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Kaimala S, Lootah SS, Mehra N, Kumar CA, Marzooqi SA, Sampath P, Ansari SA, Emerald BS. The Long Non-Coding RNA Obesity-Related (Obr) Contributes To Lipid Metabolism Through Epigenetic Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401939. [PMID: 38704700 PMCID: PMC11234455 DOI: 10.1002/advs.202401939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Indexed: 05/07/2024]
Abstract
Obesity is a multifactorial disease that is part of today's epidemic and also increases the risk of other metabolic diseases. Long noncoding RNAs (lncRNAs) provide one tier of regulatory mechanisms to maintain metabolic homeostasis. Although lncRNAs are a significant constituent of the mammalian genome, studies aimed at their metabolic significance, including obesity, are only beginning to be addressed. Here, a developmentally regulated lncRNA, termed as obesity related (Obr), whose expression in metabolically relevant tissues such as skeletal muscle, liver, and pancreas is altered in diet-induced obesity, is identified. The Clone 9 cell line and high-fat diet-induced obese Wistar rats are used as a model system to verify the function of Obr. By using stable expression and antisense oligonucleotide-mediated downregulation of the expression of Obr followed by different molecular biology experiments, its role in lipid metabolism is verified. It is shown that Obr associates with the cAMP response element-binding protein (Creb) and activates different transcription factors involved in lipid metabolism. Its association with the Creb histone acetyltransferase complex, which includes the cAMP response element-binding protein (CBP) and p300, positively regulates the transcription of genes involved in lipid metabolism. In addition, Obr is regulated by Pparγ in response to lipid accumulation.
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Affiliation(s)
- Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Shareena Saeed Lootah
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Neha Mehra
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Challagandla Anil Kumar
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
| | - Saeeda Al Marzooqi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Prabha Sampath
- A*STAR Skin Research Laboratory, Agency for Science Technology & Research (A*STAR), Singapore, 138648, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Genome Institute of Singapore, Agency for Science Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, UAE University, Al Ain, P.O. Box 15551, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
- ASPIRE Precision Medicine, Research Institute Abu Dhabi, Al Ain, Abu Dhabi, P.O. Box 15551, UAE
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2
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Hauck AK, Mehmood R, Carpenter BJ, Frankfurter MT, Tackenberg MC, Inoue SI, Krieg MK, Cassim Bawa FN, Midha MK, Zundell DM, Batmanov K, Lazar MA. Nuclear receptor corepressors non-canonically drive glucocorticoid receptor-dependent activation of hepatic gluconeogenesis. Nat Metab 2024; 6:825-836. [PMID: 38622413 DOI: 10.1038/s42255-024-01029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Nuclear receptor corepressors (NCoRs) function in multiprotein complexes containing histone deacetylase 3 (HDAC3) to alter transcriptional output primarily through repressive chromatin remodelling at target loci1-5. In the liver, loss of HDAC3 causes a marked hepatosteatosis largely because of de-repression of genes involved in lipid metabolism6,7; however, the individual roles and contribution of other complex members to hepatic and systemic metabolic regulation are unclear. Here we show that adult loss of both NCoR1 and NCoR2 (double knockout (KO)) in hepatocytes phenocopied the hepatomegalic fatty liver phenotype of HDAC3 KO. In addition, double KO livers exhibited a dramatic reduction in glycogen storage and gluconeogenic gene expression that was not observed with hepatic KO of individual NCoRs or HDAC3, resulting in profound fasting hypoglycaemia. This surprising HDAC3-independent activation function of NCoR1 and NCoR2 is due to an unexpected loss of chromatin accessibility on deletion of NCoRs that prevented glucocorticoid receptor binding and stimulatory effect on gluconeogenic genes. These studies reveal an unanticipated, non-canonical activation function of NCoRs that is required for metabolic health.
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Affiliation(s)
- Amy K Hauck
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rashid Mehmood
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryce J Carpenter
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maxwell T Frankfurter
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C Tackenberg
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin-Ichi Inoue
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria K Krieg
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fathima N Cassim Bawa
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohit K Midha
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Delaine M Zundell
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirill Batmanov
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Sponchiado M, Bonilla AL, Mata L, Jasso-Johnson K, Liao YSJ, Fagan A, Moncada V, Reznikov LR. Club cell CREB regulates the goblet cell transcriptional network and pro-mucin effects of IL-1B. Front Physiol 2023; 14:1323865. [PMID: 38173934 PMCID: PMC10761479 DOI: 10.3389/fphys.2023.1323865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Club cells are precursors for mucus-producing goblet cells. Interleukin 1β (IL-1B) is an inflammatory mediator with pro-mucin activities that increases the number of mucus-producing goblet cells. IL-1B-mediated mucin production in alveolar adenocarcinoma cells requires activation of the cAMP response element-binding protein (CREB). Whether the pro-mucin activities of IL-1B require club cell CREB is unknown. Methods: We challenged male mice with conditional loss of club cell Creb1 and wild type littermates with intra-airway IL-1B or vehicle. Secondarily, we studied human "club cell-like" H322 cells. Results: IL-1B increased whole lung mRNA of secreted (Mucin 5ac, Mucin 5b) and tethered (Mucin 1, Mucin 4) mucins independent of genotype. However, loss of club cell Creb1 increased whole lung mRNA of member RAS oncogene family (Rab3D), decreased mRNA of the muscarinic receptor 3 (M3R) and prevented IL-1B mediated increases in purinergic receptor P2Y, (P2ry2) mRNA. IL-1B increased the density of goblet cells containing neutral mucins in wildtype mice but not in mice with loss of club cell Creb1. These findings suggested that club cell Creb1 regulated mucin secretion. Loss of club cell Creb1 also prevented IL-1B-mediated impairments in airway mechanics. Four days of pharmacologic CREB inhibition in H322 cells increased mRNA abundance of forkhead box A2 (FOXA2), a repressor of goblet cell expansion, and decreased mRNA expression of SAM pointed domain containing ETS transcription factor (SPDEF), a driver of goblet cell expansion. Chromatin immunoprecipitation demonstrated that CREB directly bound to the promoter region of FOXA2, but not to the promoter region of SPDEF. Treatment of H322 cells with IL-1B increased cAMP levels, providing a direct link between IL-1B and CREB signaling. Conclusion: Our findings suggest that club cell Creb1 regulates the pro-mucin properties of IL-1B through pathways likely involving FOXA2.
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Affiliation(s)
| | | | | | | | | | | | | | - Leah R. Reznikov
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
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4
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Kitamoto T, Accili D. Unraveling the mysteries of hepatic insulin signaling: deconvoluting the nuclear targets of insulin. Endocr J 2023; 70:851-866. [PMID: 37245960 DOI: 10.1507/endocrj.ej23-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
Over 100 years have passed since insulin was first administered to a diabetic patient. Since then great strides have been made in diabetes research. It has determined where insulin is secreted from, which organs it acts on, how it is transferred into the cell and is delivered to the nucleus, how it orchestrates the expression pattern of the genes, and how it works with each organ to maintain systemic metabolism. Any breakdown in this system leads to diabetes. Thanks to the numerous researchers who have dedicated their lives to cure diabetes, we now know that there are three major organs where insulin acts to maintain glucose/lipid metabolism: the liver, muscles, and fat. The failure of insulin action on these organs, such as insulin resistance, result in hyperglycemia and/or dyslipidemia. The primary trigger of this condition and its association among these tissues still remain to be uncovered. Among the major organs, the liver finely tunes the glucose/lipid metabolism to maintain metabolic flexibility, and plays a crucial role in glucose/lipid abnormality due to insulin resistance. Insulin resistance disrupts this tuning, and selective insulin resistance arises. The glucose metabolism loses its sensitivity to insulin, while the lipid metabolism maintains it. The clarification of its mechanism is warranted to reverse the metabolic abnormalities due to insulin resistance. This review will provide a brief historical review for the progress of the pathophysiology of diabetes since the discovery of insulin, followed by a review of the current research clarifying our understanding of selective insulin resistance.
