Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues

Abstract

Thyroid hormone (T3) plays a central role in vertebrate post-embryonic development, and amphibian metamorphosis provides a unique opportunity to examine T3-dependent developmental changes. To establish a molecular framework for understanding T3-induced morphological change, we identified a set of gene expression profiles controlled by T3 in the intestine via microarray analysis. Samples were obtained from premetamorphic Xenopus laevis tadpole intestines after 0, 1, 3, and 6 days of T3 treatment, which induces successive cell death and proliferation essential for intestinal remodeling. Using a set of 21,807 60-mer oligonucleotide probes representing >98% of the Unigene clusters, we found that 1997 genes were differentially regulated by 1.5-fold or more during this remodeling process and were clustered into four temporal expression profiles; transiently up- or downregulated and late up- or downregulated. Gene Ontology categories most significantly associated with these clusters were proteolysis, cell cycle, development and transcription, and electron transport and metabolism, respectively. These categories are common with those found for T3-regulated genes from brain, limb, and tail, although more than 70% of T3-regulated genes are tissue-specific, likely due to the fact that not all genes are annotated into GO categories and that GO categories common to different organs also contain genes regulated by T3 tissue specifically. Finally, a core set of upregulated genes, most previously unknown to be T3-regulated, were identified and enriched in genes involved in transcription and cell signaling.

Thyroid hormones and the control of cell proliferation or cell differentiation: Paradox or duality?

“…This underlies the existence of a similar regulatory loop in different genders of vertebrates. A paper by Shi's laboratory recently reported a genome-wide analysis of the intestine during its remodeling at metamorphosis (Buchholz et al, 2007). They analyzed early and late stages after TH-induced intestinal remodeling and also compared the transcriptional programs triggered by THs at one specific stage in different organs such as brain, limb, tail and intestine.…”

Identification of Direct Thyroid Hormone Response Genes Reveals the Earliest Gene Regulation Programs during Frog Metamorphosis

“…2 g RNA from each sample was used to prepare cDNA, and then Cy3-labeled cRNA using a Low RNA Input Linear Amplification Kit from Agilent Technologies was used. The Cy3-labeled cRNA and Cy5-labeled X. laevis Universal Reference cRNA (made from mRNA isolated from tadpoles at multiple stages of development) (31,32) were hybridized together onto the X. laevis 60-mer oligonucleotide microarray from Agilent Technologies (AMADID# 013665) using the Microarray Hybridization kit (Agilent Technologies) with a two-color reference design system as described (31,32). After 17-h hybridization at 65°C, microarray slides were washed according to manufacturer's instructions and scanned with an Agilent Technologies Microarray scanner.…”

“…For qRT-PCR based on SYBR Green detection, 2 l of cDNA was used for each reaction, and EF1␣ was used as the control. The primer sequences are listed in Table 1 or as published previously (31,43).…”

“…The gene symbols were derived from the homologous human genes as described before (31,32). GoMiner software (57) was used to find these enriched GO categories with p value set at Ͻ0.05.…”

Regulation of adult intestinal epithelial stem cell development by thyroid hormone during Xenopus laevis metamorphosis

“…Furthermore, as mentioned above, the larval-to-adult intestinal remodeling in the X. laevis anterior intestine can be organ-autonomously reproduced by TH in vitro (IshizuyaOka and Shimozawa, 1992). Therefore, in this animal model, the molecular mechanisms of intestinal epithelial remodeling including the tissue interactions may be easily approached by studying TH response genes, many of which have been isolated from the Xenopus intestine since the 1990s (Table 1; Shi and Brown, 1993;Shimizu et al, 2002;Buchholz et al, 2007). Although precise functions of these TH response genes remain mostly unknown, in situ hybridization (ISH) analysis has identified some genes whose expression profiles correlate well spatially and temporally with the adult epithelial development.…”