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Ramamoorthy K, Sabui S, Manzon KI, Balamurugan AN, Said HM. miR-122-5p is involved in posttranscriptional regulation of the mitochondrial thiamin pyrophosphate transporter ( SLC25A19) in pancreatic acinar cells. Am J Physiol Gastrointest Liver Physiol 2023; 325:G347-G355. [PMID: 37529835 PMCID: PMC10642993 DOI: 10.1152/ajpgi.00106.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Thiamin (vitamin B1) plays a vital role in cellular energy metabolism/ATP production. Pancreatic acinar cells (PACs) obtain thiamin from circulation and convert it to thiamin pyrophosphate (TPP) in the cytoplasm. TPP is then taken up by the mitochondria via a carrier-mediated process that involves the mitochondrial TPP transporter (MTPPT; encoded by the gene SLC25A19). We have previously characterized different aspects of the mitochondrial carrier-mediated TPP uptake process, but nothing is known about its possible regulation at the posttranscriptional level. We address this issue in the current investigations focusing on the role of miRNAs in this regulation. First, we subjected the human (and rat) 3'-untranslated region (3'-UTR) of the SLC25A19 to three in-silico programs, and all have identified putative binding sites for miR-122-5p. Transfecting pmirGLO-hSLC25A19 3'-UTR into rat PAC AR42J resulted in a significant reduction in luciferase activity compared with cells transfected with pmirGLO-empty vector. Mutating as well as truncating the putative miR-122-5p binding sites in the hSLC25A19 3'-UTR led to abrogation of inhibition in luciferase activity in PAC AR42J. Furthermore, transfecting/transducing PAC AR42J and human primary PACs with mimic of miR-122-5p led to a significant inhibition in the level of expression of the MTPPT mRNA and protein as well as in mitochondrial carrier-mediated TPP uptake. Conversely, transfecting PAC AR42J with an inhibitor of miR-122-5p increased MTPPT expression and function. These findings show, for the first time, that expression and function of the MTPPT in PACs are subject to posttranscriptional regulation by miR-122-5p.NEW & NOTEWORTHY This study shows that the expression and function of mitochondrial TPP transporter (MTPPT) are subject to posttranscriptional regulation by miRNA-122-5p in pancreatic acinar cells.
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Affiliation(s)
- Kalidas Ramamoorthy
- Department of Physiology/Biophysics, University of California, Irvine, California, United States
| | - Subrata Sabui
- Department of Physiology/Biophysics, University of California, Irvine, California, United States
- Department of Medical Research, Tibor Rubin Veterans Affairs Medical Center, Long Beach, California, United States
| | - Kameron I Manzon
- Department of Physiology/Biophysics, University of California, Irvine, California, United States
| | - Appakalai N Balamurugan
- Center for Clinical and Translational Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Hamid M Said
- Department of Medicine, University of California, Irvine, California, United States
- Department of Physiology/Biophysics, University of California, Irvine, California, United States
- Department of Medical Research, Tibor Rubin Veterans Affairs Medical Center, Long Beach, California, United States
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Samur MB, Gumus G, Canpolat M, Gumus H, Per H, Caglayan AO. Clinical and genetic studies of thiamine metabolism dysfunction syndrome-4: case series and review of the literature. Clin Dysmorphol 2022; 31:125-131. [PMID: 35102031 PMCID: PMC9188987 DOI: 10.1097/mcd.0000000000000411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Thiamine metabolism dysfunction syndrome-4 (THMD-4) is an autosomal recessive inherited rare disease (OMIM #613710) characterized by febrile illness associated episodic encephalopathy, leading to transient neurological dysfunction and progressive polyneuropathy. We report three patients from two different families with normal development, episodic encephalopathy, gait disorder, progressive chronic polyneuropathy characterized by motor difficulties, distal weakness, and hoarseness (dysphonia). We identified a homozygous missense c.576G>C, p.(Gln192His) variant in the SLC25A19 gene in both families by whole-exome sequencing. Following genetic diagnosis, thiamine replacement therapy was started, and improvement was observed in all affected patients. We highlight the associated phenotypes of an SCL25A19 mutation leading to clinical features of THMD-4.