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Affiliation(s)
- Takumi Kitamoto
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Domenico Accili
- Department of Medicine and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
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5
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Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka KI, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S. Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. iScience 2022; 25:103787. [PMID: 35243212 PMCID: PMC8859528 DOI: 10.1016/j.isci.2022.103787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Glucose homeostasis is maintained by modulation of metabolic flux. Enzymes and metabolites regulate the involved metabolic pathways. Dysregulation of glucose homeostasis is a pathological event in obesity. Analyzing metabolic pathways and the mechanisms contributing to obesity-associated dysregulation in vivo is challenging. Here, we introduce OMELET: Omics-Based Metabolic Flux Estimation without Labeling for Extended Trans-omic Analysis. OMELET uses metabolomic, proteomic, and transcriptomic data to identify relative changes in metabolic flux, and to calculate contributions of metabolites, enzymes, and transcripts to the changes in metabolic flux. By evaluating the livers of fasting ob/ob mice, we found that increased metabolic flux through gluconeogenesis resulted primarily from increased transcripts, whereas that through the pyruvate cycle resulted from both increased transcripts and changes in substrates of metabolic enzymes. With OMELET, we identified mechanisms underlying the obesity-associated dysregulation of metabolic flux in the liver. We developed OMELET to infer metabolic flux from label-free multi-omic data Contributions of metabolites, enzymes, and transcripts for flux were inferred Gluconeogenic flux increased in fasting ob/ob mice by increased transcripts Increased pyruvate cycle fluxes were led by increased transcripts and substrates
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Affiliation(s)
- Saori Uematsu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Satoshi Ohno
- Molecular Genetic Research Laboratory, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kaori Y Tanaka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Toshiya Kokaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.,Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ken-Ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.,Molecular Genetic Research Laboratory, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Arige V, Terry LE, Malik S, Knebel TR, Wagner II LE, Yule DI. CREB regulates the expression of type 1 inositol 1,4,5-trisphosphate receptors. J Cell Sci 2021; 134:jcs258875. [PMID: 34533188 PMCID: PMC8601716 DOI: 10.1242/jcs.258875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) play a central role in regulating intracellular Ca2+ signals in response to a variety of internal and external cues. Dysregulation of IP3R signaling is the underlying cause for numerous pathological conditions. It is well established that the activities of IP3Rs are governed by several post-translational modifications, including phosphorylation by protein kinase A (PKA). However, the long-term effects of PKA activation on expression of IP3R subtypes remains largely unexplored. In this report, we investigate the effects of chronic stimulation and tonic activity of PKA on the expression of IP3R subtypes. We demonstrate that expression of the type 1 IP3R (IP3R1) is augmented upon prolonged activation of PKA or upon ectopic overexpression of cyclic AMP-response element-binding protein (CREB) without altering IP3R2 and IP3R3 abundance. By contrast, inhibition of PKA or blocking CREB diminished IP3R1 expression. We also demonstrate that agonist-induced Ca2+-release mediated by IP3R1 is significantly attenuated upon blocking of CREB. Moreover, CREB - by regulating the expression of KRAS-induced actin-interacting protein (KRAP) - ensures correct localization and licensing of IP3R1. Overall, we report a crucial role for CREB in governing both the expression and correct localization of IP3R1. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | | | | | | | | | - David I. Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
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7
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Korenfeld N, Finkel M, Buchshtab N, Bar-Shimon M, Charni-Natan M, Goldstein I. Fasting Hormones Synergistically Induce Amino Acid Catabolism Genes to Promote Gluconeogenesis. Cell Mol Gastroenterol Hepatol 2021; 12:1021-1036. [PMID: 33957303 PMCID: PMC8346669 DOI: 10.1016/j.jcmgh.2021.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS Gluconeogenesis from amino acids (AAs) maintains glucose homeostasis during fasting. Although glucagon is known to regulate AA catabolism, the contribution of other hormones to it and the scope of transcriptional regulation dictating AA catabolism are unknown. We explored the role of the fasting hormones glucagon and glucocorticoids in transcriptional regulation of AA catabolism genes and AA-dependent gluconeogenesis. METHODS We tested the RNA expression of AA catabolism genes and glucose production in primary mouse hepatocytes treated with fasting hormones (glucagon, corticosterone) and feeding hormones (insulin, fibroblast growth factor 19). We analyzed genomic data of chromatin accessibility and chromatin immunoprecipitation in mice and primary mouse hepatocytes. We performed chromatin immunoprecipitation in livers of fasted mice to show binding of cAMP responsive element binding protein (CREB) and the glucocorticoid receptor (GR). RESULTS Fasting induced the expression of 31 genes with various roles in AA catabolism. Of them, 15 were synergistically induced by co-treatment of glucagon and corticosterone. Synergistic gene expression relied on the activity of both CREB and GR and was abolished by treatment with either insulin or fibroblast growth factor 19. Enhancers adjacent to synergistically induced genes became more accessible and were bound by CREB and GR on fasting. Akin to the gene expression pattern, gluconeogenesis from AAs was synergistically induced by glucagon and corticosterone in a CREB- and GR-dependent manner. CONCLUSIONS Transcriptional regulation of AA catabolism genes during fasting is widespread and is driven by glucagon (via CREB) and corticosterone (via GR). Glucose production in hepatocytes is also synergistically augmented, showing that glucagon alone is insufficient in fully activating gluconeogenesis.
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Affiliation(s)
- Noga Korenfeld
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Finkel
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Nufar Buchshtab
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Bar-Shimon
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel.
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8
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Abstract
Mammals undergo regular cycles of fasting and feeding that engage dynamic transcriptional responses in metabolic tissues. Here we review advances in our understanding of the gene regulatory networks that contribute to hepatic responses to fasting and feeding. The advent of sequencing and -omics techniques have begun to facilitate a holistic understanding of the transcriptional landscape and its plasticity. We highlight transcription factors, their cofactors, and the pathways that they impact. We also discuss physiological factors that impinge on these responses, including circadian rhythms and sex differences. Finally, we review how dietary modifications modulate hepatic gene expression programs.
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Affiliation(s)
- Lara Bideyan
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Rohith Nagari
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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9
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Buurstede JC, van Weert LTCM, Colucci P, Gentenaar M, Viho EMG, Koorneef LL, Schoonderwoerd RA, Lanooij SD, Moustakas I, Balog J, Mei H, Kielbasa SM, Campolongo P, Roozendaal B, Meijer OC. Hippocampal glucocorticoid target genes associated with enhancement of memory consolidation. Eur J Neurosci 2021; 55:2666-2683. [PMID: 33840130 PMCID: PMC9292385 DOI: 10.1111/ejn.15226] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/04/2021] [Indexed: 12/16/2022]
Abstract
Glucocorticoids enhance memory consolidation of emotionally arousing events via largely unknown molecular mechanisms. This glucocorticoid effect on the consolidation process also requires central noradrenergic neurotransmission. The intracellular pathways of these two stress mediators converge on two transcription factors: the glucocorticoid receptor (GR) and phosphorylated cAMP response element‐binding protein (pCREB). We therefore investigated, in male rats, whether glucocorticoid effects on memory are associated with genomic interactions between the GR and pCREB in the hippocampus. In a two‐by‐two design, object exploration training or no training was combined with post‐training administration of a memory‐enhancing dose of corticosterone or vehicle. Genomic effects were studied by chromatin immunoprecipitation followed by sequencing (ChIP‐seq) of GR and pCREB 45 min after training and transcriptome analysis after 3 hr. Corticosterone administration induced differential GR DNA‐binding and regulation of target genes within the hippocampus, largely independent of training. Training alone did not result in long‐term memory nor did it affect GR or pCREB DNA‐binding and gene expression. No strong evidence was found for an interaction between GR and pCREB. Combination of the GR DNA‐binding and transcriptome data identified a set of novel, likely direct, GR target genes that are candidate mediators of corticosterone effects on memory consolidation. Cell‐specific expression of the identified target genes using single‐cell expression data suggests that the effects of corticosterone reflect in part non‐neuronal cells. Together, our data identified new GR targets associated with memory consolidation that reflect effects in both neuronal and non‐neuronal cells.
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Affiliation(s)
- Jacobus C Buurstede
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Lisa T C M van Weert
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands.,Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Paola Colucci
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Max Gentenaar
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva M G Viho
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Lisa L Koorneef
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin A Schoonderwoerd
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Suzanne D Lanooij
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Ioannis Moustakas
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M Kielbasa
- Department of Medical Statistics and Bioinformatics, Bioinformatics Center of Expertise, Leiden University Medical Center, Leiden, The Netherlands
| | - Patrizia Campolongo
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Benno Roozendaal
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Onno C Meijer
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
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10
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Præstholm SM, Correia CM, Grøntved L. Multifaceted Control of GR Signaling and Its Impact on Hepatic Transcriptional Networks and Metabolism. Front Endocrinol (Lausanne) 2020; 11:572981. [PMID: 33133019 PMCID: PMC7578419 DOI: 10.3389/fendo.2020.572981] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Glucocorticoids (GCs) and the glucocorticoid receptor (GR) are important regulators of development, inflammation, stress response and metabolism, demonstrated in various diseases including Addison's disease, Cushing's syndrome and by the many side effects of prolonged clinical administration of GCs. These conditions include severe metabolic challenges in key metabolic organs like the liver. In the liver, GR is known to regulate the transcription of key enzymes in glucose and lipid metabolism and contribute to the regulation of circadian-expressed genes. Insights to the modes of GR regulation and the underlying functional mechanisms are key for understanding diseases and for the development of improved clinical uses of GCs. The activity and function of GR is regulated at numerous levels including ligand availability, interaction with heat shock protein (HSP) complexes, expression of GR isoforms and posttranslational modifications. Moreover, recent genomics studies show functional interaction with multiple transcription factors (TF) and coregulators in complex transcriptional networks controlling cell type-specific gene expression by GCs. In this review we describe the different regulatory steps important for GR activity and discuss how different TF interaction partners of GR selectively control hepatic gene transcription and metabolism.
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Affiliation(s)
| | | | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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11
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Role of Marek's Disease Virus (MDV)-Encoded U S3 Serine/Threonine Protein Kinase in Regulating MDV Meq and Cellular CREB Phosphorylation. J Virol 2020; 94:JVI.00892-20. [PMID: 32581093 DOI: 10.1128/jvi.00892-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022] Open
Abstract
Marek's disease (MD) is a neoplastic disease of chickens caused by Marek's disease virus (MDV), a member of the subfamily Alphaherpesvirinae Like other alphaherpesviruses, MDV encodes a serine/threonine protein kinase, US3. The functions of US3 have been extensively studied in other alphaherpesviruses; however, the biological functions of MDV US3 and its substrates have not been studied in detail. In this study, we investigated potential cellular pathways that are regulated by MDV US3 and identified chicken CREB (chCREB) as a substrate of MDV US3. We show that wild-type MDV US3, but not kinase-dead US3 (US3-K220A), increases CREB phosphorylation, leading to recruitment of phospho-CREB (pCREB) to the promoter of the CREB-responsive gene and activation of CREB target gene expression. Using US3 deletion and US3 kinase-dead recombinant MDV, we identified US3-responsive MDV genes during infection and found that the majority of US3-responsive genes were located in the MDV repeat regions. Chromatin immunoprecipitation sequencing (ChIP-seq) studies determined that some US3-regulated genes colocalized with Meq (an MDV-encoded oncoprotein) recruitment sites. Chromatin immunoprecipitation-PCR (ChIP-PCR) further confirmed Meq binding to the ICP4/LAT region, which is also regulated by US3. Furthermore, biochemical studies demonstrated that MDV US3 interacts with Meq in transfected cells and MDV-infected chicken embryonic fibroblasts in a phosphorylation-dependent manner. Finally, in vitro kinase studies revealed that Meq is a US3 substrate. MDV US3 thus acts as an upstream kinase of the CREB signaling pathway to regulate the transcription function of the CREB/Meq heterodimer, which targets cellular and viral gene expression.IMPORTANCE MDV is a potent oncogenic herpesvirus that induces T-cell lymphoma in infected chickens. Marek's disease continues to have a significant economic impact on the poultry industry worldwide. US3 encoded by alphaherpesviruses is a multifunctional kinase involved in the regulation of various cellular pathways. Using an MDV genome quantitative reverse transcriptase PCR (qRT-PCR) array and chromatin immunoprecipitation, we elucidated the role of MDV US3 in viral and cellular gene regulation. Our results provide insights into how viral kinase regulates host cell signaling pathways to activate both viral and host gene expression. This is an important step toward understanding host-pathogen interaction through activation of signaling cascades.
