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Kyono Y, Raj S, Sifuentes CJ, Buisine N, Sachs L, Denver RJ. DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain. Dev Biol 2020; 462:180-196. [PMID: 32240642 PMCID: PMC7251973 DOI: 10.1016/j.ydbio.2020.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/23/2020] [Indexed: 01/07/2023]
Abstract
Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. There is mounting evidence that DNA methylation can be modulated by hormone signaling. We analyzed genome-wide changes in DNA methylation and their relationship to gene regulation in the brain of Xenopus tadpoles during metamorphosis, a thyroid hormone-dependent developmental process. We studied the region of the tadpole brain containing neurosecretory neurons that control pituitary hormone secretion, a region that is highly responsive to thyroid hormone action. Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). During the pre-to pro-metamorphic period, the number of DMRs was lowest (1,163), with demethylation predominating. From pre-metamorphosis to metamorphic climax DMRs nearly doubled (2,204), with methylation predominating. The largest changes in DNA methylation were seen from metamorphic climax to the completion of metamorphosis (2960 DMRs), with 80% of the DMRs representing demethylation. Using RNA sequencing, we found negative correlations between differentially expressed genes and DMRs localized to gene bodies and regions upstream of transcription start sites. DNA demethylation at metamorphosis revealed by MethylCap-seq was corroborated by increased immunoreactivity for the DNA demethylation intermediates 5-hydroxymethylcytosine and 5-carboxymethylcytosine, and the methylcytosine dioxygenase ten eleven translocation 3 that catalyzes DNA demethylation. Our findings show that the genome of tadpole neural cells undergoes significant changes in DNA methylation during metamorphosis, and these changes likely influence chromatin architecture, and gene regulation programs occurring during this developmental period.
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Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samhitha Raj
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher J Sifuentes
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Buisine
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Laurent Sachs
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Robert J Denver
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA.
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Ohba K, Leow MKS, Singh BK, Sinha RA, Lesmana R, Liao XH, Ghosh S, Refetoff S, Sng JCG, Yen PM. Desensitization and Incomplete Recovery of Hepatic Target Genes After Chronic Thyroid Hormone Treatment and Withdrawal in Male Adult Mice. Endocrinology 2016; 157:1660-72. [PMID: 26866609 PMCID: PMC4816733 DOI: 10.1210/en.2015-1848] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Clinical symptoms may vary and not necessarily reflect serum thyroid hormone (TH) levels during acute and chronic hyperthyroidism as well as recovery from hyperthyroidism. We thus examined changes in hepatic gene expression and serum TH/TSH levels in adult male mice treated either with a single T3 (20 μg per 100 g body weight) injection (acute T3) or daily injections for 14 days (chronic T3) followed by 10 days of withdrawal. Gene expression arrays from livers harvested at these time points showed that among positively-regulated target genes, 320 were stimulated acutely and 429 chronically by T3. Surprisingly, only 69 of 680 genes (10.1%) were induced during both periods, suggesting desensitization of the majority of acutely stimulated target genes. About 90% of positively regulated target genes returned to baseline expression levels after 10 days of withdrawal; however, 67 of 680 (9.9%) did not return to baseline despite normalization of serum TH/TSH levels. Similar findings also were observed for negatively regulated target genes. Chromatin immunoprecipitation analysis of representative positively regulated target genes suggested that acetylation of H3K9/K14 was associated with acute stimulation, whereas trimethylation of H3K4 was associated with chronic stimulation. In an in vivo model of chronic intrahepatic hyperthyroidism since birth, adult male monocarboxylate transporter-8 knockout mice also demonstrated desensitization of most acutely stimulated target genes that were examined. In summary, we have identified transcriptional desensitization and incomplete recovery of gene expression during chronic hyperthyroidism and recovery. Our findings may be a potential reason for discordance between clinical symptoms and serum TH levels observed in these conditions.
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Affiliation(s)
- Kenji Ohba
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Melvin Khee-Shing Leow
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Brijesh Kumar Singh
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Rohit Anthony Sinha
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Ronny Lesmana
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Xiao-Hui Liao
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Sujoy Ghosh
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Samuel Refetoff
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Judy Chia Ghee Sng
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
| | - Paul Michael Yen
- Cardiovascular and Metabolic Disorders Program (K.O., B.K.S., R.A.S., R.L., S.G., P.M.Y.), Duke-NUS Medical School, Singapore, Singapore 169857; Department of Endocrinology (M.K.-S.L.), Tan Tock Seng Hospital, Singapore, Singapore 229899; Singapore Institute for Clinical Sciences (M.K.-S.L.), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore 117609; Department of Physiology (R.L.), Universitas Padjadjaran, Bandung, West Java 45363, Indonesia; Departments of Medicine (X.-H.L., S.R.) and Pediatrics and Committee on Genetics (S.R.), The University of Chicago, Chicago, Illinois 60637; and Department of Pharmacology (J.C.G.S.), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 119228
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