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Chowdhury MAR, Haq MM, Lee JH, Jeong S. Multi-faceted regulation of CREB family transcription factors. Front Mol Neurosci 2024; 17:1408949. [PMID: 39165717 PMCID: PMC11333461 DOI: 10.3389/fnmol.2024.1408949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/12/2024] [Indexed: 08/22/2024] Open
Abstract
cAMP response element-binding protein (CREB) is a ubiquitously expressed nuclear transcription factor, which can be constitutively activated regardless of external stimuli or be inducibly activated by external factors such as stressors, hormones, neurotransmitters, and growth factors. However, CREB controls diverse biological processes including cell growth, differentiation, proliferation, survival, apoptosis in a cell-type-specific manner. The diverse functions of CREB appear to be due to CREB-mediated differential gene expression that depends on cAMP response elements and multi-faceted regulation of CREB activity. Indeed, the transcriptional activity of CREB is controlled at several levels including alternative splicing, post-translational modification, dimerization, specific transcriptional co-activators, non-coding small RNAs, and epigenetic regulation. In this review, we present versatile regulatory modes of CREB family transcription factors and discuss their functional consequences.
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Affiliation(s)
- Md Arifur Rahman Chowdhury
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
| | - Md Mazedul Haq
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Sangyun Jeong
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
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Lin TA, How CM, Yen PL, Liao VHC. Sulfate-modified nanosized polystyrene impairs memory by inhibiting ionotropic glutamate receptors and the cAMP-response element binding protein (CREB) pathway in Caenorhabditis elegans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162404. [PMID: 36868277 DOI: 10.1016/j.scitotenv.2023.162404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Nanoplastic contamination is an emerging environmental concern worldwide. In particular, sulfate anionic surfactants often appear along with nanosized plastic particles in personal care products, suggesting that sulfate-modified nanosized polystyrene (S-NP) may occur, remain, and spread into the environment. However, whether S-NP adversely affects learning and memory is unknown. In this study, we used a positive butanone training protocol to evaluate the effects of S-NP exposure on short-term associative memory (STAM) and long-term associative memory (LTAM) in Caenorhabditis elegans. We observed that long-term S-NP exposure impairs both STAM and LTAM in C. elegans. We also observed that mutations in the glr-1, nmr-1, acy-1, unc-43, and crh-1 genes eliminated the STAM and LTAM impairment induced by S-NP, and the mRNA levels of these genes were also decreased upon S-NP exposure. These genes encode ionotropic glutamate receptors (iGluRs), cyclic adenosine monophosphate (cAMP)/Ca2+ signaling proteins, and cAMP-response element binding protein (CREB)/CRH-1 signaling proteins. Moreover, S-NP exposure inhibited the expression of the CREB-dependent LTAM genes nid-1, ptr-15, and unc-86. Our findings provide new insights into long-term S-NP exposure and the impairment of STAM and LTAM, which involve the highly conserved iGluRs and CRH-1/CREB signaling pathways.
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Affiliation(s)
- Ting-An Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chun Ming How
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Pei-Ling Yen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Vivian Hsiu-Chuan Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 106, Taiwan.
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Inflammasome Genetic Variants Are Associated with Protection to Clinical Severity of COVID-19 among Patients from Rio de Janeiro, Brazil. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9082455. [PMID: 36105941 PMCID: PMC9467712 DOI: 10.1155/2022/9082455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022]
Abstract
COVID-19 has a broad spectrum of clinical manifestations, from asymptomatic or mild/moderate symptoms to severe symptoms and death. The mechanisms underlying its clinical evolution are still unclear. Upon SARS-CoV-2 infection, host factors, such as the inflammasome system, are activated by the presence of the virus inside host cells. The search for COVID-19 risk factors is of relevance for clinical management. In this study, we investigated the impact of inflammasome single-nucleotide polymorphisms (SNPs) in SARS-CoV-2-infected individuals with distinct severity profiles at clinical presentation. Patients were divided into two groups according to disease severity at clinical presentation based on the WHO Clinical Progression Scale. Group 1 included patients with mild/moderate disease (WHO < 6; n = 76), and group 2 included patients with severe/critical COVID-19 (WHO ≥ 6; n = 357). Inpatients with moderate to severe/critical profiles were recruited and followed-up at Hospital Center for COVID-19 Pandemic – National Institute of Infectology (INI)/FIOCRUZ, RJ, Brazil, from June 2020 to March 2021. Patients with mild disease were recruited at Oswaldo Cruz Institute (IOC)/FIOCRUZ, RJ, Brazil, in August 2020. Genotyping of 11 inflammasome SNPs was determined by real-time PCR. Protection and risk estimation were performed using unconditional logistic regression models. Significant differences in NLRP3 rs1539019 and CARD8 rs2043211 were observed between the two groups. Protection against disease severity was associated with the A/A genotype (ORadj = 0.36; P = 0.032), allele A (ORadj = 0.93; P = 0.010), or carrier-A (ORadj = 0.45; P = 0.027) in the NLRP3 rs1539019 polymorphism; A/T genotype (ORadj = 0.5; P = 0.045), allele T (ORadj = 0.93; P = 0.018), or carrier-T (ORadj = 0.48; P = 0.029) in the CARD8 rs2043211 polymorphism; and the A-C-G-C-C (ORadj = 0.11; P = 0.018), A-C-G-C-G (ORadj = 0.23; P = 0.003), C-C-G-C-C (ORadj = 0.37; P = 0.021), and C-T-G-A-C (ORadj = 0.04; P = 0.0473) in NLRP3 genetic haplotype variants. No significant associations were observed for the other polymorphisms. To the best of our knowledge, this is the first study demonstrating an association between CARD8 and NLRP3 inflammasome genetic variants and protection against COVID-19 severity, contributing to the discussion of the impact of inflammasomes on COVID-19 outcomes.