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12
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Homer1a Undergoes Bimodal Transcriptional Regulation by CREB and the Circadian Clock. Neuroscience 2020; 434:161-170. [DOI: 10.1016/j.neuroscience.2020.03.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
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13
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Perie L, Verma N, Xu L, Ma X, Mueller E. Transcriptional Regulation of ZNF638 in Thermogenic Cells by the cAMP Response Element Binding Protein in Male Mice. J Endocr Soc 2019; 3:2326-2340. [PMID: 31745529 PMCID: PMC6855216 DOI: 10.1210/js.2019-00238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Zinc finger factors are implicated in a variety of cellular processes, including adipose tissue differentiation and thermogenesis. We have previously demonstrated that zinc finger protein 638 (ZNF638) is a transcriptional coactivator acting as an early regulator of adipogenesis in vitro. In this study, we show, to our knowledge for the first time, that, in vivo, ZNF638 abounds selectively in mature brown and subcutaneous fat tissues and in fully differentiated thermogenic adipocytes. Furthermore, gene expression studies revealed that ZNF638 is upregulated by cAMP modulators in vitro and by cold exposure and by pharmacological stimulation of β-adrenergic signaling in vivo. In silico analysis of the upstream regulatory region of the ZNF638 gene identified two putative cAMP response elements within 500 bp of the ZNF638 transcription start site. Detailed molecular analysis involving EMSA and chromatin immunoprecipitation assays demonstrated that cAMP response element binding protein (CREB) binds to these cAMP response element regions of the ZNF638 promoter, and functional studies revealed that CREB is necessary and sufficient to regulate the levels of ZNF638 transcripts. Taken together, these results demonstrate that ZNF638 is selectively expressed in mature thermogenic adipocytes and tissues and that its induction in response to classic stimuli that promote heat generation is mediated via CREB signaling, pointing to a possible novel role of ZNF638 in brown and beige fat tissues.
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Affiliation(s)
- Luce Perie
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, New York University, New York, New York
| | - Narendra Verma
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, New York University, New York, New York
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Elisabetta Mueller
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, New York University, New York, New York
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14
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Cohen DM, Lim HW, Won KJ, Steger DJ. Shared nucleotide flanks confer transcriptional competency to bZip core motifs. Nucleic Acids Res 2019; 46:8371-8384. [PMID: 30085281 PMCID: PMC6144830 DOI: 10.1093/nar/gky681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022] Open
Abstract
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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Beytebiere JR, Trott AJ, Greenwell BJ, Osborne CA, Vitet H, Spence J, Yoo SH, Chen Z, Takahashi JS, Ghaffari N, Menet JS. Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions. Genes Dev 2019; 33:294-309. [PMID: 30804225 PMCID: PMC6411008 DOI: 10.1101/gad.322198.118] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022]
Abstract
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the various biological functions under clock control, rhythmic gene expression is tissue-specific despite an identical clockwork mechanism in every cell. Here we show that BMAL1 DNA binding is largely tissue-specific, likely because of differences in chromatin accessibility between tissues and cobinding of tissue-specific transcription factors. Our results also indicate that BMAL1 ability to drive tissue-specific rhythmic transcription is associated with not only the activity of BMAL1-bound enhancers but also the activity of neighboring enhancers. Characterization of physical interactions between BMAL1 enhancers and other cis-regulatory regions by RNA polymerase II chromatin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 target gene expression correlates with rhythmic chromatin interactions. These data thus support that much of BMAL1 target gene transcription depends on BMAL1 capacity to rhythmically regulate a network of enhancers.
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Affiliation(s)
- Joshua R Beytebiere
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Alexandra J Trott
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Ben J Greenwell
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Collin A Osborne
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Helene Vitet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Jessica Spence
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noushin Ghaffari
- Center for Bioinformatics and Genomic Systems Engineering (CBGSE), Texas A&M AgriLife Research, College Station, Texas 77845, USA
- AgriLife Genomics and Bioinformatics, Texas A&M AgriLife Research, College Station, Texas 77845, USA
| | - Jerome S Menet
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, Texas 77843, USA
- Program of Genetics, Texas A&M University, College Station, Texas 77843, USA
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16
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Kalvisa A, Siersbæk MS, Præstholm SM, Christensen LJL, Nielsen R, Stohr O, Vettorazzi S, Tuckermann J, White M, Mandrup S, Grøntved L. Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver. PLoS Biol 2018; 16:e2006249. [PMID: 30532187 PMCID: PMC6301715 DOI: 10.1371/journal.pbio.2006249] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 12/20/2018] [Accepted: 11/16/2018] [Indexed: 02/01/2023] Open
Abstract
Hepatic circadian gene transcription is tightly coupled to feeding behavior, which has a profound impact on metabolic disorders associated with diet-induced obesity. Here, we describe a genomics approach to uncover mechanisms controlling hepatic postprandial gene expression. Combined transcriptomic and cistromic analysis identified hundreds of circadian-regulated genes and enhancers controlled by feeding. Postprandial suppression of enhancer activity was associated with reduced glucocorticoid receptor (GR) and Forkhead box O1 (FOXO1) occupancy of chromatin correlating with reduced serum corticosterone levels and increased serum insulin levels. Despite substantial co-occupancy of feeding-regulated enhancers by GR and FOXO1, selective disruption of corticosteroid and/or insulin signaling resulted in dysregulation of specific postprandial regulated gene programs. In combination, these signaling pathways operate a major part of the genes suppressed by feeding. Importantly, the feeding response was disrupted in diet-induced obese animals, which was associated with dysregulation of several corticosteroid- and insulin-regulated genes, providing mechanistic insights to dysregulated circadian gene transcription associated with obesity. The liver is an essential organ regulating metabolic homeostasis in response to fluctuations of metabolites induced by daily rhythms of food intake. Homeostasis is maintained by precise dynamic regulation of signaling pathways controlling a wealth of enzymatic reactions involving lipid, bile acid, amino acid and glucose synthesis, storage, and redistribution in hepatocytes. Precise temporal expression of hepatic enzymes is crucial for metabolic homeostasis; a major part of circadian hepatic protein expression is regulated by precisely timed gene transcription. Here, we use a genomics approach to identify genes and regulatory regions of the genome involved in feeding-regulated gene expression. We find that transcription factors acting downstream of glucocorticoid and insulin signaling are enriched at regulatory regions repressed by feeding. Importantly, insulin and glucocorticoid signaling operate to cooperatively control the majority of feeding-mediated gene repression, and these signaling pathways are dysregulated in diet-induced obesity impacting dynamic hepatic gene expression.
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Affiliation(s)
- Adrija Kalvisa
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Majken S. Siersbæk
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Stine M. Præstholm
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Line J. L. Christensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Oliver Stohr
- Division of Endocrinology, Boston Children's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sabine Vettorazzi
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Jan Tuckermann
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Morris White
- Division of Endocrinology, Boston Children's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- * E-mail:
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17
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Larabee JL, Hauck G, Ballard JD. Unique, Intersecting, and Overlapping Roles of C/EBP β and CREB in Cells of the Innate Immune System. Sci Rep 2018; 8:16931. [PMID: 30446701 PMCID: PMC6240029 DOI: 10.1038/s41598-018-35184-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
CREB and C/EBP β signaling pathways are modulated during inflammation and also targeted by Bacillus anthracis edema toxin (ET), but how these factors individually and jointly contribute to changes in immune cell function is poorly understood. Using CRISPR/Cas9 gene editing, macrophage cell lines lacking CREB and isoforms of C/EBP β were generated and analyzed for changes in responses to LPS, ET, and IL-4. Macrophages lacking C/EBP β suppressed induction of IL-10 and Arg1, while IL-6 was increased in these cells following exposure to LPS. Examination of C/EBP β isoforms indicated the 38 kDa isoform was necessary for the expression of IL-10 and Arg1. ChIP-Seq analysis of CREB and C/EBP β binding to targets on the chromosome of human PBMC identified several regions where both factors overlapped in their binding, suggesting similar gene targeting or cooperative effects. Based on the ChIP-Seq data, a panel of previously unknown targets of CREB and C/EBP β was identified and includes genes such as VNN2, GINS4, CTNNBL1, and SULF2. Isoforms of a transcriptional corepressor, transducin-like enhancer of Split (TLE), were also found to have CREB and C/EBP β binding their promoter and were up regulated by ET. Finally, we explore a possible layer of C/EBP β regulation by a protein complex consisting of adenomatous polyposis coli (APC) and PKA. Collectively, these data provide new insights into the role of CREB and C/EBP β as immunosignaling regulators and targets of an important bacterial virulence factor.
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Affiliation(s)
- Jason L Larabee
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73190, USA
| | - Garrett Hauck
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73190, USA
| | - Jimmy D Ballard
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73190, USA.
