporal regulation of amphibian metamorphosis: roles of thyroid hormone and its receptors. 1996, Pubmed , Xenbase
Shi, Regulation of apoptosis during development: input from the extracellular matrix (review). 1998, Pubmed , Xenbase
Stolow, Identification and characterization of a novel collagenase in Xenopus laevis: possible roles during frog development. 1996, Pubmed , Xenbase
Su, Thyroid hormone induces apoptosis in primary cell cultures of tadpole intestine: cell type specificity and effects of extracellular matrix. 1997, Pubmed , Xenbase
Tata, Gene expression during metamorphosis: an ideal model for post-embryonic development. 1993, Pubmed
Timpl, Supramolecular assembly of basement membranes. 1996, Pubmed
Tomita, Recruitment of N-CoR/SMRT-TBLR1 corepressor complex by unliganded thyroid hormone receptor for gene repression during frog development. 2004, Pubmed , Xenbase
Tsai, Molecular mechanisms of action of steroid/thyroid receptor superfamily members. 1994, Pubmed
Vukicevic, Identification of multiple active growth factors in basement membrane Matrigel suggests caution in interpretation of cellular activity related to extracellular matrix components. 1992, Pubmed
Wang, Thyroid hormone-induced gene expression program for amphibian tail resorption. 1993, Pubmed , Xenbase
Wen, Unliganded thyroid hormone receptor α controls developmental timing in Xenopus tropicalis. 2015, Pubmed , Xenbase
Wen, Regulation of growth rate and developmental timing by Xenopus thyroid hormone receptor α. 2016, Pubmed , Xenbase
Wen, Thyroid Hormone Receptor α Controls Developmental Timing and Regulates the Rate and Coordination of Tissue-Specific Metamorphosis in Xenopus tropicalis. 2017, Pubmed , Xenbase
Werb, Extracellular matrix remodeling and the regulation of epithelial-stromal interactions during differentiation and involution. 1996, Pubmed
Wong, A role for nucleosome assembly in both silencing and activation of the Xenopus TR beta A gene by the thyroid hormone receptor. 1995, Pubmed , Xenbase
Wong, Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase. 1998, Pubmed , Xenbase
Wong, Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: hormone-regulated chromatin disruption is not sufficient for transcriptional activation. 1997, Pubmed , Xenbase
Wood, The transient expression of type II collagen at tissue interfaces during mammalian craniofacial development. 1991, Pubmed
Yen, Unliganded TRs regulate growth and developmental timing during early embryogenesis: evidence for a dual function mechanism of TR action. 2015, Pubmed , Xenbase
Yen, Physiological and molecular basis of thyroid hormone action. 2001, Pubmed