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Association between rs738408, rs738409 and rs139051polymorphisms in PNPLA3 gene and non-alcoholic fatty liver disease. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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APOC3 rs2070667 Associates with Serum Triglyceride Profile and Hepatic Inflammation in Nonalcoholic Fatty Liver Disease. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8869674. [PMID: 33294458 PMCID: PMC7718051 DOI: 10.1155/2020/8869674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) of apolipoprotein C3 (APOC3) play important role in lipid metabolism, and dyslipidemia underlies nonalcoholic fatty liver disease (NAFLD). But the correlation of serum lipidomics, APOC3 SNPs, and NAFLD remains limited understood. Enrolling thirty-four biopsy-proven NAFLD patients from Tianjin, Shanghai, Fujian, we investigated their APOC3 genotype and serum lipid profile by DNA sequencing and ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), respectively. Scoring of hepatocyte steatosis, ballooning, lobular inflammation, and liver fibrosis was then performed to reveal the role of lipidomics-affecting APOC3 SNPs in NAFLD-specific pathological alterations. Here, we reported that APOC3 SNPs (rs4225, rs4520, rs5128, rs2070666, and rs2070667) intimately correlated to serum lipidomics in NAFLD patients. A allele instead of G allele at rs2070667, which dominated the SNPs underlying lipidomic alteration, exhibited downregulatory effect on triacylglycerols (TGs: TG 54 : 7, TG 54 : 8, and TG 56 : 9) containing polyunsaturated fatty acid (PUFA). Moreover, subjects with low-level PUFA-containing TGs were predisposed to high-grade lobular inflammation (TG 54 : 7, rho = -0.454 and P = 0.007; TG 54 : 8, rho = -0.411 and P =0.016; TG 56 : 9, rho = -0.481 and P = 0.004). The significant correlation of APOC3 rs2070667 and inflammation grading [G/G vs. G/A+A/A: 0.00 (0.00 and 1.00) vs. 1.50 (0.75 and 2.00), P = 0.022] further confirmed its pathological action on the basis of lipidomics-impacting activity. These findings suggest an inhibitory effect of A allele at APOC3 rs2070667 on serum levels of PUFA-containing TGs, which are associated with high-grade lobular inflammation in NAFLD patients.
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Liu H, Fu L, He D, Deng J, Zhu J, Xu K, Hu D, Li J, Wang Y, Hu W, Xiao S. RUNX3 Polymorphisms Affect the Risk of Ankylosing Spondylitis. Med Sci Monit 2020; 26:e919528. [PMID: 32355155 PMCID: PMC7212810 DOI: 10.12659/msm.919528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background We aimed to assess the potential association of runt-related transcription factor 3 (RUNX3) gene variants with ankylosing spondylitis (AS) susceptibility among Chinese Han people. Material/Methods Genotyping for RUNX3 variants was accomplished through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 115 AS patients and 102 healthy controls. Genotypes distributions of the polymorphisms in controls was assessed for their deviation from Hardy-Weinberg equilibrium (HWE). Moreover, odds ratio (OR) with 95% confidence interval (95%CI) was achieved using chi-square analysis to evaluate AS risk related to RUNX3 polymorphisms. Additionally, logistic regression analysis produced adjusted OR values. Results Genotypes distribution of rs760805 and rs11249206 polymorphisms conformed to HWE in the control group (P>0.05). TT genotype of rs760805 appeared more frequently among AS cases than in controls (P=0.033), indicating its significant association with increased risk of AS onset (OR=2.309, 95%CI=1.069–4.892). The carriage of T allele in rs760805 also heightened AS incidence, in comparison to A allele (OR=1.578, 95%CI=1.075–2.316, P=0.020). Moreover, the carriage of AT+TT genotype in rs760805 and TT genotype in rs11249206 obviously increased risk of AS onset (OR=2.585, 95%CI=1.062–6.288). Conclusions RUNX3 rs760805 polymorphism can contribute to AS incidence in Chinese Han people. The interaction of the 2 polymorphisms may be a risk factor for AS.