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18
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The nuclear bile acid receptor FXR is a PKA- and FOXA2-sensitive activator of fasting hepatic gluconeogenesis. J Hepatol 2018; 69:1099-1109. [PMID: 29981427 DOI: 10.1016/j.jhep.2018.06.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/14/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Embedded into a complex signaling network that coordinates glucose uptake, usage and production, the nuclear bile acid receptor FXR is expressed in several glucose-processing organs including the liver. Hepatic gluconeogenesis is controlled through allosteric regulation of gluconeogenic enzymes and by glucagon/cAMP-dependent transcriptional regulatory pathways. We aimed to elucidate the role of FXR in the regulation of fasting hepatic gluconeogenesis. METHODS The role of FXR in hepatic gluconeogenesis was assessed in vivo and in mouse primary hepatocytes. Gene expression patterns in response to glucagon and FXR agonists were characterized by quantitative reverse transcription PCR and microarray analysis. FXR phosphorylation by protein kinase A was determined by mass spectrometry. The interaction of FOXA2 with FXR was identified by cistromic approaches and in vitro protein-protein interaction assays. The functional impact of the crosstalk between FXR, the PKA and FOXA2 signaling pathways was assessed by site-directed mutagenesis, transactivation assays and restoration of FXR expression in FXR-deficient hepatocytes in which gene expression and glucose production were assessed. RESULTS FXR positively regulates hepatic glucose production through two regulatory arms, the first one involving protein kinase A-mediated phosphorylation of FXR, which allowed for the synergistic activation of gluconeogenic genes by glucagon, agonist-activated FXR and CREB. The second arm involves the inhibition of FXR's ability to induce the anti-gluconeogenic nuclear receptor SHP by the glucagon-activated FOXA2 transcription factor, which physically interacts with FXR. Additionally, knockdown of Foxa2 did not alter glucagon-induced and FXR agonist enhanced expression of gluconeogenic genes, suggesting that the PKA and FOXA2 pathways regulate distinct subsets of FXR responsive genes. CONCLUSIONS Thus, hepatic glucose production is regulated during physiological fasting by FXR, which integrates the glucagon/cAMP signal and the FOXA2 signal, by being post-translationally modified, and by engaging in protein-protein interactions, respectively. LAY SUMMARY Activation of the nuclear bile acid receptor FXR regulates gene expression networks, controlling lipid, cholesterol and glucose metabolism, which are mostly effective after eating. Whether FXR exerts critical functions during fasting is unknown. The results of this study show that FXR transcriptional activity is regulated by the glucagon/protein kinase A and the FOXA2 signaling pathways, which act on FXR through phosphorylation and protein-protein interactions, respectively, to increase hepatic glucose synthesis.
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19
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Tolerance to sustained activation of the cAMP/Creb pathway activity in osteoblastic cells is enabled by loss of p53. Cell Death Dis 2018; 9:844. [PMID: 30154459 PMCID: PMC6113249 DOI: 10.1038/s41419-018-0944-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
Abstract
The loss of p53 function is a central event in the genesis of osteosarcoma (OS). How mutation of p53 enables OS development from osteoblastic lineage cells is poorly understood. We and others have reported a key role for elevated and persistent activation of the cAMP/PKA/Creb1 pathway in maintenance of OS. In view of the osteoblast lineage being the cell of origin of OS, we sought to determine how these pathways interact within the context of the normal osteoblast. Normal osteoblasts (p53 WT) rapidly underwent apoptosis in response to acute elevation of cAMP levels or activity, whereas p53-deficient osteoblasts tolerated this aberrant cAMP/Creb level and activity. Using the p53 activating small-molecule Nutlin-3a and cAMP/Creb1 activator forskolin, we addressed the question of how p53 responds to the activation of cAMP. We observed that p53 acts dominantly to protect cells from excessive cAMP accumulation. We identify a Creb1-Cbp complex that functions together with and interacts with p53. Finally, translating these results we find that a selective small-molecule inhibitor of the Creb1-Cbp interaction demonstrates selective toxicity to OS cells where this pathway is constitutively active. This highlights the cAMP/Creb axis as a potentially actionable therapeutic vulnerability in p53-deficient tumors such as OS. These results define a mechanism through which p53 protects normal osteoblasts from excessive or abnormal cAMP accumulation, which becomes fundamentally compromised in OS.
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20
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Gadupudi GS, Elser BA, Sandgruber FA, Li X, Gibson-Corley KN, Robertson LW. PCB126 Inhibits the Activation of AMPK-CREB Signal Transduction Required for Energy Sensing in Liver. Toxicol Sci 2018; 163:440-453. [PMID: 29474705 PMCID: PMC5974782 DOI: 10.1093/toxsci/kfy041] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
3,3',4,4',5-pentachlorobiphenyl (PCB126), a dioxin-like PCB, elicits toxicity through a wide array of noncarcinogenic effects, including metabolic syndrome, wasting, and nonalcoholic fatty-liver disease. Previously, we reported decreases in the transcription of several enzymes involved in gluconeogenesis, before the early onset of lipid accumulation. Hence, this study was aimed at understanding the impact of resultant decreases gluconeogenic enzymes on growth, weight, and metabolism in the liver, upon extended exposure. Male Sprague Dawley rats (75-100 g), fed a defined AIN-93G diet, were injected (ip) with single dose of soy oil (5 ml/kg body weight; n = 14) or PCB126 (5 µmol/kg; n = 15), 28 days, prior euthanasia. A subset of rats from each group were fasted for 12 h (vehicle [n = 6] and PCB126 [n = 4]). Rats only showed significant weight loss between days 14 and 28 (p < .05) and some mortality (p = .0413). As in our previous studies, the expression levels of enzymes involved in gluconeogenesis (Pepck-c, G6Pase, Sds, Pc, and Ldh-A) and glycogenolysis (Pygl) were strongly downregulated. The decreased expression of these enzymes in PCB126-treated rats after a 12 h fast decreased hepatic glucose production from glycogen and gluconeogenic substrates, exacerbating the hypoglycemia. Additionally, PCB126 caused hepatic steatosis and decreased the expression of the transcription factor Pparα and its targets, necessary for fatty-acid oxidation. The observed metabolic disruption across multiple branches of fasting metabolism resulted from inhibition in the activation of enzyme AMPK and transcription factor CREB signaling, necessary for "sensing" energy-deprivation and the induction of enzymes that respond to the PCB126 triggered fuel crisis in liver.
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Affiliation(s)
- Gopi S Gadupudi
- Interdisciplinary Graduate Program in Human Toxicology, Graduate College, The University of Iowa, Iowa City, Iowa
- Department of Occupational and Environmental Health, College of Public Health
| | - Benjamin A Elser
- Interdisciplinary Graduate Program in Human Toxicology, Graduate College, The University of Iowa, Iowa City, Iowa
- Department of Occupational and Environmental Health, College of Public Health
| | - Fabian A Sandgruber
- Department of Occupational and Environmental Health, College of Public Health
| | - Xueshu Li
- Department of Occupational and Environmental Health, College of Public Health
| | | | - Larry W Robertson
- Interdisciplinary Graduate Program in Human Toxicology, Graduate College, The University of Iowa, Iowa City, Iowa
- Department of Occupational and Environmental Health, College of Public Health
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21
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Luo WJ, Cheng TY, Wong KI, Fang WH, Liao KM, Hsieh YT, Su KY. Novel therapeutic drug identification and gene correlation for fatty liver disease using high-content screening: Proof of concept. Eur J Pharm Sci 2018; 121:106-117. [PMID: 29800612 DOI: 10.1016/j.ejps.2018.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/13/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a problem in obese people caused by increasing intake of high-calorie food such as fructose implicated in the elevated prevalence. It is necessary to identify novel drugs to develop effective therapies. In this study, we combined LOPAC® (The Library of Pharmacologically Active Compounds) and High-Content screening to identify compounds that significantly reduced intracellular lipid droplets (LD) after high fat medium (HFM) treatment. Among 1280 compounds, we identified 239 compounds that reduced LD by >50%. Of these, 17 maintained cell viability. Nine of them were selected for validation using normal primary hepatocytes, of which five compounds showed dose-dependent efficacy. Whole genome transcriptomic network analysis was performed to construct the underlying regulatory network. There were 831 (711 up-regulated and 120 down-regulated genes) and 3480 (2009 up-regulated and 1471 down-regulated genes) genes that showed a significant change (>2-fold; p < 0.05) after 12 and 24 h HFM treatment, respectively. Gene enrichment and pathway analysis showed several immune responses mediated by MIF, IL-17, TLR, and IL-6. These compounds modulate lipogenesis via GSK3β and CREB1, which is followed by an alteration in the expression of several downstream genes related to hepatocellular carcinoma and hepatitis. CREB1 is a core transcription factor and may be a potential therapeutic target for liver disease. In conclusion, this proof of concept provides a strategy for identifying novel drugs for treatment of fatty liver disease as well as elucidates their underlying mechanisms. This research provides opportunity for developing future pharmaceutical therapeutics.
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Affiliation(s)
- Wei-Jia Luo
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Yu Cheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Keng-Ieng Wong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Woei-Horng Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Keng-Mao Liao
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yun-Ting Hsieh
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan; Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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22
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Jung HJ, Raghuram V, Lee JW, Knepper MA. Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBP β in Vasopressin-Sensitive Collecting Duct Cells. J Am Soc Nephrol 2018; 29:1490-1500. [PMID: 29572403 DOI: 10.1681/asn.2017050545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/18/2018] [Indexed: 11/03/2022] Open
Abstract
Background Renal water excretion is controlled by vasopressin, in part through regulation of the transcription of the aquaporin-2 gene (Aqp2).Methods To identify enhancer regions likely to be involved in the regulation of Aqp2 and other principal cell-specific genes, we used several next generation DNA-sequencing techniques in a well characterized cultured cell model of collecting duct principal cells (mpkCCD). To locate enhancers, we performed the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) to identify accessible regions of DNA and integrated the data with data generated by chromatin immunoprecipitation followed by next generation DNA-sequencing (ChIP-Seq) for CCCTC binding factor (CTCF) binding, histone H3 lysine-27 acetylation, and RNA polymerase II.Results We identified two high-probability enhancers centered 81 kb upstream and 5.8 kb downstream from the Aqp2 transcriptional start site. Motif analysis of these regions and the Aqp2 promoter identified several potential transcription factor binding sites, including sites for two b-ZIP transcription factors: CCAAT/enhancer binding protein-β (C/EBPβ) and cAMP-responsive element binding protein (CREB). To identify genomic binding sites for both, we conducted ChIP-Seq using well characterized antibodies. In the presence of vasopressin, C/EBPβ, a pioneer transcription factor critical to cell-specific gene expression, bound strongly at the identified enhancer downstream from Aqp2 However, over multiple replicates, we found no detectable CREB binding sites within 390 kb of Aqp2 Thus, any role for CREB in the regulation of Aqp2 gene transcription is likely to be indirect.Conclusions The analysis identified two enhancer regions pertinent to transcriptional regulation of the Aqp2 gene and showed C/EBPβ (but not CREB) binding.
