1
|
Hao Y, Han L, Wu A, Bochkis IM. Pioneer Factor Foxa2 Mediates Chromatin Conformation Changes for Activation of Bile Acid Targets of FXR. Cell Mol Gastroenterol Hepatol 2023; 17:237-249. [PMID: 37879405 PMCID: PMC10765059 DOI: 10.1016/j.jcmgh.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND & AIMS Transcription factors regulate gene expression that orchestrates liver physiology. Many bind at distal enhancers and chromatin looping is required to activate their targets. Chromatin architecture has been linked to essential functions of the liver, including metabolism and sexually dimorphic gene expression. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors farnesoid X receptor (FXR) and liver X receptor-α during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation and performed genome-wide studies to test this hypothesis. METHODS We performed Foxa2 HiChIP (Hi-C and ChIP) to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. RESULTS HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, topological associated domains, and intrachromosomal and interchromosomal Foxa2-anchored loops, drastically changes on addition of FXR agonist. Additional Foxa2 binding in ligand-activated state leads to formation of Foxa2-anchored loops, leading to distal interactions and activation of gene expression of FXR targets. CONCLUSIONS Ligand activation of FXR, and likely of related receptors, requires global changes in chromatin architecture. We determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.
Collapse
Affiliation(s)
- Yi Hao
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Lu Han
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Anqi Wu
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia.
| |
Collapse
|
2
|
Hao Y, Han L, Wu A, Bochkis IM. Pioneer factor Foxa2 mediates chromatin conformation changes in ligand-dependent activation of nuclear receptor FXR. bioRxiv 2023:2023.03.06.531297. [PMID: 36945375 PMCID: PMC10028776 DOI: 10.1101/2023.03.06.531297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Activation of nuclear receptors, a family of ligand-dependent transcription factors, is used extensively in development of drug targets. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXRα during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation. We performed Foxa2 HiChIP to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of FXR agonist. Hence, we determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.
Collapse
|
3
|
Wei X, Murphy MA, Reddy NA, Hao Y, Eggertsen TG, Saucerman JJ, Bochkis IM. Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease. Genome Res 2022; 32:1981-1992. [PMID: 36522168 PMCID: PMC9808618 DOI: 10.1101/gr.277149.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent in type 2 diabetes mellitus and the elderly, impacting 40% of individuals over 70. Regulation of heterochromatin at the nuclear lamina has been associated with aging and age-dependent metabolic changes. We previously showed that changes at the lamina in aged hepatocytes and laminopathy models lead to redistribution of lamina-associated domains (LADs), opening of repressed chromatin, and up-regulation of genes regulating lipid synthesis and storage, culminating in fatty liver. Here, we test the hypothesis that change in the expression of lamina-associated proteins and nuclear shape leads to redistribution of LADs, followed by altered binding of pioneer factor FOXA2 and by up-regulation of lipid synthesis and storage, culminating in steatosis in younger NAFLD patients (aged 21-51). Changes in nuclear morphology alter LAD partitioning and reduced lamin B1 signal correlate with increased FOXA2 binding before severe steatosis in young mice placed on a western diet. Nuclear shape is also changed in younger NAFLD patients. LADs are redistrubted and lamin B1 signal decreases similarly in mild and severe steatosis. In contrast, FOXA2 binding is similar in normal and NAFLD patients with moderate steatosis and is repositioned only in NAFLD patients with more severe lipid accumulation. Hence, changes at the nuclear lamina reshape FOXA2 binding with progression of the disease. Our results suggest a role for nuclear lamina in etiology of NAFLD, irrespective of aging, with potential for improved stratification of patients and novel treatments aimed at restoring nuclear lamina function.