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Affiliation(s)
- Huawei Liu
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Ligong Fu
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Dawei He
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Jiuzheng Deng
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Jianjin Zhu
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Kai Xu
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Dong Hu
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
| | - Jing Li
- Department of Orthopedics, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China (mainland)
| | - Yan Wang
- Department of Orthopedics, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China (mainland)
| | - Wenhao Hu
- Department of Orthopedics, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China (mainland)
| | - Songhua Xiao
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China (mainland)
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Ceramide Kinase Is Upregulated in Metastatic Breast Cancer Cells and Contributes to Migration and Invasion by Activation of PI 3-Kinase and Akt. Int J Mol Sci 2020; 21:ijms21041396. [PMID: 32092937 PMCID: PMC7073039 DOI: 10.3390/ijms21041396] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/28/2020] [Accepted: 02/12/2020] [Indexed: 01/04/2023] Open
Abstract
Ceramide kinase (CerK) is a lipid kinase that converts the proapoptotic ceramide to ceramide 1-phosphate, which has been proposed to have pro-malignant properties and regulate cell responses such as proliferation, migration, and inflammation. We used the parental human breast cancer cell line MDA-MB-231 and two single cell progenies derived from lung and bone metastasis upon injection of the parental cells into immuno-deficient mice. The lung and the bone metastatic cell lines showed a marked upregulation of CerK mRNA and activity when compared to the parental cell line. The metastatic cells also had increased migratory and invasive activity, which was dose-dependently reduced by the selective CerK inhibitor NVP-231. A similar reduction of migration was seen when CerK was stably downregulated with small hairpin RNA (shRNA). Conversely, overexpression of CerK in parental MDA-MB-231 cells enhanced migration, and this effect was also observed in the non-metastatic cell line MCF7 upon CerK overexpression. On the molecular level, CerK overexpression increased the activation of protein kinase Akt. The increased migration of CerK overexpressing cells was mitigated by the CerK inhibitor NVP-231, by inhibition of the phosphoinositide 3-kinase (PI3K)/Akt pathway and the Rho kinase, but not by inhibition of the classical extracellular signal-regulated kinase (ERK) pathway. Altogether, our data demonstrate for the first time that CerK promotes migration and invasion of metastatic breast cancer cells and that targeting of CerK has potential to counteract metastasis in breast cancer.
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Muñiz LC, Molina CA. The transcriptional repressor ICER binds to multiple loci throughout the genome. Biochem Biophys Res Commun 2016; 478:1462-5. [PMID: 27590584 DOI: 10.1016/j.bbrc.2016.08.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 08/26/2016] [Indexed: 11/27/2022]
Abstract
The events culminating in ovulation are controlled by the cyclical actions of hormones such as Follical Stimulating Hormone (FSH) and Luteinizing Hormone (LH). The secondary messenger, cyclic AMP (cAMP) conveys the intracellular activity of these hormones. It is well established that a family of transcription factors facilitate cAMP mediated gene expression, yet it remains unknown how these factors directly affect ovulation. One of these factors, Inducible cAMP Early Repressor (ICER) has been implicated in the transcriptional regulation of cAMP inducible genes during folliculogenesis and ovulation. In order to better determine the role of ICER in ovarian function we have identified novel targets using a genome-wide approach. Using a modification of the chromatin immunoprecipitation (ChIP) assay we directly cloned and sequenced the immunoprecipitated ICER-associated DNAs from an immortalized mouse granulose cell line (GRMO2). The analysis of the immunoprecipitated DNA fragments has revealed that ICER's binding to DNA has the following distribution; 16% within the promoter region, 31% within an intron, 14% were not within a gene, 6% were within 20 kb of a promoter and 3% were within the 3' end of genes.
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Affiliation(s)
- Luis C Muñiz
- Department of Biochemistry and Molecular Biology, Rutgers-New Jersey Medical School, Newark, NJ, 07103, USA
| | - Carlos A Molina
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA.
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Zhang RN, Zheng RD, Mi YQ, Zhou D, Shen F, Chen GY, Zhu CY, Pan Q, Fan JG. APOC3 rs2070666 Is Associated with the Hepatic Steatosis Independently of PNPLA3 rs738409 in Chinese Han Patients with Nonalcoholic Fatty Liver Diseases. Dig Dis Sci 2016; 61:2284-2293. [PMID: 27059980 DOI: 10.1007/s10620-016-4120-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/06/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIM The association between nonalcoholic fatty liver disease (NAFLD) and apolipoprotein C3 gene (APOC3) promoter region single-nucleotide polymorphisms (SNPs) rs2854117 and rs2854116 is controversial. The aim of this study was to investigate the relationship between other polymorphisms of APOC3 and NAFLD in Chinese. METHODS Fifty-nine liver biopsy-proven NAFLD patients and 72 healthy control subjects were recruited to a cohort representing Chinese Han population. The polymorphisms in the exons and flanking regions of APOC3 and patatin-like phospholipase domain-containing protein 3 (PNPLA3) rs738409 polymorphisms were genotyped. RESULTS Among the five SNPs (rs4225, rs4520, rs5128, rs2070666, and rs2070667) in APOC3, only rs2070666 (c.179 + 62 T/A) was significantly different in genotype and allele frequency (both p < 0.01) between groups of NAFLD and control. After adjusting for sex, age, serum triglycerides, total cholesterol, body mass index, and the PNPLA3 rs738409 polymorphism, the APOC3 rs2070666 A allele was an independent risk factor for NAFLD with an odds ratio (OR) of 3.683 and 95 % confidence interval (CI) of 1.037-13.084. The APOC3 rs2070666 A allele was linked to the fourth quartile of the controlled attenuation parameter values (OR 2.769, 95 % CI 1.002-7.651) in 131 subjects, and also linked to the significant histological steatosis (OR 4.986, 95 % CI 1.020-24.371), but neither to liver stiffness measurement values nor to hepatic histological activity and fibrosis in NAFLD patients. CONCLUSIONS The APOC3 rs2070666 A allele is a risk factor for NAFLD independent of obesity, dyslipidemia, and PNPLA3 rs738409, and it might contribute to increased liver fat content in Chinese Han population.