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Affiliation(s)
- Hyun Jun Jung
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Jae Wook Lee
- National Cancer Center, Goyang, Gyeonggi-do, Republic of Korea
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
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23
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Thierion E, Odom DT. Charting the transcriptional regulatory changes in mouse liver during fasting. Hepatology 2018; 67:436-438. [PMID: 28833286 DOI: 10.1002/hep.29474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/20/2017] [Accepted: 08/15/2017] [Indexed: 12/07/2022]
Affiliation(s)
- Elodie Thierion
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
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24
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Goldstein I, Hager GL. The Three Ds of Transcription Activation by Glucagon: Direct, Delayed, and Dynamic. Endocrinology 2018; 159:206-216. [PMID: 29077799 PMCID: PMC6283435 DOI: 10.1210/en.2017-00521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022]
Abstract
Upon lowered blood glucose occurring during fasting, glucagon is secreted from pancreatic islets, exerting various metabolic effects to normalize glucose levels. A considerable portion of these effects is mediated by glucagon-activated transcription factors (TFs) in liver. Glucagon directly activates several TFs via immediate cyclic adenosine monophosphate (cAMP)- and calcium-dependent signaling events. Among these TFs, cAMP response element-binding protein (CREB) is a major factor. CREB recruits histone-modifying enzymes and cooperates with other TFs on the chromatin template to increase the rate of gene transcription. In addition to direct signal transduction, the transcriptional effects of glucagon are also influenced by dynamic TF cross talk. Specifically, assisted loading of one TF by a companion TF leads to increased binding and activity. Lastly, transcriptional regulation by glucagon is also exerted by TF cascades by which a primary TF induces the gene expression of secondary TFs that bring about their activity a few hours after the initial glucagon signal. This mechanism of a delayed response may be instrumental in establishing the temporal organization of the fasting response by which distinct metabolic events separate early from prolonged fasting. In this mini-review, we summarize recent advances and critical discoveries in glucagon-dependent gene regulation with a focus on direct TF activation, dynamic TF cross talk, and TF cascades.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
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25
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Rossi M, Spichty M, Attorri L, Distante C, Nervi C, Salvati S, Vitelli L. Eicosapentaenoic acid modulates the synergistic action of CREB1 and ID/E2A family members in the rat pup brain and mouse embryonic stem cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:870-884. [PMID: 28666847 DOI: 10.1016/j.bbagrm.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/01/2017] [Accepted: 06/20/2017] [Indexed: 12/13/2022]
Abstract
The aim of this study was to investigate the molecular mechanism by which eicosapentaenoic acid (EPA) may exert neuroprotective effects through an "EPA-cyclic AMP response element-binding protein (CREB)" signaling pathway. The current study reveals that EPA modulates the exquisite interplay of interaction of CREB1 with the inhibitor of DNA binding (ID) and E2A family members, thereby delivering mechanistic insights into specific neural differentiation program. In this scenario, our work provides evidence for the capability of CREB1 to sequester ID:E2A family members in brain tissues and neural differentiating mouse embryonic stem cells (mESCs) through formation of a [CREB1]2:ID2:E47 tetrameric complex.In essence, the molecular function of CREB1 is to dynamically regulate the location-specific assembly or disassembly of basic-helix-loop-helix (bHLH):HLH protein complexes to mediate the activation of neural/glial target genes. Together, these findings support the one-to-many binding mechanism of CREB1 and indicate that EPA treatment potentiates the integration of CREB dependent signaling with HLH/bHLH transcriptional network, adding specificity to the CREB1-mediated gene regulation during neural/glial differentiation. Our current research on the EPA-CREB axis could reveal new molecular targets for treating neurogenerative disease.
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Affiliation(s)
- Maurizio Rossi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Martin Spichty
- Laboratory of Biology and Modelling of the Cell, Lyon University, ENS Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 allée d'Italie, Site Jacques Monod, F-69007 Lyon, France
| | - Lucilla Attorri
- Department of Public Veterinary Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Chiara Distante
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, 04100, Latina, Italy
| | - Serafina Salvati
- Department of Public Veterinary Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Luigi Vitelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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26
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Cohen DM, Steger DJ. Nuclear Receptor Function through Genomics: Lessons from the Glucocorticoid Receptor. Trends Endocrinol Metab 2017; 28:531-540. [PMID: 28495406 PMCID: PMC5505657 DOI: 10.1016/j.tem.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Unlocking the therapeutic potential of the glucocorticoid receptor (GR) has motivated a search for small molecules that selectively modulate its ability to activate or repress gene transcription. Recently, breakthrough studies in the field of genomics have reinvigorated debate over longstanding transcriptional models explaining how GR controls tissue-specific gene expression. Here, we highlight these genomic studies with the dual goals of advancing understanding of nuclear receptor-mediated transcription and stimulating thought on the development of anti-inflammatory and immunosuppressive ligands for GR that have reduced harmful effects on metabolism.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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27
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Byun S, Kim YC, Zhang Y, Kong B, Guo G, Sadoshima J, Ma J, Kemper B, Kemper JK. A postprandial FGF19-SHP-LSD1 regulatory axis mediates epigenetic repression of hepatic autophagy. EMBO J 2017; 36:1755-1769. [PMID: 28446510 DOI: 10.15252/embj.201695500] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 12/19/2022] Open
Abstract
Lysosome-mediated autophagy is essential for cellular survival and homeostasis upon nutrient deprivation, but is repressed after feeding. Despite the emerging importance of transcriptional regulation of autophagy by nutrient-sensing factors, the role for epigenetic control is largely unexplored. Here, we show that Small Heterodimer Partner (SHP) mediates postprandial epigenetic repression of hepatic autophagy by recruiting histone demethylase LSD1 in response to a late fed-state hormone, FGF19 (hFGF19, mFGF15). FGF19 treatment or feeding inhibits macroautophagy, including lipophagy, but these effects are blunted in SHP-null mice or LSD1-depleted mice. In addition, feeding-mediated autophagy inhibition is attenuated in FGF15-null mice. Upon FGF19 treatment or feeding, SHP recruits LSD1 to CREB-bound autophagy genes, including Tfeb, resulting in dissociation of CRTC2, LSD1-mediated demethylation of gene-activation histone marks H3K4-me2/3, and subsequent accumulation of repressive histone modifications. Both FXR and SHP inhibit hepatic autophagy interdependently, but while FXR acts early, SHP acts relatively late after feeding, which effectively sustains postprandial inhibition of autophagy. This study demonstrates that the FGF19-SHP-LSD1 axis maintains homeostasis by suppressing unnecessary autophagic breakdown of cellular components, including lipids, under nutrient-rich postprandial conditions.
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Affiliation(s)
- Sangwon Byun
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Young-Chae Kim
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yang Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bo Kong
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Grace Guo
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jian Ma
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Byron Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jongsook Kim Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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28
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Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol 2017; 15:e2001069. [PMID: 28414715 PMCID: PMC5393560 DOI: 10.1371/journal.pbio.2001069] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022] Open
Abstract
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription. Using chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq), we found that hypersensitivity cycled in phase with RNA polymerase II (Pol II) loading and H3K27ac histone marks. We then combined the DHSs with temporal Pol II profiles in wild-type (WT) and Bmal1-/- livers to computationally identify transcription factors through which the core clock and feeding-fasting cycles control diurnal rhythms in transcription. While a similar number of mRNAs accumulated rhythmically in Bmal1-/- compared to WT livers, the amplitudes in Bmal1-/- were generally lower. The residual rhythms in Bmal1-/- reflected transcriptional regulators mediating feeding-fasting responses as well as responses to rhythmic systemic signals. Finally, the analysis of DNase I cuts at nucleotide resolution showed dynamically changing footprints consistent with dynamic binding of CLOCK:BMAL1 complexes. Structural modeling suggested that these footprints are driven by a transient heterotetramer binding configuration at peak activity. Together, our temporal DNase I mappings allowed us to decipher the global regulation of diurnal transcription rhythms in the mouse liver.
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Affiliation(s)
- Jonathan Aryeh Sobel
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Irina Krier
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Teemu Andersin
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Sunil Raghav
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Federica Gilardi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Styliani Kalantzi
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Rey
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Benjamin Weger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ueli Schibler
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Bart Deplancke
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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29
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Lo YH, Chung E, Li Z, Wan YW, Mahe MM, Chen MS, Noah TK, Bell KN, Yalamanchili HK, Klisch TJ, Liu Z, Park JS, Shroyer NF. Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine. Cell Mol Gastroenterol Hepatol 2016; 3:51-71. [PMID: 28174757 PMCID: PMC5247424 DOI: 10.1016/j.jcmgh.2016.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/13/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND & AIMS The transcription factor atonal homolog 1 (ATOH1) controls the fate of intestinal progenitors downstream of the Notch signaling pathway. Intestinal progenitors that escape Notch activation express high levels of ATOH1 and commit to a secretory lineage fate, implicating ATOH1 as a gatekeeper for differentiation of intestinal epithelial cells. Although some transcription factors downstream of ATOH1, such as SPDEF, have been identified to specify differentiation and maturation of specific cell types, the bona fide transcriptional targets of ATOH1 still largely are unknown. Here, we aimed to identify ATOH1 targets and to identify transcription factors that are likely to co-regulate gene expression with ATOH1. METHODS We used a combination of chromatin immunoprecipitation and messenger RNA-based high-throughput sequencing (ChIP-seq and RNA-seq), together with cell sorting and transgenic mice, to identify direct targets of ATOH1, and establish the epistatic relationship between ATOH1 and SPDEF. RESULTS By using unbiased genome-wide approaches, we identified more than 700 genes as ATOH1 transcriptional targets in adult small intestine and colon. Ontology analysis indicated that ATOH1 directly regulates genes involved in specification and function of secretory cells. De novo motif analysis of ATOH1 targets identified SPDEF as a putative transcriptional co-regulator of ATOH1. Functional epistasis experiments in transgenic mice show that SPDEF amplifies ATOH1-dependent transcription but cannot independently initiate transcription of ATOH1 target genes. CONCLUSIONS This study unveils the direct targets of ATOH1 in the adult intestines and illuminates the transcriptional events that initiate the specification and function of intestinal secretory lineages.