Collapse
Affiliation(s)
- Xiaolong Wei
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Megan A Murphy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Nihal A Reddy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Yi Hao
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Taylor G Eggertsen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jeffrey J Saucerman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| |
Collapse
|
4
|
Granade ME, Hargett SR, Lank DS, Lemke MC, Luse MA, Isakson BE, Bochkis IM, Linden J, Harris TE. Feeding desensitizes A1 adenosine receptors in adipose through FOXO1-mediated transcriptional regulation. Mol Metab 2022; 63:101543. [PMID: 35811051 PMCID: PMC9304768 DOI: 10.1016/j.molmet.2022.101543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE Adipose tissue is a critical regulator of energy balance that must rapidly shift its metabolism between fasting and feeding to maintain homeostasis. Adenosine has been characterized as an important regulator of adipocyte metabolism primarily through its actions on A1 adenosine receptors (A1R). We sought to understand the role A1R plays specifically in adipocytes during fasting and feeding to regulate glucose and lipid metabolism. METHODS We used Adora1 floxed mice with an inducible, adiponectin-Cre to generate FAdora1-/- mice, where F designates a fat-specific deletion of A1R. We used these FAdora1-/- mice along with specific agonists and antagonists of A1R to investigate changes in adenosine signaling within adipocytes between the fasted and fed state. RESULTS We found that the adipose tissue response to adenosine is not static, but changes dynamically according to nutrient conditions through the insulin-Akt-FOXO1 axis. We show that under fasted conditions, FAdora1-/- mice had impairments in the suppression of lipolysis by insulin on normal chow and impaired glucose tolerance on high-fat diet. FAdora1-/- mice also exhibited a higher lipolytic response to isoproterenol than WT controls when fasted, however this difference was lost after a 4-hour refeeding period. We demonstrate that FOXO1 binds to the A1R promoter, and refeeding leads to a rapid downregulation of A1R transcript and desensitization of adipocytes to A1R agonism. Obesity also desensitizes adipocyte A1R, and this is accompanied by a disruption of cyclical changes in A1R transcription between fasting and refeeding. CONCLUSIONS We propose that FOXO1 drives high A1R expression under fasted conditions to limit excess lipolysis during stress and augment insulin action upon feeding. Subsequent downregulation of A1R under fed conditions leads to desensitization of these receptors in adipose tissue. This regulation of A1R may facilitate reentrance into the catabolic state upon fasting.
Collapse
Affiliation(s)
- Mitchell E Granade
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Stefan R Hargett
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Daniel S Lank
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Melissa A Luse
- Department of Molecular Physiology and Biophysics, University of Virginia, Charlottesville, VA, USA
| | - Brant E Isakson
- Department of Molecular Physiology and Biophysics, University of Virginia, Charlottesville, VA, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - Joel Linden
- Department of Medicine, Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, VA, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
5
|
Upchurch CM, Yeudall S, Pavelec CM, Merk D, Greulich J, Manjegowda M, Raghavan SS, Bochkis IM, Scott MM, Perez-Reyes E, Leitinger N. Targeting oxidized phospholipids by AAV-based gene therapy in mice with established hepatic steatosis prevents progression to fibrosis. Sci Adv 2022; 8:eabn0050. [PMID: 35857497 PMCID: PMC9286512 DOI: 10.1126/sciadv.abn0050] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/03/2022] [Indexed: 05/06/2023]
Abstract
Oxidized phosphatidylcholines (OxPCs) are implicated in chronic tissue damage. Hyperlipidemic LDL-R--deficient mice transgenic for an OxPC-recognizing IgM fragment (scFv-E06) are protected against nonalcoholic fatty liver disease (NAFLD). To examine the effect of OxPC elimination at different stages of NAFLD progression, we used cre-dependent, adeno-associated virus serotype 8-mediated expression of the single-chain variable fragment of E06 (AAV8-scFv-E06) in hepatocytes of albumin-cre mice. AAV8-induced expression of scFv-E06 at the start of FPC diet protected mice from developing hepatic steatosis. Independently, expression of scFv-E06 in mice with established steatosis prevented the progression to hepatic fibrosis. Mass spectrometry-based oxophospho-lipidomics identified individual OxPC species that were reduced by scFv-E06 expression. In vitro, identified OxPC species dysregulated mitochondrial metabolism and gene expression in hepatocytes and hepatic stellate cells. We demonstrate that individual OxPC species independently affect disease initiation and progression from hepatic steatosis to steatohepatitis, and that AAV-mediated expression of scFv-E06 is an effective therapeutic intervention.