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Affiliation(s)
- Rui-Nan Zhang
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Rui-Dan Zheng
- Department of Hepatology, Zhengxing Hospital, Zhangzhou, 363000, China
| | - Yu-Qiang Mi
- Department of Infective Disease, Tianjin Infectious Disease Hospital, Tianjin, 300192, China
| | - Da Zhou
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Feng Shen
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Guang-Yu Chen
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Chan-Yan Zhu
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Qin Pan
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.
| | - Jian-Gao Fan
- Department of Gastroenterology and Center for Fatty Liver, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.
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Transcriptional and Posttranscriptional Programming by Long Noncoding RNAs. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2016; 51:1-27. [PMID: 21287131 DOI: 10.1007/978-3-642-16502-3_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recently, several lines of evidence have suggested that noncoding RNAs, which include both small and long noncoding RNAs (ncRNAs), contribute to a significant portion of the transcriptome in eukaryotic organisms. However, the functional significance of this wide-spread occurrence of ncRNAs, and in particular, the long ncRNAs (lncRNAs), for organismal development and differentiation is unclear. The available evidence from a subset of lncRNAs suggests that certain lncRNAs, and/or the act of their transcription, are involved in important biological functions at the transcriptional and posttranscriptional level. This chapter discusses the epigenetic and nonepigenetic mechanisms by which lncRNAs and/or their transcription are involved in the programming of various biological functions in model systems, from yeast to mammals.
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Sugo N, Morimatsu M, Arai Y, Kousoku Y, Ohkuni A, Nomura T, Yanagida T, Yamamoto N. Single-Molecule Imaging Reveals Dynamics of CREB Transcription Factor Bound to Its Target Sequence. Sci Rep 2015; 5:10662. [PMID: 26039515 PMCID: PMC4454023 DOI: 10.1038/srep10662] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 04/22/2015] [Indexed: 12/31/2022] Open
Abstract
Proper spatiotemporal gene expression is achieved by selective DNA binding of transcription factors in the genome. The most intriguing question is how dynamic interactions between transcription factors and their target sites contribute to gene regulation by recruiting the basal transcriptional machinery. Here we demonstrate individual binding and dissociation events of the transcription factor cAMP response element-binding protein (CREB), both in vitro and in living cells, using single-molecule imaging. Fluorescent–tagged CREB bound to its target sequence cAMP-response element (CRE) for a remarkably longer period (dissociation rate constant: 0.21 s-1) than to an unrelated sequence (2.74 s-1). Moreover, CREB resided at restricted positions in the living cell nucleus for a comparable period. These results suggest that CREB stimulates transcription by binding transiently to CRE in the time range of several seconds.
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Affiliation(s)
- Noriyuki Sugo
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Yoshiyuki Arai
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Yoshinori Kousoku
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Aya Ohkuni
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Taishin Nomura
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Toshio Yanagida
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan [2] Riken Quantitative Biological Center (QBic), Osaka, Japan
| | - Nobuhiko Yamamoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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Zhu L, Zhu J, Liu Y, Chen Y, Li Y, Huang L, Chen S, Li T, Dang Y, Chen T. Methamphetamine induces alterations in the long non-coding RNAs expression profile in the nucleus accumbens of the mouse. BMC Neurosci 2015; 16:18. [PMID: 25884509 PMCID: PMC4399149 DOI: 10.1186/s12868-015-0157-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 03/13/2015] [Indexed: 01/01/2023] Open
Abstract
Background Repeated exposure to addictive drugs elicits long-lasting cellular and molecular changes. It has been reported that the aberrant expression of long non-coding RNAs (lncRNAs) is involved in cocaine and heroin addiction, yet the expression profile of lncRNAs and their potential effects on methamphetamine (METH)-induced locomotor sensitization are largely unknown. Results Using high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq), here we examined the alterations in the lncRNAs expression profile in the nucleus accumbens (NAc) of METH-sensitized mice. We found that the expression levels of 6246 known lncRNAs (6215 down-regulated, 31 up-regulated) and 8442 novel lncRNA candidates (8408 down-regulated, 34 up-regulated) were significantly altered in the METH-sensitized mice. Based on characterizations of the genomic contexts of the lncRNAs, we further showed that there were 5139 differentially expressed lncRNAs acted via cis mechanisms, including sense intronic (4295 down-regulated and one up-regulated), overlapping (25 down-regulated and one up-regulated), natural antisense transcripts (NATs, 148 down-regulated and eight up-regulated), long intergenic non-coding RNAs (lincRNAs, 582 down-regulated and five up-regulated), and bidirectional (72 down-regulated and two up-regulated). Moreover, using the program RNAplex, we identified 3994 differentially expressed lncRNAs acted via trans mechanisms. Gene ontology (GO) and KEGG pathway enrichment analyses revealed that the predicted cis- and trans- associated genes were significantly enriched during neuronal development, neuronal plasticity, learning and memory, and reward and addiction. Conclusions Taken together, our results suggest that METH can elicit global changes in lncRNA expressions in the NAc of sensitized mice that might be involved in METH-induced locomotor sensitization and addiction. Electronic supplementary material The online version of this article (doi:10.1186/s12868-015-0157-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Zhu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
| | - Jie Zhu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
| | - Yufeng Liu
- Beijing Genomics Institute, Shenzhen, 518083, PR China.
| | - Yanjiong Chen
- Departments of Immunology and Pathogenic Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China.
| | - Yanlin Li
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
| | - Liren Huang
- Beijing Genomics Institute, Shenzhen, 518083, PR China.
| | - Sisi Chen
- Beijing Genomics Institute, Shenzhen, 518083, PR China.
| | - Tao Li
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
| | - Yonghui Dang
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
| | - Teng Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, PR China. .,The Key Laboratory of Health Ministry for Forensic Science, Xi'an Jiaotong University, Shaanxi, PR China.
