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Shou W, Zhang C, Shi J, Wu H, Huang W. Fine genetic mapping of the chromosome 11q23.3 region in a Han Chinese population: insights into the apolipoprotein genes underlying the blood lipid-lipoprotein variances. J Genet Genomics 2020; 47:756-769. [PMID: 33753020 DOI: 10.1016/j.jgg.2020.11.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/09/2020] [Accepted: 11/20/2020] [Indexed: 12/01/2022]
Abstract
The unusual chromosome 11q23.3 harboring the apolipoprotein (APO) gene cluster has been well documented for its essential roles in plasma lipid-related traits and atherosclerotic cardiovascular diseases. However, its genetic architecture and the potential biological mechanisms underlying complex phenotypes have not been well assessed. We conducted a study for this target region in a Han Chinese population through a stepwise forward framework based on massive parallel sequencing, association analyses, genetic fine mapping, and functional interpretation. The present study identified new meaningful genetic associations that were not simply determined by statistical significance. In addition to the APOA5 gene, we found robust evidence of the genetic commitments of APOC3 and APOA1 to blood lipids. Several variants with high confidence were prioritized along with the potential biological mechanism interpretations in the wake of adaptive fine-mapping analyses. rs2849174 in the APOC3 enhancer was discovered with an unrivaled posterior probability of causality for triglyceride levels and could mediate APOC3 expression through enhancer activity modulated by a combination of histone modifications and transcription factor accessibility. Similarly, multiple lines of evidence converged in favor of rs3741297 as a causal variant influencing high-density lipoprotein cholesterol. Our findings provided novel insights into this genomic locus in the Chinese population.
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Affiliation(s)
- Weihua Shou
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China.
| | - Chenhui Zhang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China
| | - Hong Wu
- Department of Cardiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai 200025, China.
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Guardiola M, Oliva I, Guillaumet A, Martín-Trujillo Á, Rosales R, Vallvé JC, Sabench F, Del Castillo D, Zaina S, Monk D, Ribalta J. Tissue-specific DNA methylation profiles regulate liver-specific expression of the APOA1/C3/A4/A5 cluster and can be manipulated with demethylating agents on intestinal cells. Atherosclerosis 2014; 237:528-35. [PMID: 25463085 DOI: 10.1016/j.atherosclerosis.2014.10.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/17/2014] [Accepted: 10/19/2014] [Indexed: 12/16/2022]
Abstract
OBJECTIVE The tissue-specific expression profiles of genes within the APOA1/C3/A4/A5 cluster play an important role in lipid metabolism regulation. We hypothesize that the tissue-specific expression of the APOA1/C3/A4/A5 gene cluster will show an inverse pattern with DNA methylation, and that repression in non- or low-expressing tissue, such as the intestine, can be reversed using epigenetic drugs. METHODS AND RESULTS We analyzed DNA samples from different human adult tissues (liver, intestine, leukocytes, brain, kidney, pancreas, muscle and sperm) using the Infinium HumanMethyation450 BeadChip array. DNA methylation profiles in APOA1/C3/A4/A5 gene cluster were confirmed by bisulfite PCR and pyrosequencing. To determine whether the observed tissue-specific methylation was associated with the expression profile we exposed intestinal TC7/Caco-2 cells to the demethylating agent 5-Aza-2'-deoxycytidine and monitored intestinal APOA1/C3/A4/A5 transcript re-expression by RT-qPCR. The promoters of APOA1, APOC3 and APOA5 genes were less methylated in liver compared to other tissues, and APOA4 gene was highly methylated in most tissues and partially methylated in liver and intestine. In TC7/Caco-2 cells, 5-Aza-2'-deoxycytidine treatment induced a decrease between 37 and 24% in the methylation levels of APOA1/C3/A4/A5 genes and a concomitant re-expression mainly in APOA1, APOA4 and APOA5 genes ranging from 22 to 600%. CONCLUSIONS We have determined the methylation patterns of the APOA1/C3/A4/A5 cluster that may be directly involved in the transcriptional regulation of this cluster. DNA demethylation of intestinal cells increases the RNA levels especially of APOA1, APOA4 and APOA5 genes.