Collapse
Affiliation(s)
- Clint M. Upchurch
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Scott Yeudall
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Caitlin M. Pavelec
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Dennis Merk
- Environmentally-Induced Cardiovascular Degeneration, Clinical Chemistry and Laboratory Diagnostics, Medical Faculty, University Hospital and Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jan Greulich
- Environmentally-Induced Cardiovascular Degeneration, Clinical Chemistry and Laboratory Diagnostics, Medical Faculty, University Hospital and Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
- IUF-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mohan Manjegowda
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Shyam S. Raghavan
- Department of Pathology, University of Virginia, Charlottesville, VA 22904, USA
| | - Irina M. Bochkis
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Michael M. Scott
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Edward Perez-Reyes
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| | - Norbert Leitinger
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22904, USA
| |
Collapse
|
6
|
Upchurch CM, Yeudall S, Pavelec CM, Manjegowda M, Bochkis IM, Scott M, Perez‐Reyes E, Leitinger N. Virus‐induced Hepatic Expression of an Oxidized Phospholipid‐binding Antibody Fragment Prevents Initiation of Hepatic Steatosis and Progression to Fibrosis. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l8081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
7
|
Kain J, Wei X, Reddy NA, Price AJ, Woods C, Bochkis IM. Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRα. Mol Metab 2021; 53:101291. [PMID: 34246806 PMCID: PMC8350412 DOI: 10.1016/j.molmet.2021.101291] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Objective Type II nuclear hormone receptors, including farnesoid X receptors (FXR), liver X receptors (LXR), and peroxisome proliferator-activated receptors (PPAR), which serve as drug targets for metabolic diseases, are permanently positioned in the nucleus and thought to be bound to DNA regardless of the ligand status. However, recent genome-wide location analysis showed that LXRα and PPARα binding in the liver is largely ligand-dependent. We hypothesized that pioneer factor Foxa2 evicts nucleosomes to enable ligand-dependent binding of type II nuclear receptors and performed genome-wide studies to test this hypothesis. Methods ATAC-Seq was used to profile chromatin accessibility; ChIP-Seq was performed to assess transcription factors (Foxa2, FXR, LXRα, and PPARα) binding; and RNA-Seq analysis determined differentially expressed genes in wildtype and Foxa2 mutants treated with a ligand (GW4064 for FXR, GW3965, and T09 for LXRα). Results We reveal that chromatin accessibility, FXR binding, LXRα occupancy, and ligand-responsive activation of gene expression by FXR and LXRα require Foxa2. Unexpectedly, Foxa2 occupancy is drastically increased when either receptor, FXR or LXRα, is bound by an agonist. In addition, co-immunoprecipitation experiments demonstrate that Foxa2 interacts with either receptor in a ligand-dependent manner, suggesting that Foxa2 and the receptor, bind DNA as an interdependent complex during ligand activation. Furthermore, PPARα binding is induced in Foxa2 mutants treated with FXR and LXR ligands, leading to the activation of PPARα targets. Conclusions Our model requires pioneering activity for ligand activation that challenges the existing ligand-independent binding mechanism. We also demonstrate that Foxa2 is required to achieve activation of the proper receptor – one that binds the added ligand – by repressing the activity of a competing receptor. Foxa2 opens chromatin for FXR and LXRα binding during acute ligand activation. Ligand-dependent activation of FXR & LXR-dependent gene expression requires Foxa2. Foxa2 interacts with FXR and LXRα in a ligand-dependent manner. Foxa2 restricts binding of competing receptor PPARα to ensure proper ligand-dependent activation of FXR and LXRα.
Collapse
Affiliation(s)
- Jessica Kain
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaolong Wei
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nihal A Reddy
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Andrew J Price
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Claire Woods
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
8
|
Price AJ, Manjegowda MC, Kain J, Anandh S, Bochkis IM. Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver. Aging Cell 2020; 19:e13092. [PMID: 31858687 PMCID: PMC6996956 DOI: 10.1111/acel.13092] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 11/05/2019] [Accepted: 11/23/2019] [Indexed: 01/21/2023] Open
Abstract
Post‐translational modifications of histone tails play a crucial role in gene regulation. Here, we performed chromatin profiling by quantitative targeted mass spectrometry to assess all possible modifications of the core histones. We identified a bivalent combination, a dually marked H3K9me3/H3K14ac modification in the liver, that is significantly decreased in old hepatocytes. Subsequent sequential ChIP‐Seq identified dually marked single nucleosome regions, with reduced number of sites and decreased signal in old livers, confirming mass spectrometry results. We detected H3K9me3 and H3K14ac bulk ChIP‐Seq signal in reChIP nucleosome regions, suggesting a correlation between H3K9me3/H3K14ac bulk bivalent genomic regions and dually marked single nucleosomes. Histone H3K9 deacetylase Hdac3, as well as H3K9 methyltransferase Setdb1, found in complex Kap1, occupied both bulk and single nucleosome bivalent regions in both young and old livers, correlating to presence of H3K9me3. Expression of genes associated with bivalent regions in young liver, including those regulating cholesterol secretion and triglyceride synthesis, is upregulated in old liver once the bivalency is lost. Hence, H3K9me3/H3K14ac dually marked regions define a poised inactive state that is resolved with loss of one or both of the chromatin marks, which subsequently leads to change in gene expression.