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Lakhina V, Arey RN, Kaletsky R, Kauffman A, Stein G, Keyes W, Xu D, Murphy CT. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs. Neuron 2015; 85:330-45. [PMID: 25611510 DOI: 10.1016/j.neuron.2014.12.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2014] [Indexed: 12/30/2022]
Abstract
Induced CREB activity is a hallmark of long-term memory, but the full repertoire of CREB transcriptional targets required specifically for memory is not known in any system. To obtain a more complete picture of the mechanisms involved in memory, we combined memory training with genome-wide transcriptional analysis of C. elegans CREB mutants. This approach identified 757 significant CREB/memory-induced targets and confirmed the involvement of known memory genes from other organisms, but also suggested new mechanisms and novel components that may be conserved through mammals. CREB mediates distinct basal and memory transcriptional programs at least partially through spatial restriction of CREB activity: basal targets are regulated primarily in nonneuronal tissues, while memory targets are enriched for neuronal expression, emanating from CREB activity in AIM neurons. This suite of novel memory-associated genes will provide a platform for the discovery of orthologous mammalian long-term memory components.
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Affiliation(s)
- Vanisha Lakhina
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rachel N Arey
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Amanda Kauffman
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Geneva Stein
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - William Keyes
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Daniel Xu
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA.
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14
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The neuronal activity-driven transcriptome. Mol Neurobiol 2014; 51:1071-88. [PMID: 24935719 DOI: 10.1007/s12035-014-8772-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/01/2014] [Indexed: 10/25/2022]
Abstract
Activity-driven transcription is a key event associated with long-lasting forms of neuronal plasticity. Despite the efforts to investigate the regulatory mechanisms that control this complex process and the important advances in the knowledge of the function of many activity-induced genes in neurons, as well as the specific contribution of activity-regulated transcription factors, our understanding of how activity-driven transcription operates at the systems biology level is still very limited. This review focuses on the research of neuronal activity-driven transcription from an "omics" perspective. We will discuss the different high-throughput approaches undertaken to characterize the gene programs downstream of specific activity-regulated transcription factors, including CREB, SRF, MeCP2, Fos, Npas4, and others, and the interplay between epigenetic and transcriptional mechanisms underlying neuronal plasticity changes. Although basic questions remain unanswered and important challenges still lie ahead, the refinement of genome-wide techniques for investigating the neuronal transcriptome and epigenome promises great advances.
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Iversen ES, Lipton G, Clyde MA, Monteiro ANA. Functional annotation signatures of disease susceptibility loci improve SNP association analysis. BMC Genomics 2014; 15:398. [PMID: 24886216 PMCID: PMC4041996 DOI: 10.1186/1471-2164-15-398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/13/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the phenotype. To date, functional annotations of the genetic variants have rarely played more than an indirect role in assessing evidence for association. Here, we demonstrate how these data can be systematically integrated into an association study's analysis plan. RESULTS We developed a Bayesian statistical model for the prior probability of phenotype-genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a binary regression of association status on a set of annotation variables whose coefficients were estimated through an analysis of associated SNPs in the GWAS Catalog (GC). The functional predictors examined included measures that have been demonstrated to correlate with the association status of SNPs in the GC and some whose utility in this regard is speculative: summaries of the UCSC Human Genome Browser ENCODE super-track data, dbSNP function class, sequence conservation summaries, proximity to genomic variants in the Database of Genomic Variants and known regulatory elements in the Open Regulatory Annotation database, PolyPhen-2 probabilities and RegulomeDB categories. Because we expected that only a fraction of the annotations would contribute to predicting association, we employed a penalized likelihood method to reduce the impact of non-informative predictors and evaluated the model's ability to predict GC SNPs not used to construct the model. We show that the functional data alone are predictive of a SNP's presence in the GC. Further, using data from a genome-wide study of ovarian cancer, we demonstrate that their use as prior data when testing for association is practical at the genome-wide scale and improves power to detect associations. CONCLUSIONS We show how diverse functional annotations can be efficiently combined to create 'functional signatures' that predict the a priori odds of a variant's association to a trait and how these signatures can be integrated into a standard genome-wide-scale association analysis, resulting in improved power to detect truly associated variants.
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Affiliation(s)
- Edwin S Iversen
- Department of Statistical Science, Duke University, Box 90251, 27708-0251 Durham, NC, USA.