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Key Words
- ATOH1
- ATOH1, atonal homolog 1
- Atoh1Flag
- Atoh1GFP
- CRC, colorectal cancer
- ChIP, chromatin immunoprecipitation
- ChIP-seq, chromatin immunoprecipitation sequencing
- DBZ, dibenzazepine
- FACS, fluorescence-activated cell sorting
- FDR, false-discovery rate
- GFP, green fluorescent protein
- GO, gene ontology
- Gfi1, growth factor independent 1
- ISC, intestinal stem cell
- Intestinal Epithelium
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- QES, Q-enrichment-score
- RT-qPCR, reverse-transcription quantitative polymerase chain reaction
- SPDEF
- Spdef, SAM pointed domain containing ETS transcription factor
- TRE-Spdef
- TSS, transcription start site
- Transcription
- Villin-creER
- mRNA, messenger RNA
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Affiliation(s)
- Yuan-Hung Lo
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Eunah Chung
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zhaohui Li
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas
| | - Maxime M. Mahe
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Min-Shan Chen
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Taeko K. Noah
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kristin N. Bell
- Graduate Program in Molecular Developmental Biology, University of Cincinnati, Cincinnati, Cincinnati, Ohio
| | | | - Tiemo J. Klisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Zhandong Liu
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joo-Seop Park
- Division of Pediatric Urology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Joo-Seop Park, PhD, Divisions of Pediatric Urology and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.Divisions of Pediatric Urology and Developmental BiologyCincinnati Children's Hospital Medical CenterCincinnatiOhio
| | - Noah F. Shroyer
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
- Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
- Correspondence Address correspondence to: Noah F. Shroyer, PhD, Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas.Division of MedicineSection of Gastroenterology and HepatologyBaylor College of MedicineHoustonTexas
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30
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Sandoval PC, Claxton JS, Lee JW, Saeed F, Hoffert JD, Knepper MA. Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin. Sci Rep 2016; 6:34863. [PMID: 27725713 PMCID: PMC5057153 DOI: 10.1038/srep34863] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/16/2016] [Indexed: 11/09/2022] Open
Abstract
Vasopressin-mediated regulation of renal water excretion is defective in a variety of water balance disorders in humans. It occurs in part through long-term mechanisms that regulate the abundance of the aquaporin-2 water channel in renal collecting duct cells. Here, we use deep DNA sequencing in mouse collecting duct cells to ask whether vasopressin signaling selectively increases Aqp2 gene transcription or whether it triggers a broadly targeted transcriptional network. ChIP-Seq quantification of binding sites for RNA polymerase II was combined with RNA-Seq quantification of transcript abundances to identify genes whose transcription is regulated by vasopressin. (View curated dataset at https://helixweb.nih.gov/ESBL/Database/Vasopressin/). The analysis revealed only 35 vasopressin-regulated genes (of 3659) including Aqp2. Increases in RNA polymerase II binding and mRNA abundances for Aqp2 far outstripped corresponding measurements for all other genes, consistent with the conclusion that vasopressin-mediated transcriptional regulation is highly selective for Aqp2. Despite the overall selectivity of the net transcriptional response, vasopressin treatment was associated with increased RNA polymerase II binding to the promoter proximal region of a majority of expressed genes, suggesting a nearly global positive regulation of transcriptional initiation with transcriptional pausing. Thus, the overall net selectivity appears to be a result of selective control of transcriptional elongation.
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Affiliation(s)
- Pablo C Sandoval
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
| | - J'Neka S Claxton
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
| | - Jae Wook Lee
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
- National Cancer Center, Goyang Gyeonggi-do, Korea
| | - Fahad Saeed
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
| | - Jason D Hoffert
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD 20892-1603, USA
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31
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Heo HJ, Tozour JN, Delahaye F, Zhao Y, Cui L, Barzilai N, Einstein FH. Advanced aging phenotype is revealed by epigenetic modifications in rat liver after in utero malnutrition. Aging Cell 2016; 15:964-72. [PMID: 27470058 PMCID: PMC5013021 DOI: 10.1111/acel.12505] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 02/06/2023] Open
Abstract
Adverse environmental exposures of mothers during fetal period predispose offspring to a range of age-related diseases earlier in life. Here, we set to determine whether a deregulated epigenetic pattern is similar in young animals whose mothers' nutrition was modulated during fetal growth to that acquired during normal aging in animals. Using a rodent model of maternal undernutrition (UN) or overnutrition (ON), we examined cytosine methylation profiles of liver from young female offspring and compared them to age-matched young controls and aged (20-month-old) animals. HELP-tagging, a genomewide restriction enzyme and sequencing assay demonstrates that fetal exposure to two different maternal diets is associated with nonrandom dysregulation of methylation levels with profiles similar to those seen in normal aging animals and occur in regions mapped to genes relevant to metabolic diseases and aging. Functional consequences were assessed by gene expression at 9 weeks old with more significant changes at 6 months of age. Early developmental exposures to unfavorable maternal diets result in altered methylation profiles and transcriptional dysregulation in Prkcb, Pc, Ncor2, and Smad3 that is also seen with normal aging. These Notch pathway and lipogenesis genes may be useful for prediction of later susceptibility to chronic disease.
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Affiliation(s)
- Hye J. Heo
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Jessica N. Tozour
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Fabien Delahaye
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Yongmei Zhao
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Lingguang Cui
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Nir Barzilai
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Francine Hughes Einstein
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
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32
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Tahara Y, Shibata S. Circadian rhythms of liver physiology and disease: experimental and clinical evidence. Nat Rev Gastroenterol Hepatol 2016; 13:217-26. [PMID: 26907879 DOI: 10.1038/nrgastro.2016.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The circadian clock system consists of a central clock located in the suprachiasmatic nucleus in the hypothalamus and peripheral clocks in peripheral tissues. Peripheral clocks in the liver have fundamental roles in maintaining liver homeostasis, including the regulation of energy metabolism and the expression of enzymes controlling the absorption and metabolism of xenobiotics. Over the past two decades, research has investigated the molecular mechanisms linking circadian clock genes with the regulation of hepatic physiological functions, using global clock-gene-knockout mice, or mice with liver-specific knockout of clock genes or clock-controlled genes. Clock dysfunction accelerates the development of liver diseases such as fatty liver diseases, cirrhosis, hepatitis and liver cancer, and these disorders also disrupt clock function. Food is an important regulator of circadian clocks in peripheral tissues. Thus, controlling the timing of food consumption and food composition, a concept known as chrononutrition, is one area of active research to aid recovery from many physiological dysfunctions. In this Review, we focus on the molecular mechanisms of hepatic circadian gene regulation and the relationships between hepatic circadian clock systems and liver physiology and disease. We concentrate on experimental data obtained from cell or mice and rat models and discuss how these findings translate into clinical research, and we highlight the latest developments in chrononutritional studies.
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Affiliation(s)
- Yu Tahara
- Waseda Institute for Advanced Study, Waseda University, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Shigenobu Shibata
- Laboratory of Physiology and Pharmacology, School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo, 162-8480, Japan
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Krasnov GS, Dmitriev AA, Melnikova NV, Zaretsky AR, Nasedkina TV, Zasedatelev AS, Senchenko VN, Kudryavtseva AV. CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res 2016; 44:e62. [PMID: 26773058 PMCID: PMC4838350 DOI: 10.1093/nar/gkv1478] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA–miRNA and gene–transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF–gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource. Similarly, CrossHub identifies mRNA–miRNA pairs with predicted or validated binding sites (TargetScan, mirSVR, PicTar, DIANA microT, miRTarBase) and strong negative expression correlations. We observed partial consistency between ChIP-Seq or miRNA target predictions and gene–TF/miRNA co-expression, demonstrating a link between these indicators. Additionally, CrossHub expression-methylation correlation analysis can be used to identify hypermethylated CpG sites or regions with the greatest potential impact on gene expression. Thus, CrossHub is capable of outlining molecular portraits of a specific gene and determining the three most common sources of expression regulation: promoter/enhancer methylation, miRNA interference and TF-mediated activation or repression. CrossHub generates formatted Excel workbooks with the detailed results. CrossHub is freely available at https://sourceforge.net/projects/crosshub/.