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Affiliation(s)
- M. Bahadir Samur
- Department of Pediatrics, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Gulsum Gumus
- Department of Pediatrics, Division of Pediatric Radiology, Erciyes University, Faculty of Medicine, Kayseri, Turkey
| | - Mehmet Canpolat
- Department of Pediatrics, Division of Pediatric Neurology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Hakan Gumus
- Department of Pediatrics, Division of Pediatric Neurology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Huseyin Per
- Department of Pediatrics, Division of Pediatric Neurology, Erciyes University Faculty of Medicine, Kayseri, Turkey
| | - Ahmet Okay Caglayan
- Department of Medical Genetics, School of Medicine, Dokuz Eylul University, Izmir, Turkey
- Department of Neurosurgery, Yale School of Medicine, CT, USA
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Hou L, Guan S, Jin Y, Sun W, Wang Q, Du Y, Zhang R. Cell metabolomics to study the cytotoxicity of carbon black nanoparticles on A549 cells using UHPLC-Q/TOF-MS and multivariate data analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134122. [PMID: 31505349 DOI: 10.1016/j.scitotenv.2019.134122] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/30/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Carbon black nanoparticles (CBNPs) are core component of fine particulate matter (PM2.5) in the atmosphere. It was reported that the particle in the atmosphere with smaller size and the larger the specific surface area are easier to reach the deep respiratory tract or even the alveoli through the respiratory barrier and cause lung injury. Therefore, it has been believed that ultrafine or nanometer particles with more toxic than those with larger particle sizes. Moreover, it was confirmed that CBNPs could induce inflammation, oxidative stress and changes in cell signaling and gene expression in mammalian cells and organs. However, the cytotoxicity mechanism of them has been uncertain so far. The aim of the present study was to explore the underlying mechanism of cytotoxicity induced by CBNPs on A549 cells. In the current research, the viabilities of A549 cells were detected by Cell Counting Kit-8 (CCK-8) assay. The further metabolomics studies were conducted to detect the cytotoxic effect of CBNPs on A549 cells with an IC50 value of 70 μg/mL for 48 h. Potential differential compounds were identified and quantified using a novel on-line acquisition method based on ultra-liquid chromatography quadrupole time-of-flight mass spectrometry(UHPLC-Q-TOF/MS). The cytotoxicity mechanism of CBNPs on A549 cells was evaluated by multivariate data analysis and statistics. As a result, a total of 32 differential compounds were identified between CBNPs exposure and control groups. In addition, pathway analysis showed the metabolic changes were involved in the tricarboxylic acid (TCA) cycle, alanine, aspartate and glutamate metabolism, histidine metabolism and so on. It is also suggested that CBNPs may induce cytotoxicity by affecting the normal process of energy metabolism and disturbing several vital signaling pathways and finally induce cell apoptosis.
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Affiliation(s)
- Ludan Hou
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China
| | - Shuai Guan
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, PR China
| | - Yiran Jin
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China; The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, PR China
| | - Wenjing Sun
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China
| | - Qiao Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China
| | - Yingfeng Du
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China.
| | - Rong Zhang
- Department of Occupational and Environmental Health, The School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, PR China
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Tao S, Zhou T, Saelao P, Wang Y, Zhu Y, Li T, Zhou H, Wang J. Intrauterine Growth Restriction Alters the Genome-Wide DNA Methylation Profiles in Small Intestine, Liver and Longissimus Dorsi Muscle of Newborn Piglets. Curr Protein Pept Sci 2019; 20:713-726. [PMID: 30678618 DOI: 10.2174/1389203720666190124165243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 01/20/2023]
Abstract
Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.
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Affiliation(s)
- Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianjiao Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Yuhua Zhu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tiantian Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Sabui S, Subramanian VS, Kapadia R, Said HM. Adaptive regulation of pancreatic acinar mitochondrial thiamin pyrophosphate uptake process: possible involvement of epigenetic mechanism(s). Am J Physiol Gastrointest Liver Physiol 2017; 313:G448-G455. [PMID: 28729247 PMCID: PMC5792211 DOI: 10.1152/ajpgi.00192.2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 01/31/2023]
Abstract
The essentiality of thiamin stems from its roles as a cofactor [mainly in the form of thiamin pyrophosphate (TPP)] in critical metabolic reactions including oxidative energy metabolism and reduction of cellular oxidative stress. Like other mammalian cells, pancreatic acinar cells (PAC) obtain thiamin from their surroundings and convert it to TPP; mitochondria then take up TPP by a carrier-mediated process that involves the mitochondrial TPP (MTPP) transporter (MTPPT; product of SLC25A19 gene). Previous studies have characterized different physiological/biological aspects of the MTPP uptake process, but little is known about its possible adaptive regulation. We addressed this issue using pancreatic acinar 266-6 cells (PAC 266-6) maintained under thiamin-deficient (DEF) and oversupplemented (OS) conditions, as well as thiamin-DEF and -OS transgenic mice carrying the SLC25A19 promoter. We found that maintaining PAC 266-6 under the thiamin-DEF condition leads to a significant induction in mitochondrial [3H]TPP uptake, as well as in the level of expression of the MTPPT protein and mRNA compared with thiamin-OS cells. Similar findings were observed in mitochondria from thiamin-DEF mice compared with thiamin-OS. Subsequently, we demonstrated that adaptive regulation of MTTP protein was partly mediated via transcriptional mechanism(s) via studies with PAC 266-6 transfected with the SLC25A19 promoter and transgenic mice carrying the SLC25A19 promoter. This transcriptional regulation appeared to be, at least in part, mediated via epigenetic mechanism(s) involving histone modifications. These studies report, for the first time, that the PAC mitochondrial TPP uptake process is adaptively regulated by the prevailing thiamin level and that this regulation is transcriptionally mediated and involves epigenetic mechanism(s).NEW & NOTEWORTHY Our findings show, for the first time, that the mitochondrial thiamin pyrophosphate (MTPP) uptake process is adaptively regulated by the prevailing thiamin level in pancreatic acinar cells and this regulation is mediated, at least in part, by transcriptional and epigenetic mechanism(s) affecting the SLC25A19 promoter.