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Kreydiyyeh SI, Dakroub Z. Ceramide and its metabolites modulate time-dependently the activity of the Na⁺/K⁺ ATPase in HepG2 cells. Int J Biochem Cell Biol 2014; 53:102-7. [PMID: 24819540 DOI: 10.1016/j.biocel.2014.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 04/17/2014] [Accepted: 04/30/2014] [Indexed: 02/03/2023]
Abstract
Ceramide is involved in the regulation of many cellular processes including cell proliferation and apoptosis, which are accompanied respectively with a decrease and an increase in the activity of the Na(+)/K(+) ATPase. These antagonistic effects may be time-dependent and due to different signaling pathways requiring different time intervals to be activated. While we showed previously a ceramide-induced inhibition of the ATPase in HepG2 cells during the first hour, we study here the effect of ceramide thereafter. Ceramide stimulated the Na(+)/K(+) ATPase between 1 and 4h with a peak at 2h. This stimulation was maintained in the simultaneous presence of an inhibitor of ceramidase (CAY 10466) but disappeared when ceramide kinase was inhibited, suggesting a role of ceramide-1-phosphate (cer-1-P) in the observed effect. Exogenous cer-1-P caused a similar stimulation of the ATPase which was not affected by an inhibition of JNK but changed into a decrease in presence of PDTC, a specific inhibitor of NF-κB, and disappeared when NF-κB and JNK were inhibited simultaneously. It was concluded that cer-1-P activates both JNK and NF-κB. While JNK exerts an inhibitory effect on the ATPase, NF-κB increases its activity and abrogates the stimulatory effect of the sphingolipid on JNK leading thus to an additional increase in the ATPase activity.
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Affiliation(s)
| | - Zeina Dakroub
- Department of Biology, Faculty of Arts & Sciences, American University of Beirut, Beirut, Lebanon
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Han M, Xiao X, Yang Y, Huang RY, Cao H, Zhao ZQ, Zhang YQ. SIP30 is required for neuropathic pain-evoked aversion in rats. J Neurosci 2014; 34:346-55. [PMID: 24403136 PMCID: PMC6608160 DOI: 10.1523/jneurosci.3160-13.2014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 11/04/2013] [Accepted: 11/07/2013] [Indexed: 11/21/2022] Open
Abstract
SIP30 (SNAP25 interacting protein of 30) is a SNAP25 interaction protein of 30 kDa that functions in neurotransmitter release. Using a chronic constriction injury (CCI) model of neuropathic pain, we profiled gene expression in the rat spinal cord and brain and identified sip30, which was upregulated after CCI. Here, we show that CCI induced a bilateral increase of SIP30 in the rostral anterior cingulate cortex (rACC), a key brain region that has been implicated in pain affect. We put rats in a chamber with one half painted white (light area) and the other half painted black (dark area), and measured neuropathic pain-evoked place escape/avoidance paradigm (PEAP) to quantify the level of negative emotion evoked by painful stimuli using a Von Frey hair. Inhibition of CCI-mediated induction of SIP30 by intra-rACC injection of shRNA targeting the rat sip30 gene reduced PEAP. Interestingly, knockdown of SIP30 did not affect CCI-induced evoked pain such as heat hyperalgesia and mechanical allodynia. Neither did it affect general learning and memory. CCI-induced upregulation of SIP30 was correlated with activation of ERK, PKA, and CREB in the rACC. Intra-rACC administration of PKA or ERK inhibitors suppressed CCI-induced SIP30 upregulation and blocked the induction of PEAP. Additionally, knockdown of SIP30 suppressed the frequency of mEPSCs and increased paired-pulse ratios in rACC slices and decreased extracellular glutamate concentrations. Together, our results highlight SIP30 as a target of PKA and ERK in the rACC to mediate neuropathic pain-evoked negative emotion via modulation of glutamate release and excitatory synaptic transmission.
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Affiliation(s)
- Mei Han
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
| | - Xiao Xiao
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
| | - Yan Yang
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
| | - Ru-Yi Huang
- Department of Life Science, Fudan University, Shanghai 200433, China
| | - Hong Cao
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
| | - Zhi-Qi Zhao
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
| | - Yu-Qiu Zhang
- Institute of Neurobiology, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China, and
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Peng XE, Wu YL, Lu QQ, Hu ZJ, Lin X. MTTP polymorphisms and susceptibility to non-alcoholic fatty liver disease in a Han Chinese population. Liver Int 2014; 34:118-28. [PMID: 23738963 DOI: 10.1111/liv.12220] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 05/11/2013] [Indexed: 12/29/2022]
Abstract
BACKGROUND The microsomal triglyceride transfer protein (MTP) is required for the assembly and secretion of apolipoprotein B (ApoB)-containing lipoproteins from the liver and intestine. Previous studies showed that functional polymorphisms in the MTTP gene correspond to lower LDL levels and protect against other traits of the metabolic syndrome. AIMS Here, we aimed to investigate whether MTTP single nucleotide polymorphisms (SNPs) and their predicted haplotypes of linkage disequilibrium blocks contribute to non-alcoholic fatty liver disease (NAFLD) susceptibility in a Han Chinese population. METHODS Seven tag SNPs in the MTTP gene were selected and genotyped in a frequency-matched case-control study in a population from Fuzhou City, China. We enrolled 580 patients with NAFLD and 580 healthy controls. RESULTS In the multivariate logistic regression analysis, the rs1800804 (-164 T/C) was associated with an increased risk of NAFLD, while the rs1057613 A/G and rs3805335 C/T SNPs were associated with a decreased risk of NAFLD. The cumulative effect of the rs1800804 (-164 T/C), rs1057613 and rs3805335 was estimated, and a significant increased trend in the risk of NAFLD with increasing genetic risk score was observed (adjusted P(trend) = 0.014). Furthermore, the results of haplotype analysis suggested that the haplotype GC in block 1 containing the -164 C allele was associated with an increased risk of NAFLD, while haplotype TGTTC in block 2 was associated with a decreased risk of NAFLD. CONCLUSIONS Our data show that MTTP genetic polymorphisms influence the susceptibility to developing NAFLD independently or jointly in the Han Chinese population.