Collapse
Affiliation(s)
- Andrew J. Price
- Department of Pharmacology University of Virginia Charlottesville VA USA
| | | | - Jessica Kain
- Department of Pharmacology University of Virginia Charlottesville VA USA
| | - Swetha Anandh
- Department of Pharmacology University of Virginia Charlottesville VA USA
| | - Irina M. Bochkis
- Department of Pharmacology University of Virginia Charlottesville VA USA
| |
Collapse
|
9
|
Whitton H, Singh LN, Patrick MA, Price AJ, Osorio FG, López‐Otín C, Bochkis IM. Changes at the nuclear lamina alter binding of pioneer factor Foxa2 in aged liver. Aging Cell 2018; 17:e12742. [PMID: 29484800 PMCID: PMC5946061 DOI: 10.1111/acel.12742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2018] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that regulation of heterochromatin at the nuclear envelope underlies metabolic disease susceptibility and age-dependent metabolic changes, but the mechanism is unknown. Here, we profile lamina-associated domains (LADs) using lamin B1 ChIP-Seq in young and old hepatocytes and find that, although lamin B1 resides at a large fraction of domains at both ages, a third of lamin B1-associated regions are bound exclusively at each age in vivo. Regions occupied by lamin B1 solely in young livers are enriched for the forkhead motif, bound by Foxa pioneer factors. We also show that Foxa2 binds more sites in Zmpste24 mutant mice, a progeroid laminopathy model, similar to increased Foxa2 occupancy in old livers. Aged and Zmpste24-deficient livers share several features, including nuclear lamina abnormalities, increased Foxa2 binding, de-repression of PPAR- and LXR-dependent gene expression, and fatty liver. In old livers, additional Foxa2 binding is correlated to loss of lamin B1 and heterochromatin (H3K9me3 occupancy) at these loci. Our observations suggest that changes at the nuclear lamina are linked to altered Foxa2 binding, enabling opening of chromatin and de-repression of genes encoding lipid synthesis and storage targets that contribute to etiology of hepatic steatosis.
Collapse
Affiliation(s)
| | - Larry N. Singh
- Center for Mitochondrial and Epigenomic MedicineChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | | | - Andrew J. Price
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Fernando G. Osorio
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
| | - Carlos López‐Otín
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
- Centro de Investigación Biomédica en Red de CáncerMadridSpain
| | - Irina M. Bochkis
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
| |
Collapse
|
10
|
Bochkis IM, Przybylski D, Chen J, Regev A. Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Rep 2014; 9:996-1006. [PMID: 25437555 PMCID: PMC4250828 DOI: 10.1016/j.celrep.2014.09.048] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/15/2014] [Accepted: 09/24/2014] [Indexed: 12/27/2022] Open
Abstract
Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that derepression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix transcription factor Foxa2 and nuclear receptor corepressor Hdac3 exhibit a reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.
Collapse
Affiliation(s)
- Irina M Bochkis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
11
|
Bochkis IM, Schug J, Ye DZ, Kurinna S, Stratton SA, Barton MC, Kaestner KH. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PLoS Genet 2012; 8:e1002770. [PMID: 22737085 PMCID: PMC3380847 DOI: 10.1371/journal.pgen.1002770] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/02/2012] [Indexed: 01/04/2023] Open
Abstract
Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1-only sites are enriched for p53 binding sites and are frequently found near genes important to cell cycle regulation, while Foxa2-restricted sites show only a limited match to the forkhead consensus and are found in genes involved in steroid and lipid metabolism. Thus, Foxa1 and Foxa2, while redundant during development, have evolved divergent roles in the adult liver, ensuring the maintenance of both genes during evolution. The duplication of a gene from a common ancestor, resulting in two copies known as paralogs, plays an important role in evolution. Newly duplicated genes must acquire new functions in order to remain relevant, otherwise they are lost via mutation over time. We have performed genome-wide location analysis (ChIP–Seq) in adult liver to examine the differences between two paralogous DNA binding proteins, Foxa1 and Foxa2. While Foxa1 and Foxa2 bind a number of common genomic locations, each protein also localizes to distinct regulatory regions. Sites specific for Foxa1 also contain a DNA motif bound by tumor suppressor p53 and are found near genes important to cell cycle regulation, while Foxa2-only sites are found near genes essential to steroid and lipid metabolism. Hence, Foxa1 and Foxa2 have developed unique functions in adult liver, contributing to the maintenance of both genes during evolution.