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Affiliation(s)
- George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119121, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Andrew R Zaretsky
- M.M. Shemyakin-Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatiana V Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Vera N Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
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Sunkel B, Wu D, Chen Z, Wang CM, Liu X, Ye Z, Horning AM, Liu J, Mahalingam D, Lopez-Nicora H, Lin CL, Goodfellow PJ, Clinton SK, Jin VX, Chen CL, Huang THM, Wang Q. Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. Nucleic Acids Res 2016; 44:4105-22. [PMID: 26743006 PMCID: PMC4872073 DOI: 10.1093/nar/gkv1528] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/22/2015] [Indexed: 01/22/2023] Open
Abstract
Identifying prostate cancer-driving transcription factors (TFs) in addition to the androgen receptor promises to improve our ability to effectively diagnose and treat this disease. We employed an integrative genomics analysis of master TFs CREB1 and FoxA1 in androgen-dependent prostate cancer (ADPC) and castration-resistant prostate cancer (CRPC) cell lines, primary prostate cancer tissues and circulating tumor cells (CTCs) to investigate their role in defining prostate cancer gene expression profiles. Combining genome-wide binding site and gene expression profiles we define CREB1 as a critical driver of pro-survival, cell cycle and metabolic transcription programs. We show that CREB1 and FoxA1 co-localize and mutually influence each other's binding to define disease-driving transcription profiles associated with advanced prostate cancer. Gene expression analysis in human prostate cancer samples found that CREB1/FoxA1 target gene panels predict prostate cancer recurrence. Finally, we showed that this signaling pathway is sensitive to compounds that inhibit the transcription co-regulatory factor MED1. These findings not only reveal a novel, global transcriptional co-regulatory function of CREB1 and FoxA1, but also suggest CREB1/FoxA1 signaling is a targetable driver of prostate cancer progression and serves as a biomarker of poor clinical outcomes.
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Affiliation(s)
- Benjamin Sunkel
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Dayong Wu
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Zhong Chen
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiangtao Liu
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Zhenqing Ye
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Aaron M Horning
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Joseph Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Devalingam Mahalingam
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Horacio Lopez-Nicora
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Paul J Goodfellow
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Steven K Clinton
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qianben Wang
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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Somvanshi PR, Patel AK, Bhartiya S, Venkatesh KV. Influence of plasma macronutrient levels on hepatic metabolism: role of regulatory networks in homeostasis and disease states. RSC Adv 2016. [DOI: 10.1039/c5ra18128c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multilevel regulations by metabolic, signaling and transcription pathways form a complex network that works to provide robust metabolic regulation in the liver. This analysis indicates that dietary perturbations in these networks can lead to insulin resistance.
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Affiliation(s)
- Pramod R. Somvanshi
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - Anilkumar K. Patel
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - Sharad Bhartiya
- Control Systems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - K. V. Venkatesh
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
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Abstract
Mammals have at least 210 histologically diverse cell types (Alberts, Molecular biology of the cell. Garland Science, New York, 2008) and the number would be even higher if functional differences are taken into account. The genome in each of these cell types is differentially programmed to express the specific set of genes needed to fulfill the phenotypical requirements of the cell. Furthermore, in each of these cell types, the gene program can be differentially modulated by exposure to external signals such as hormones or nutrients. The basis for the distinct gene programs relies on cell type-selective activation of transcriptional enhancers, which in turn are particularly sensitive to modulation. Until recently we had only fragmented insight into the regulation of a few of these enhancers; however, the recent advances in high-throughput sequencing technologies have enabled the development of a large number of technologies that can be used to obtain genome-wide insight into how genomes are reprogrammed during development and in response to specific external signals. By applying such technologies, we have begun to reveal the cross-talk between metabolism and the genome, i.e., how genomes are reprogrammed in response to metabolites, and how the regulation of metabolic networks is coordinated at the genomic level.
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Affiliation(s)
- Alexander Rauch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark.
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37
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Hill MJ, Suzuki S, Segars JH, Kino T. CRTC2 Is a Coactivator of GR and Couples GR and CREB in the Regulation of Hepatic Gluconeogenesis. Mol Endocrinol 2016; 30:104-17. [PMID: 26652733 PMCID: PMC4695631 DOI: 10.1210/me.2015-1237] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
Glucocorticoid hormones play essential roles in the regulation of gluconeogenesis in the liver, an adaptive response that is required for the maintenance of circulating glucose levels during fasting. Glucocorticoids do this by cooperating with glucagon, which is secreted from pancreatic islets to activate the cAMP-signaling pathway in hepatocytes. The cAMP-response element-binding protein (CREB)-regulated transcription coactivator 2 (CRTC2) is a coactivator known to be specific to CREB and plays a central role in the glucagon-mediated activation of gluconeogenesis in the early phase of fasting. We show here that CRTC2 also functions as a coactivator for the glucocorticoid receptor (GR). CRTC2 strongly enhances GR-induced transcriptional activity of glucocorticoid-responsive genes. CRTC2 physically interacts with the ligand-binding domain of the GR through a region spanning amino acids 561-693. Further, CRTC2 is required for the glucocorticoid-associated cooperative mRNA expression of the glucose-6-phosphatase, a rate-limiting enzyme for hepatic gluconeogenesis, by facilitating the attraction of GR and itself to its promoter region already occupied by CREB. CRTC2 is required for the maintenance of blood glucose levels during fasting in mice by enhancing the GR transcriptional activity on both the G6p and phosphoenolpyruvate carboxykinase (Pepck) genes. Finally, CRTC2 modulates the transcriptional activity of the progesterone receptor, indicating that it may influence the transcriptional activity of other steroid/nuclear receptors. Taken together, these results reveal that CRTC2 plays an essential role in the regulation of hepatic gluconeogenesis through coordinated regulation of the glucocorticoid/GR- and glucagon/CREB-signaling pathways on the key genes G6P and PEPCK.
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Affiliation(s)
- Micah J Hill
- Program in Reproductive and Adult Endocrinology (M.J.H., S.S., J.H.S., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Division of Reproductive Endocrinology and Infertility (M.J.H.), Walter Reed National Military Medical Center, Bethesda, Maryland 20889; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Reproductive Sciences and Women's Health Research (J.H.S.), Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Shigeru Suzuki
- Program in Reproductive and Adult Endocrinology (M.J.H., S.S., J.H.S., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Division of Reproductive Endocrinology and Infertility (M.J.H.), Walter Reed National Military Medical Center, Bethesda, Maryland 20889; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Reproductive Sciences and Women's Health Research (J.H.S.), Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha 26999, Qatar
| | - James H Segars
- Program in Reproductive and Adult Endocrinology (M.J.H., S.S., J.H.S., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Division of Reproductive Endocrinology and Infertility (M.J.H.), Walter Reed National Military Medical Center, Bethesda, Maryland 20889; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Reproductive Sciences and Women's Health Research (J.H.S.), Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Tomoshige Kino
- Program in Reproductive and Adult Endocrinology (M.J.H., S.S., J.H.S., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Division of Reproductive Endocrinology and Infertility (M.J.H.), Walter Reed National Military Medical Center, Bethesda, Maryland 20889; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Reproductive Sciences and Women's Health Research (J.H.S.), Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha 26999, Qatar
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Chen Q, Lu M, Monks BR, Birnbaum MJ. Insulin Is Required to Maintain Albumin Expression by Inhibiting Forkhead Box O1 Protein. J Biol Chem 2015; 291:2371-8. [PMID: 26668316 DOI: 10.1074/jbc.m115.677351] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 01/07/2023] Open
Abstract
Diabetes is accompanied by dysregulation of glucose, lipid, and protein metabolism. In recent years, much effort has been spent on understanding how insulin regulates glucose and lipid metabolism, whereas the effect of insulin on protein metabolism has received less attention. In diabetes, hepatic production of serum albumin decreases, and it has been long established that insulin positively controls albumin gene expression. In this study, we used a genetic approach in mice to identify the mechanism by which insulin regulates albumin gene transcription. Albumin expression was decreased significantly in livers with insulin signaling disrupted by ablation of the insulin receptor or Akt. Concomitant deletion of Forkhead Box O1 (Foxo1) in these livers rescued the decreased albumin secretion. Furthermore, activation of Foxo1 in the liver is sufficient to suppress albumin expression. These results suggest that Foxo1 acts as a repressor of albumin expression.
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Affiliation(s)
- Qing Chen
- From the Institute for Diabetes, Obesity, and Metabolism, Department of Biochemistry and Biophysics, and Graduate Group of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and
| | - Mingjian Lu
- From the Institute for Diabetes, Obesity, and Metabolism
| | - Bobby R Monks
- From the Institute for Diabetes, Obesity, and Metabolism
| | - Morris J Birnbaum
- From the Institute for Diabetes, Obesity, and Metabolism, Department of Biochemistry and Biophysics, and Graduate Group of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 and the Cardiovascular and Metabolic Disease Research Unit, Pfizer Inc., Cambridge, Massachusetts 02140
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39
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Goldstein I, Hager GL. Transcriptional and Chromatin Regulation during Fasting - The Genomic Era. Trends Endocrinol Metab 2015; 26:699-710. [PMID: 26520657 PMCID: PMC4673016 DOI: 10.1016/j.tem.2015.09.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/10/2015] [Accepted: 09/12/2015] [Indexed: 12/21/2022]
Abstract
An elaborate metabolic response to fasting is orchestrated by the liver and is heavily reliant on transcriptional regulation. In response to hormones (glucagon, glucocorticoids) many transcription factors (TFs) are activated and regulate various genes involved in metabolic pathways aimed at restoring homeostasis: gluconeogenesis, fatty acid oxidation, ketogenesis, and amino acid shuttling. We summarize recent discoveries regarding fasting-related TFs with an emphasis on genome-wide binding patterns. Collectively, the findings we discuss reveal a large degree of cooperation between TFs during fasting that occurs at motif-rich DNA sites bound by a combination of TFs. These new findings implicate transcriptional and chromatin regulation as major determinants of the response to fasting and unravels the complex, multi-TF nature of this response.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National institutes of Health, Bethesda, MD, 20892, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National institutes of Health, Bethesda, MD, 20892, USA.