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Affiliation(s)
- Montse Guardiola
- Unitat de Recerca en Lípids i Arteriosclerosi, Universitat Rovira i Virgili, IISPV, CIBERDEM, Spain.
| | - Iris Oliva
- Unitat de Recerca en Lípids i Arteriosclerosi, Universitat Rovira i Virgili, IISPV, CIBERDEM, Spain.
| | - Amy Guillaumet
- Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.
| | - Álex Martín-Trujillo
- Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.
| | - Roser Rosales
- Unitat de Recerca en Lípids i Arteriosclerosi, Universitat Rovira i Virgili, IISPV, CIBERDEM, Spain.
| | - Joan Carles Vallvé
- Unitat de Recerca en Lípids i Arteriosclerosi, Universitat Rovira i Virgili, IISPV, CIBERDEM, Spain.
| | - Fàtima Sabench
- Unitat de Recerca en Cirurgia, Universitat Rovira i Virgili, IISPV, Spain.
| | | | - Silvio Zaina
- Cancer Epigenetics Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain; Department of Medical Sciences, Division of Health Sciences, León Campus, University of Guanajuato, Mexico.
| | - David Monk
- Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.
| | - Josep Ribalta
- Unitat de Recerca en Lípids i Arteriosclerosi, Universitat Rovira i Virgili, IISPV, CIBERDEM, Spain.
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Zhang Z, Liu J, Xi Y, Yang R, Chen H, Li Z, Liu D, Liang C. Two novel cis-elements involved in hepatocyte nuclear factor 4α regulation of acyl-coenzyme A:cholesterol acyltransferase 2 expression. Acta Biochim Biophys Sin (Shanghai) 2012; 44:162-71. [PMID: 22155889 DOI: 10.1093/abbs/gmr102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acyl-coenzyme A:cholesterol acyltransferase 2 (ACAT2) is important for cholesterol ester synthesis and secretion. A previous study revealed that ACAT2 gene promoter activity was upregulated by hepatocyte nuclear factor 4α (HNF4α) through two sites around -247 and -311 of ACAT2 gene promoter. Here, we identified two novel cis-elements, site I (-1006 to -898) and site II (-38 to -29), which are important for HNF4α effect. In HepG2 cells, mutation of site I decreased ACAT2 gene promoter activity to one-fifth of that of the wild type, while mutation of site II reduced promoter activity to less than one-tenth of that of the wild type. In 293T cells, mutation of these two cis-elements profoundly impaired the HNF4α induction effect. When either of these two elements was inserted into pGL3-promoter, HNF4α induced promoter activity through the inserted element, while mutation of the element impaired HNF4α induction effect. In electrophoretic mobility shift assay and chromatin immunoprecipitation experiment, HNF4α bound to these two elements. Thus, the two cis-elements are important for HNF4α effect on ACAT2 gene transcription. We also showed that HNF4α positively regulates ACAT2 gene expression at mRNA level. Overexpression of HNF4α increased ACAT2 expression, whereas knockdown of HNF4α decreased ACAT2 expression. Peroxisome proliferator-activated receptor gamma coactivator 1α (PCG1α), a coactivator of HNF4α, increased ACAT2 expression, while small heterodimer partner (SHP), a corepressor of HNF4α, decreased ACAT2 expression. These results provide more insights into transcriptional regulation of ACAT2 expression.