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Affiliation(s)
- Subrata Sabui
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
| | - Veedamali S. Subramanian
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
| | - Rubina Kapadia
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
| | - Hamid M. Said
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
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Srinivasan P, Thrower EC, Gorelick FS, Said HM. Inhibition of pancreatic acinar mitochondrial thiamin pyrophosphate uptake by the cigarette smoke component 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Am J Physiol Gastrointest Liver Physiol 2016; 310:G874-83. [PMID: 26999808 PMCID: PMC4888549 DOI: 10.1152/ajpgi.00461.2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/11/2016] [Indexed: 01/31/2023]
Abstract
Thiamin is essential for normal metabolism in pancreatic acinar cells (PAC) and is obtained from their microenvironment through specific plasma-membrane transporters, converted to thiamin pyrophosphate (TPP) in the cytoplasm, followed by uptake of TPP by mitochondria through the mitochondrial TPP (MTPP) transporter (MTPPT; product of SLC25A19 gene). TPP is essential for normal mitochondrial function. We examined the effect of long-term/chronic exposure of PAC in vitro (pancreatic acinar 266-6 cells) and in vivo (wild-type or transgenic mice carrying the SLC25A19 promoter) of the cigarette smoke toxin, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), on the MTPP uptake process. Our in vitro and in vivo findings demonstrate that NNK negatively affects MTPP uptake and reduced expression of MTPPT protein, MTPPT mRNA, and heterogenous nuclear RNA, as well as SLC25A19 promoter activity. The effect of NNK on Slc25a19 transcription was neither mediated by changes in expression of transcriptional factor NFY-1 (known to drive SLC25A19 transcription), nor due to changes in methylation profile of the Slc25a19 promoter. Rather, it appears to be due to changes in histone modifications that involve significant decreases in histone H3K4-trimethylation and H3K9-acetylation (activation markers). The effect of NNK on MTPPT function is mediated through the nonneuronal α7-nicotinic acetylcholine receptor (α7-nAChR), as indicated by both in vitro (using the nAChR antagonist mecamylamine) and in vivo (using an α7-nAchR(-/-) mouse model) studies. These findings demonstrate that chronic exposure of PAC to NNK negatively impacts PAC MTPP uptake. This effect appears to be exerted at the level of Slc25a19 transcription, involve epigenetic mechanism(s), and is mediated through the α7-nAchR.