Collapse
Affiliation(s)
- Irina M. Bochkis
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jonathan Schug
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Diana Z. Ye
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Svitlana Kurinna
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sabrina A. Stratton
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Michelle C. Barton
- Center for Stem Cell and Developmental Biology, Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Klaus H. Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
12
|
Bochkis IM, Schug J, Rubins NE, Chopra AR, O'Malley BW, Kaestner KH. Foxa2-dependent hepatic gene regulatory networks depend on physiological state. Physiol Genomics 2009; 38:186-95. [PMID: 19417011 DOI: 10.1152/physiolgenomics.90376.2008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bile acids are powerful detergents produced by the liver to aid in the absorption of dietary lipids. We recently reported a novel role for Foxa2 in bile acid metabolism. The winged helix transcription factor Foxa2 is required to prevent intrahepatic cholestasis and liver injury in mice fed a cholic acid-enriched diet. Here, we use functional genomics to study how Foxa2 regulates its targets in a cholic acid-dependent manner. We found that multiple signaling pathways essential for the hepatic response to acute liver injury are impaired in livers of Foxa2-deficient mice, suggesting that the deletion of Foxa2 in the hepatocyte affects the liver on a large scale. We also discovered distinct feed-forward regulatory loops controlling Foxa2-dependent targets in a cholic acid-dependent or -independent manner. We show that Foxa2 interacts with different transcription factors to achieve gene expression responses appropriate for each physiologic state.
Collapse
Affiliation(s)
- Irina M Bochkis
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | |
Collapse
|
13
|
Behr R, Sackett SD, Bochkis IM, Le PP, Kaestner KH. Impaired male fertility and atrophy of seminiferous tubules caused by haploinsufficiency for Foxa3. Dev Biol 2007; 306:636-45. [PMID: 17488644 PMCID: PMC1952241 DOI: 10.1016/j.ydbio.2007.03.525] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 03/15/2007] [Accepted: 03/30/2007] [Indexed: 11/22/2022]
Abstract
Foxa1, 2 and 3 (formerly HNF-3alpha, -beta and -gamma) constitute a sub-family of winged helix transcription factors with multiple roles in mammalian organ development. While all three Foxa mRNAs are present in endoderm derivatives including liver and pancreas, only Foxa3 is expressed in the testis. Here we demonstrate by genetic lineage tracing that Foxa3 is expressed in postmeiotic germ and interstitial Leydig cells. The germinal epithelium of Foxa3-deficient testes is characterized by a loss of germ cells secondary to an increase in germ cell apoptosis that ultimately leads to a Sertoli cell-only syndrome. Remarkably, not only the Foxa3(-/-) mice but also Foxa3(+/-) mice exhibited loss of germ cells. This cellular phenotype caused significantly reduced fertility and testis weight of both Foxa3(-/-) and Foxa3(+/-) mice. Using microarray analysis, we found a dramatic downregulation of the zinc finger protein 93 and the testicular tumor-associated paraneoplastic Ma antigen (PNMA) and increased expression of a number of genes including zinc finger protein 94 and several kallikrein 1-related peptidases which could account for at least part of the observed phenotype. In summary, we have identified Foxa3 as a transcriptional regulator with a dominant phenotype in germ cell maintenance and suggest FOXA3 as a potential candidate gene for subfertility in man.
Collapse
Affiliation(s)
| | | | | | | | - Klaus H. Kaestner
- Corresponding author. Mailing address: Department of Genetics, University of Pennsylvania School of Medicine, 415 Curie Blvd. Philadelphia, PA 19104-6145, Phone: (215) 898-8759, Fax: (215) 573-5892 E-mail:
| |
Collapse
|
14
|
Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH. Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet 2005; 1:e16. [PMID: 16110340 PMCID: PMC1186734 DOI: 10.1371/journal.pgen.0010016] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 06/16/2005] [Indexed: 12/23/2022] Open
Abstract
While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address this question, we performed an orthogonal analysis to identify direct targets of the GR. First, we analyzed the expression profile of mouse livers in the presence or absence of exogenous glucocorticoid, resulting in over 1,300 differentially expressed genes. We then executed genome-wide location analysis on chromatin from the same livers, identifying more than 300 promoters that are bound by the GR. Intersecting the two lists yielded 53 genes whose expression is functionally dependent upon the ligand-bound GR. Further network and sequence analysis of the functional targets enabled us to suggest interactions between the GR and other transcription factors at specific target genes. Together, our results further our understanding of the GR and its targets, and provide the basis for more targeted glucocorticoid therapies.
Collapse
Affiliation(s)
- Phillip Phuc Le
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joshua R Friedman
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jonathan Schug
- Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - John E Brestelli
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. Brandon Parker
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Irina M Bochkis
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- *To whom correspondence should be addressed. E-mail:
| |
Collapse
|