title: Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.
abstract: Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Krüppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse tissues. We identified regions of the Xenopus and mouse Klf9 genes 5-6 kb upstream of the transcription start sites that supported synergistic transactivation by TH plus GC. Within these regions, we found an orthologous sequence of approximately 180 bp that is highly conserved among tetrapods, but absent in other chordates, and possesses chromatin marks characteristic of an enhancer element. The Xenopus and mouse approximately 180-bp DNA element conferred synergistic transactivation by hormones in transient transfection assays, so we designate this the Klf9 synergy module (KSM). We identified binding sites within the mouse KSM for TH receptor, GC receptor, and nuclear factor κB. TH strongly increased recruitment of liganded GC receptor and serine 5 phosphorylated (initiating) RNA polymerase II to chromatin at the KSM, suggesting a mechanism for transcriptional synergy. The KSM is transcribed to generate long noncoding RNAs, which are also synergistically induced by combined hormone treatment, and the KSM interacts with the Klf9 promoter and a far upstream region through chromosomal looping. Our findings support that the KSM plays a central role in hormone regulation of vertebrate Klf9 genes, it evolved in the tetrapod lineage, and has been maintained by strong stabilizing selection.
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Pia D
authors: PD
authors: Bagamasbad
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Ronald M
authors: RM
authors: Bonett
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Laurent
authors: L
authors: Sachs
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Nicolas
authors: N
authors: Buisine
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Samhitha
authors: S
authors: Raj
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Joseph R
authors: JR
authors: Knoedler
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Yasuhiro
authors: Y
authors: Kyono
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Yijun
authors: Y
authors: Ruan
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Xiaoan
authors: X
authors: Ruan
authors: Department of Molecular, Cellular and Developmental Biology (P.D.B., S.R., R.J.D.), University of Michigan, Ann Arbor, Michigan 48109; Department of Biological Science (R.M.B.), The University of Tulsa, Tulsa, Oklahoma 74104; Unité Mixte de Recherche 7221 (L.S., N.B.), Muséum National d'Histoire Naturelle, Centre Nationale de Recherche Scientifique, CP32 Paris, France; Neuroscience Graduate Program (J.R.K., Y.K., R.J.D.), The University of Michigan, Ann Arbor, Michigan 48109; Genome Institute of Singapore (Y.R., X.R.), 138672 Singapore; The Jackson Laboratory of Genomic Medicine (Y.R., X.R.), Farmington, Connecticut 06030; and Department of Genetics and Developmental Biology (Y.R., X.R.), University of Connecticut, Storrs, Connecticut 06269.
authors: Robert J
authors: RJ
authors: Denver
mesh_terms: D000107:Acetylation / Q000187:drug effects; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D017124:Conserved Sequence; D003348:Cortisone / Q000494:pharmacology; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D019143:Evolution, Molecular; D005786:Gene Expression Regulation / Q000187:drug effects; D055785:Gene Knockdown Techniques; D056426:Genetic Loci; D006657:Histones / Q000378:metabolism; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism; D008810:Mice, Inbred C57BL; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding / Q000187:drug effects; D012319:RNA Polymerase II / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics* / Q000378:metabolism; D011965:Receptors, Glucocorticoid / Q000378:metabolism; D015533:Transcriptional Activation / Q000187:drug effects; D014284:Triiodothyronine / Q000494:pharmacology; D014981:Xenopus
chemical_list: D002843:Chromatin; D006657:Histones; D051741:Kruppel-Like Transcription Factors; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D018160:Receptors, Cytoplasmic and Nuclear; D011965:Receptors, Glucocorticoid; D014284:Triiodothyronine; D012319:RNA Polymerase II; D003348:Cortisone