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Affiliation(s)
- Padmanabhan Srinivasan
- 1Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; ,2Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California;
| | - Edwin C. Thrower
- 3Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut;
| | - Fred S. Gorelick
- 4Section of Digestive Diseases, Department of Internal Medicine, Yale University, New Haven, Connecticut; and ,5Veterans Affairs Healthcare System, West Haven, Connecticut
| | - Hamid M. Said
- 1Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; ,2Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California;
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Sabui S, Subramanian VS, Kapadia R, Said HM. Structure-function characterization of the human mitochondrial thiamin pyrophosphate transporter (hMTPPT; SLC25A19): Important roles for Ile(33), Ser(34), Asp(37), His(137) and Lys(291). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1883-90. [PMID: 27188525 DOI: 10.1016/j.bbamem.2016.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 01/19/2023]
Abstract
Thiamin plays a critical role in cellular energy metabolism. Mammalian cells obtain the vitamin from their surroundings, converted it to thiamin pyrophosphate (TPP) in the cytoplasm, followed by uptake of TPP by mitochondria via a carrier-mediated process that involves the MTPPT (product of the SLC25A19 gene). Previous studies have characterized different physiological/biological aspects of the human MTPPT (hMTPPT), but less is known about structural features that are important for its function. Here, we used a protein-docking model ("Phyre2" and "DockingServer") to predict residues that may be important for function (substrate recognition) of the hMTPPT; we also examined the role of conserved positively-charged residues predicted ("PRALINE") to be in the trans-membrane domains (TMDs) in uptake of the negatively-charged TPP. Among the six residues predicted by the docking model (i.e., Thr(29), Arg(30), Ile(33), Ser(34), Asp(37) and Phe(298)), only Ile(33), Ser(34) and Asp(37) were found to be critical for function. While no change in translational efficiency/protein stability of the Ser(34) mutant was observed, both the Ile(33) and Asp(37) mutants showed a decrease in this parameter(s); there was also a decrease in the expression of the latter two mutants in mitochondria. A need for a polar residue at position 34 of the hMTPPT was evident. Our findings with the positively-charged residues (i.e., His(82), His(137), Lys(231) and Lys(291)) predicted in the TMD showed that His(137) and Lys(291) are important for function (via a role in proper delivery of the protein to mitochondria). These investigations provide important information about the structure-function relationship of the hMTPPT.
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Affiliation(s)
- Subrata Sabui
- Department of Medical Research, VA Medical Center, Long Beach, CA 90822, United States; Departments of Medicine and Physiology/Biophysics, University of California, Irvine, CA 92697, United States
| | - Veedamali S Subramanian
- Department of Medical Research, VA Medical Center, Long Beach, CA 90822, United States; Departments of Medicine and Physiology/Biophysics, University of California, Irvine, CA 92697, United States
| | - Rubina Kapadia
- Department of Medical Research, VA Medical Center, Long Beach, CA 90822, United States; Departments of Medicine and Physiology/Biophysics, University of California, Irvine, CA 92697, United States
| | - Hamid M Said
- Department of Medical Research, VA Medical Center, Long Beach, CA 90822, United States; Departments of Medicine and Physiology/Biophysics, University of California, Irvine, CA 92697, United States.
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Srinivasan P, Nabokina S, Said HM. Chronic alcohol exposure affects pancreatic acinar mitochondrial thiamin pyrophosphate uptake: studies with mouse 266-6 cell line and primary cells. Am J Physiol Gastrointest Liver Physiol 2015; 309:G750-8. [PMID: 26316591 PMCID: PMC4628969 DOI: 10.1152/ajpgi.00226.2015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/21/2015] [Indexed: 01/31/2023]
Abstract
Thiamin is essential for normal metabolic activity of all mammalian cells, including those of the pancreas. Cells obtain thiamin from their surroundings and enzymatically convert it into thiamin pyrophosphate (TPP) in the cytoplasm; TPP is then taken up by mitochondria via a specific carrier the mitochondrial TPP transporter (MTPPT; product of the SLC25A19 gene). Chronic alcohol exposure negatively impacts the health of pancreatic acinar cells (PAC), but its effect on physiological/molecular parameters of MTPPT is not known. We addressed this issue using mouse pancreatic acinar tumor cell line 266-6 and primary PAC of wild-type and transgenic mice carrying the SLC25A19 promoter that were fed alcohol chronically. Chronic alcohol exposure of 266-6 cells (but not to its nonoxidative metabolites ethyl palmitate and ethyl oleate) led to a significant inhibition in mitochondrial TPP uptake, which was associated with a decreased expression of MTPPT protein, mRNA, and activity of the SLC25A19 promoter. Similarly, chronic alcohol feeding of mice led to a significant inhibition in expression of MTPPT protein, mRNA, heterogeneous nuclear RNA, as well as in activity of SLC25A19 promoter in PAC. While chronic alcohol exposure did not affect DNA methylation of the Slc25a19 promoter, a significant decrease in histone H3 euchromatin markers and an increase in H3 heterochromatin marker were observed. These findings show, for the first time, that chronic alcohol exposure negatively impacts pancreatic MTPPT, and that this effect is exerted, at least in part, at the level of Slc25a19 transcription and appears to involve epigenetic mechanism(s).