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40
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Cieślik M, Bekiranov S. Genome-wide predictors of NF-κB recruitment and transcriptional activity. BioData Min 2015; 8:37. [PMID: 26617673 PMCID: PMC4661973 DOI: 10.1186/s13040-015-0071-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/18/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Inducible transcription factors (TFs) mediate transcriptional responses to environmental cues. In response to multiple inflammatory signals active NF-κB dimers enter the nucleus and trigger cell-type-, and stimulus-specific transcriptional programs. Although much is known about NF-κB inducing pathways and about locus-specific mechanisms of transcriptional control, it is poorly understood how the pre-existing chromatin landscape determines NF-κB target selection and activation. Specifically, it is not known which epigenetic marks and pre-bound TFs serve genome-wide as positive (negative) cues for active NF-κB. RESULTS We applied multivariate and combinatorial data mining techniques on a comprehensive dataset of DNA methylation, DNase I hypersensitivity, eight epigenetic marks, and 34 TFs to arrive at genome-wide patterns that predict NF-κB binding. Strikingly, we observed NF-κB recruitment to accessible and nucleosome-bound sites. Within nucleosomal DNA NF-κB binding was primed by H3K4me1 and H2A.Z, but also hyper-methylated DNA outside of promoters and CpG-islands. Many of these predictors showed combinatorial cooperativity and statistically significant interactions. Recruitment to pre-accessible sites was more frequent and influenced by chromatin-associated TFs. We observed that specific TF-combinations are greatly enriched for (or depleted of) NF-κB binding events. CONCLUSIONS We provide evidence of NF-κB binding within genomic regions that lack classical marks of activity. These pioneer binding events are relatively often associated with transcriptional regulation. Further, our predictive models indicate that specific combinations of epigenetic marks and transcription factors predetermine the NF-κB cistrome, supporting the feasibility of using statistical approaches to identify "histone codes".
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Affiliation(s)
- Marcin Cieślik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
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Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. Mol Cell Biol 2015; 36:50-69. [PMID: 26459762 DOI: 10.1128/mcb.00861-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/02/2015] [Indexed: 01/04/2023] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. To investigate the potential for functionality, we focused on the responses of the liver lincRNAs to growth hormone stimulation, which imparts clinically relevant sex differences to hepatic metabolism and liver disease susceptibility. Sex-biased expression characterized 247 liver lincRNAs, with many being nuclear RNA enriched and regulated by growth hormone. The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). Repression of female-specific lincRNAs in male liver, but not that of male-specific lincRNAs in female liver, was associated with enrichment of H3K27me3-associated inactive states and poised (bivalent) enhancer states. Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. Orthologs for many liver lincRNAs were identified in one or more supraprimates, including two rat lincRNAs showing the same growth hormone-regulated, sex-biased expression as their mouse counterparts. This integrative analysis of liver lincRNA chromatin states, transcription factor occupancy, and growth hormone regulation provides novel insights into the expression of sex-specific lincRNAs and their potential for regulation of sex differences in liver physiology and disease.
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42
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Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo. Cell 2015; 159:1140-1152. [PMID: 25416951 DOI: 10.1016/j.cell.2014.10.022] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/28/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of enhancer RNAs (eRNAs) that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ.
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43
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Briand LA, Lee BG, Lelay J, Kaestner KH, Blendy JA. Serine 133 phosphorylation is not required for hippocampal CREB-mediated transcription and behavior. ACTA ACUST UNITED AC 2015; 22:109-15. [PMID: 25593297 PMCID: PMC4341363 DOI: 10.1101/lm.037044.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The cAMP response element (CRE)-binding protein, CREB, is a transcription factor whose activity in the brain is critical for long-term memory formation. Phosphorylation of Ser133 in the kinase-inducible domain (KID), that in turn leads to the recruitment of the transcriptional coactivator CREB-binding protein (CBP), is thought to mediate the activation of CREB. However, the importance of phosphorylation for CREB binding to DNA and subsequent gene transcription in vivo is controversial. To definitively address the role of CREB phosphorylation in gene transcription and learning and memory, we derived mutant mice lacking the Ser133 phosphorylation site. These mice exhibit normal CREB-mediated gene transcription for a number of genes implicated in learning and memory processes. Furthermore these mice have no deficits in hippocampus- or striatum-dependent learning. Strikingly, our findings show that CREB phosphorylation at Ser133 is not necessary for CREB binding to CRE sites, CREB-mediated transcription, or CREB-mediated behavioral phenotypes associated with learning and memory.
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Affiliation(s)
- Lisa A Briand
- Department of Psychology, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Bridgin G Lee
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - John Lelay
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Julie A Blendy
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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44
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Transcriptional regulation of autophagy by an FXR-CREB axis. Nature 2014; 516:108-11. [PMID: 25383523 PMCID: PMC4257899 DOI: 10.1038/nature13949] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/08/2014] [Indexed: 02/08/2023]
Abstract
Lysosomal degradation of cytoplasmic components by autophagy is essential for cellular survival and homeostasis under nutrient-deprived conditions1–4. Acute regulation of autophagy by nutrient-sensing kinases is well defined3, 5–7, but longer-term transcriptional regulation is relatively unknown. Here we show that the fed-state sensing nuclear receptor FXR8, 9 and the fasting transcriptional activator CREB10, 11 coordinately regulate the hepatic autophagy gene network. Pharmacological activation of FXR repressed many autophagy genes and inhibited autophagy even in fasted mice and feeding-mediated inhibition of macroautophagy was attenuated in FXR-knockout mice. From mouse liver ChIP-seq data12–15, FXR and CREB binding peaks were detected at 178 and 112, respectively, of 230 autophagy-related genes, and 78 genes showed shared binding, mostly in their promoter regions. CREB promoted lipophagy, autophagic degradation of lipids16, under nutrient-deprived conditions, and FXR inhibited this response. Mechanistically, CREB upregulated autophagy genes, including Atg7, Ulk1, and Tfeb, by recruiting the coactivator CRTC2. After feeding or pharmacological activation, FXR trans-repressed these genes by disrupting the functional CREB/CRTC2 complex. This study identifies the novel FXR/CREB axis as a key physiological switch regulating autophagy, resulting in sustained nutrient regulation of autophagy during feeding/fasting cycles.
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Lee D, Le Lay J, Kaestner KH. The transcription factor CREB has no non-redundant functions in hepatic glucose metabolism in mice. Diabetologia 2014; 57:1242-8. [PMID: 24595858 DOI: 10.1007/s00125-014-3203-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
AIMS/HYPOTHESIS Excessive hepatic glucose production is a hallmark of insulin resistance in type 2 diabetes. The cAMP responsive transcription factor cAMP responsive element binding protein (CREB), thought to be a key activator of the hepatic gluconeogenic gene regulation programme, has been suggested as a therapeutic target to reduce glucose output by the liver. Here, we test directly the requirement for hepatocytic CREB for the maintenance of glucose homeostasis. METHODS We derived mice with a Creb (also known as Creb1) loxP allele for conditional, cell-type specific gene ablation. Hepatocyte-specific deletion of Creb was induced by injecting Creb (loxP/loxP) mice with Cre recombinase expression adeno-associated virus. RESULTS Strikingly, we found no difference in fed and fasted glucose levels, or in glucose, insulin and glucagon tolerance in mice fed a normal chow or a high-fat diet. In addition, mRNA levels of liver-specific genes, including several CREB target genes involved in gluconeogenesis, were not affected by CREB deficiency in the liver. CONCLUSION/INTERPRETATION Our data show that CREB has no non-redundant functions in hepatic glucose metabolism, and is therefore not likely to be a useful target for the development of glucose-lowering drugs.
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Affiliation(s)
- Dolim Lee
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, 12-126 Translational Research Center, 3400 Civic Center Boulevard, Philadelphia, PA, 19104-6145, USA
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Schupp M, Chen F, Briggs ER, Rao S, Pelzmann HJ, Pessentheiner AR, Bogner-Strauss JG, Lazar MA, Baldwin D, Prokesch A. Metabolite and transcriptome analysis during fasting suggest a role for the p53-Ddit4 axis in major metabolic tissues. BMC Genomics 2013; 14:758. [PMID: 24191950 PMCID: PMC3907060 DOI: 10.1186/1471-2164-14-758] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 10/31/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the molecular mechanisms in fasting. RESULTS We investigated the dynamic changes of liver gene expression and serum parameters of mice at several time points during a 48 hour fasting experiment and then focused on the global gene expression changes in epididymal white adipose tissue (WAT) as well as on pathways common to WAT, liver, and skeletal muscle. This approach produced several intriguing insights: (i) rather than a sequential activation of biochemical pathways in fasted liver, as current knowledge dictates, our data indicates a concerted parallel response; (ii) this first characterization of the transcriptome signature of WAT of fasted mice reveals a remarkable activation of components of the transcription apparatus; (iii) most importantly, our bioinformatic analyses indicate p53 as central node in the regulation of fasting in major metabolic tissues; and (iv) forced expression of Ddit4, a fasting-regulated p53 target gene, is sufficient to augment lipolysis in cultured adipocytes. CONCLUSIONS In summary, this combination of focused and global profiling approaches provides a comprehensive molecular characterization of the processes operating during fasting in mice and suggests a role for p53, and its downstream target Ddit4, as novel components in the transcriptional response to food deprivation.
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Affiliation(s)
- Michael Schupp
- Department of Endocrinology, Diabetes, and Nutrition and Center for Cardiovascular Research (CCR), Charité University Medicine, Hessische Str. 3-4, Berlin 10115, Germany
| | - Fang Chen
- Department of Microbiology, 201 Johnson Pavilion, Perelman School of Medicine University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Erika R Briggs
- Department of Medicine, and the Institute for Diabetes, Obesity, and Metabolism, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shilpa Rao
- Penn Bioinformatics Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Helmut J Pelzmann
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, Graz 8010, Austria
| | - Ariane R Pessentheiner
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, Graz 8010, Austria
| | - Juliane G Bogner-Strauss
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, Graz 8010, Austria
| | - Mitchell A Lazar
- Department of Medicine, and the Institute for Diabetes, Obesity, and Metabolism, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Don Baldwin
- Pathonomics LLC, Suite 200, 3160 Chestnut St., Philadelphia, PA 19104, USA
| | - Andreas Prokesch
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, Graz 8010, Austria
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