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Affiliation(s)
- Xian E Peng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
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Zhang M, Xu JJ, Zhou RL, Zhang QY. cAMP responsive element binding protein-1 is a transcription factor of lysosomal-associated protein transmembrane-4 Beta in human breast cancer cells. PLoS One 2013; 8:e57520. [PMID: 23469012 PMCID: PMC3585361 DOI: 10.1371/journal.pone.0057520] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 01/22/2013] [Indexed: 12/16/2022] Open
Abstract
Lysosomal-associated protein transmembrane-4 beta (LAPTM4B) is a potential proto-oncogene, whose overexpression is involved in cancer occurrence and progression. Its transcript is up-regulated in various types of solid tumors including breast cancer. However, its transcriptional regulation mechanism is still unclear. To investigate the mechanism of transcriptional regulation of LAPTM4B in human breast cancer cells, a series of luciferase reporter constructs and construct with mutated binding site for cAMP responsive element binding protein-1 (CREB1) were generated by PCR amplification and transiently transfected into breast cancer cells to determine the transcriptional activities of different promoter regions. The +10+292 promoter region was possessed the highest transcriptional activity. The ability of CREB1 to bind the LAPMT4B promoter was confirmed by electrophoretic mobility shift assay, super-shift and RNA interference experiments. Our study identified the core promoter region responsible for constitutive expression of LAPTM4B and clarified that CREB1 played an important role in LAPTM4B transcriptional regulation in human breast cancer cells.
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Affiliation(s)
- Meng Zhang
- Department of Clinical laboratory, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jian-Jun Xu
- Department of Clinical laboratory, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Rou-Li Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qing-Yun Zhang
- Department of Clinical laboratory, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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20
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Ding G, Liu F, Feng C, Xu J, Ding Q. [Association between the myeloperoxidase gene polymorphisms and the susceptibility to prostate cancer: a case-control study in a Chinese population]. Actas Urol Esp 2013; 37:79-82. [PMID: 23260186 DOI: 10.1016/j.acuro.2012.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 03/10/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND OBJECTIVES Prostate cancer (PCa) is the most common cancer among men in most western populations. The polymorphisms of the myeloperoxidase (MPO) gene have been correlated with abnormal MPO expression and increased risk of various types of cancers. Our study aimed to evaluate the association between the genetic polymorphisms and the risk of prostate cancer. METHODS Genotyping was carried out by using the genotyping system (MassARRAY iPLEX; Sequenom, Inc., San Diego, CA, USA) on 1,108 PCa patients and 1,525 cancer-free controls in a Chinese Han population. RESULTS Although one SNP (rs8082134, P < 0.050) was significant, it is very rare and unstable. Other SNPs had no significant difference between genotype distributions in the PCa patients and the control group. Totally, SNPs in the MPO gene is not associated with PCa risk. CONCLUSION Our data showed a limited association between the MPO SNPs and the susceptibility to PCa in population of Chinese Han population. The possible association of rs8082134 of MPO with PCa risk need further clarification.
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21
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Peng XE, Wu YL, Lin SW, Lu QQ, Hu ZJ, Lin X. Genetic variants in PNPLA3 and risk of non-alcoholic fatty liver disease in a Han Chinese population. PLoS One 2012; 7:e50256. [PMID: 23226254 PMCID: PMC3511464 DOI: 10.1371/journal.pone.0050256] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 10/17/2012] [Indexed: 02/06/2023] Open
Abstract
We investigated the possible association between genetic variants in the Patatin like phospholipase-3 (PNPLA3) gene and nonalcoholic fatty liver disease (NAFLD) in a Han Chinese population. We evaluated twelve tagging single-nucleotide polymorphisms (tSNPs) of the PNPLA3 gene in a frequency matched case–control study from Fuzhou city of China (553 cases, 553 controls). In the multivariate logistic regression analysis, the rs738409 GG or GC, and rs139051 TT genotypes were found to be associated with increased risk of NAFLD, and a significant trend of increased risk with increasing numbers of risk genotype was observed in the cumulative effect analysis of these single nucleotide polymorphisms. Furthermore, haplotype association analysis showed that, compared with the most common haplotype, the CAAGAATGCGTG and CGAAGGTGTCCG haplotypes conferred a statistically significant increased risk for NAFLD, while the CGGGAACCCGCG haplotype decreased the risk of NAFLD. Moreover, rs738409 C>G appeared to have a multiplicative joint effect with tea drinking (P<0.005) and an additive joint effect with obesity (Interaction contrast ratio (ICR) = 2.31, 95% CI: 0.7–8.86), hypertriglyceridemia (ICR = 3.07, 95% CI: 0.98–5.09) or hypertension (ICR = 1.74, 95% CI: 0.52–3.12). Our data suggests that PNPLA3 genetic polymorphisms might influence the susceptibility to NAFLD development independently or jointly in Han Chinese.