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Affiliation(s)
- Padmanabhan Srinivasan
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
| | - Svetlana Nabokina
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
| | - Hamid M. Said
- Department of Medical Research, Veterans Affairs Medical Center, Long Beach, California; and Departments of Medicine and Physiology/Biophysics, University of California, Irvine, California
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Moeinvaziri F, Shahhoseini M. Epigenetic role of CCAAT box-binding transcription factor NF-Y on ID gene family in human embryonic carcinoma cells. IUBMB Life 2015; 67:880-7. [PMID: 26509926 DOI: 10.1002/iub.1443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022]
Abstract
Nuclear factor Y (NF-Y) is a histone substitute protein that specifically binds to the CCAAT box of the target genes and thereby promotes their regulation. NF-Y transcription factor, with defined CCAAT element-binding activities, target a gene family that encodes a group of basic helix-loop-helix ID factors (ID1-ID4), with or without CCAAT box at their promoter region. In this study, the expressions of NF-Y in mRNA and protein level were evaluated in a human embryonic carcinoma cell line, named NTera2, before and after 7 days induction of differentiation. We also looked into expression levels of ID genes in NTera2 cells during differentiation because of their critical role in development. By using chromatin immunoprecipitation coupled with real-time polymerase chain reaction, NF-Y incorporation and acetylation/dimethylation of histone H3 at lysine 9 (H3K9ac/me2) was quantitatively evaluated on the regulatory regions of considered genes to monitor the changes in epigenetic markers at ID gene promoters throughout differentiation. The results demonstrated a marked down-regulation of ID1, ID2, and ID3 genes, parallel to a loss of NF-Y binding to the promoters of these genes. The data show that although the genes encoding NF-Y complex remained expressed at mRNA level, NF-YC is lost at the protein level onset of differentiation. Additionally, the epigenetic marks of H3K9ac and H3K9me2 at the target gene promoters decreased and increased, respectively, after 1 day of differentiation. It is suggested that, in the absence of NF-Y binding, the corresponding regions adopt a heterochromatic nature, whereas when NF-Y comes back after 7 days of differentiation, the ID1-3 promoters become again converted into active chromatin. The ID4 gene, lacking a CCAAT box, behaves differently and does not show any incorporation. This experiment implies for the first time that the presence of NF-Y transcription factor plays a pivotal role in transcriptional regulation of ID genes in development.
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Affiliation(s)
- Farideh Moeinvaziri
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Maryam Shahhoseini
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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Lu YH, Dallner OS, Birsoy K, Fayzikhodjaeva G, Friedman JM. Nuclear Factor-Y is an adipogenic factor that regulates leptin gene expression. Mol Metab 2015; 4:392-405. [PMID: 25973387 PMCID: PMC4420997 DOI: 10.1016/j.molmet.2015.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/05/2015] [Indexed: 12/22/2022] Open
Abstract
Objective Leptin gene expression is highly correlated with cellular lipid content in adipocytes but the transcriptional mechanisms controlling leptin expression in vivo are poorly understood. In this report, we set out to identify cis- and trans-regulatory elements controlling leptin expression. Methods Leptin-BAC luciferase transgenic mice combining with other computational and molecular techniques were used to identify transcription regulatory elements including a CCAAT-binding protein Nuclear Factor Y (NF-Y). The function of NF-Y in adipocyte was studied in vitro with 3T3-L1 cells and in vivo with adipocyte-specific knockout of NF-Y. Results Using Leptin-BAC luciferase mice, we showed that DNA sequences between −22 kb and +8.8 kb can confer quantitative expression of a leptin reporter. Computational analysis of sequences and gel shift assays identified a 32 bp sequence (chr6: 28993820–2899385) consisting a CCAAT binding site for Nuclear Factor Y (NF-Y) and this was confirmed by a ChIP assay in vivo. A deletion of this 32 bp sequence in the −22 kb to +8.8 kb leptin-luciferase BAC reporter completely abrogates luciferase reporter activity in vivo. RNAi mediated knockdown of NF-Y interfered with adipogenesis in vitro and adipocyte-specific knockout of NF-Y in mice reduced expression of leptin and other fat specific genes in vivo. Further analyses of the fat specific NF-Y knockout revealed that these animals develop a moderately severe lipodystrophy that is remediable with leptin therapy. Conclusions These studies advance our understanding of leptin gene expression and show that NF-Y controls the expression of leptin and other adipocyte genes and identifies a new form of lipodystrophy.
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Affiliation(s)
- Yi-Hsueh Lu
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olof Stefan Dallner
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Kivanc Birsoy
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gulya Fayzikhodjaeva
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jeffrey M Friedman
- Laboratory of Molecular Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA ; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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