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Affiliation(s)
- Zhuqin Zhang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences, Beijing, China
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Wei J, Ouyang H, Wang Y, Pang D, Cong NX, Wang T, Leng B, Li D, Li X, Wu R, Ding Y, Gao F, Deng Y, Liu B, Li Z, Lai L, Feng H, Liu G, Deng X. Characterization of a hypertriglyceridemic transgenic miniature pig model expressing human apolipoprotein CIII. FEBS J 2011; 279:91-9. [PMID: 22023023 DOI: 10.1111/j.1742-4658.2011.08401.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hypertriglyceridemia has recently been considered to be an independent risk factor for coronary heart disease, in which apolipoprotein (Apo)CIII is one of the major contributory factors, as it is strongly correlated with plasma triglyceride levels. Although ApoCIII transgenic mice have been generated as an animal model for the study of hypertriglyceridemia, the features of lipoprotein metabolism in mice differ greatly from those in humans. Because of the great similarity between pigs and humans with respect to lipid metabolism and cardiovascular physiology, we generated transgenic miniature pigs expressing human ApoCIII by the transfection of somatic cells combined with nuclear transfer. The expression of human ApoCIII was detected in the liver and intestine of the transgenic pigs. As compared with nontransgenic controls, transgenic pigs showed significantly increased plasma triglyceride levels (83 ± 36 versus 38 ± 4 mg·dL(-1), P < 0.01) when fed a chow diet. Plasma lipoprotein profiling by FPLC in transgenic animals showed a higher peak in large-particle fractions corresponding to very low-density lipoprotein/chylomicrons when triglyceride content in the fractions was assayed. There was not much difference in cholesterol content in FPLC fractions, although a large low-density lipoprotein peak was identified in both nontransgenic and transgenic animals, resembling that found in humans. Further analysis revealed markedly delayed clearance of plasma triglyceride, accompanied by significantly reduced lipoprotein lipase activity in post-heparin plasma, in transgenic pigs as compared with nontransgenic controls. In summary, we have successfully generated a novel hypertriglyceridemic ApoCIII transgenic miniature pig model that could be of great value for studies on hyperlipidemia in relation to atherosclerotic disorders.
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Affiliation(s)
- Jingyuan Wei
- Laboratory Animal Center, Jilin University, Changchun, China
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Mishiro T, Ishihara K, Hino S, Tsutsumi S, Aburatani H, Shirahige K, Kinoshita Y, Nakao M. Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J 2009; 28:1234-45. [PMID: 19322193 PMCID: PMC2683055 DOI: 10.1038/emboj.2009.81] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/04/2009] [Indexed: 12/31/2022] Open
Abstract
Long-range regulatory elements and higher-order chromatin structure coordinate the expression of multiple genes in cluster, and CTCF/cohesin-mediated chromatin insulator may be a key in this regulation. The human apolipoprotein (APO) A1/C3/A4/A5 gene region, whose alterations increase the risk of dyslipidemia and atherosclerosis, is partitioned at least by three CTCF-enriched sites and three cohesin protein RAD21-enriched sites (two overlap with the CTCF sites), resulting in the formation of two transcribed chromatin loops by interactions between insulators. The C3 enhancer and APOC3/A4/A5 promoters reside in the same loop, where the APOC3/A4 promoters are pointed towards the C3 enhancer, whereas the APOA1 promoter is present in the different loop. The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression and the localization of transcription factor hepatocyte nuclear factor (HNF)-4alpha and transcriptionally active form of RNA polymerase II at the APO promoters. Thus, CTCF/cohesin-mediated insulators maintain the chromatin loop formation and the localization of transcriptional apparatus at the promoters, suggesting an essential role of chromatin insulation in controlling the expression of clustered genes.
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Affiliation(s)
- Tsuyoshi Mishiro
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Gastroenterology and Hepatology, Shimane University School of Medicine, Izumo, Japan
| | - Ko Ishihara
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shinjiro Hino
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Katsuhiko Shirahige
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama City, Kanagawa, Japan
| | - Yoshikazu Kinoshita
- Department of Gastroenterology and Hepatology, Shimane University School of Medicine, Izumo, Japan
| | - Mitsuyoshi Nakao
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
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