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Affiliation(s)
- Xian-E Peng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Research Center of Molecular Medicine, Fujian Medical University, Fuzhou, China
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Yun-Li Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Research Center of Molecular Medicine, Fujian Medical University, Fuzhou, China
- Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Shao-Wei Lin
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Qing-Qing Lu
- Department of Gastroenterology, Union Hospital of Fujian Medical University, Fuzhou, China
| | - Zhi-Jian Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Research Center of Molecular Medicine, Fujian Medical University, Fuzhou, China
- Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- * E-mail:
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Abstract
The control of gene transcription is a critical level of gene expression regulation. The interactions between transcription factors (TF) and their DNA binding sites (TFBS) play a key role at this level. In order to decipher the molecular mechanism of the interactions of TFs with TFBSs and construct transcription regulatory network, it is necessary to systematically collect, save, and analyze the information of discovered TFs and their TFBSs. In recent years, multiple TF and TFBS-related databases have been established. These databeses significantly promoted the TF-related studies in the fields of molecular biology, bioinformatics, and system biology. This paper summarized the contents, characteristics, access, and advances of main TFs and TFBSs-related databases, including TRANSFAC, JASPAR, TFDB, TRRD, TRED, PAZAR, MAPPER and others.
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Ji X, Hou Z, Wang T, Jin K, Fan J, Luo C, Chen M, Han R, Ni C. Polymorphisms in inflammasome genes and risk of coal workers' pneumoconiosis in a Chinese population. PLoS One 2012; 7:e47949. [PMID: 23110140 PMCID: PMC3478280 DOI: 10.1371/journal.pone.0047949] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/18/2012] [Indexed: 01/22/2023] Open
Abstract
Background Coal workers' pneumoconiosis (CWP), resulting from the inhalation of silica-containing coal mine dust, is characterized by fibrosing nodular lesions that eventually develop into progressive pulmonary fibrosis. Recently, it has been hypothesized that inflammasomes could have a crucial role in the host response to silica and recent studies show that the inflammasome contributes to inflammation and pulmonary fibrosis. NLRP3, CARD8 are components of the NLRP3 inflammasome, which triggers caspase 1-mediated IL-1β and IL-18 release. In the present study, we investigated whether common single nucleotide polymorphisms (SNPs) in inflammasome genes are associated with CWP. Methods We performed an association study analyzing 3 NLRP3, 1 CARD8, 1 IL-1β, 2 IL-18 SNPs in a case-control study of 697 CWP and 694 controls. Genotyping was carried out by the TaqMan method. Results The NLRP3 rs1539019 TT genotype was associated with a significantly increased risk of CWP (adjusted odds ratio (OR) = 1.39, 95% confidence interval (CI) = 1.07–1.81), compared with the GG/GT genotype, in particular among smokers (adjusted OR = 1.67, 95%CI = 1.15–2.42). In addition, the polymorphism was significantly associated with risk of CWP patients with stage I. Conclusions This is the first report showing an association between the NLRP3 rs1539019 polymorphism and CWP, and suggests that this polymorphism may confer increased risk for the development of the disease. Further studies are warranted to confirm our findings.
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Affiliation(s)
- Xiaoming Ji
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiguo Hou
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Kexin Jin
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingjing Fan
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chen Luo
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Minjuan Chen
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruhui Han
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chunhui Ni
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, China
- * E-mail:
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Bini F, Frati A, Garcia-Gil M, Battistini C, Granado M, Martinesi M, Mainardi M, Vannini E, Luzzati F, Caleo M, Peretto P, Gomez-Muñoz A, Meacci E. New signalling pathway involved in the anti-proliferative action of vitamin D3 and its analogues in human neuroblastoma cells. A role for ceramide kinase. Neuropharmacology 2012; 63:524-37. [DOI: 10.1016/j.neuropharm.2012.04.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/06/2012] [Accepted: 04/21/2012] [Indexed: 01/12/2023]
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25
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Gu GM, Wang JK. [DNA-binding profiles of mammalian transcription factors]. YI CHUAN = HEREDITAS 2012; 34:950-68. [PMID: 22917900 DOI: 10.3724/sp.j.1005.2012.00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChIP-chip and ChIP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.
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Affiliation(s)
- Guang-Ming Gu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China.
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Hasler R, Perroud N, Baud P, Olié E, Guillaume S, Malafosse A, Courtet P. CREB1 modulates the influence of childhood sexual abuse on adult's anger traits. GENES BRAIN AND BEHAVIOR 2012; 11:720-6. [DOI: 10.1111/j.1601-183x.2012.00807.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Peng XE, Wu YL, Lu QQ, Hu ZJ, Lin X. Two genetic variants in FABP1 and susceptibility to non-alcohol fatty liver disease in a Chinese population. Gene 2012; 500:54-8. [DOI: 10.1016/j.gene.2012.03.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/27/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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Mitra SA, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet 2012; 3:17. [PMID: 22363342 PMCID: PMC3279698 DOI: 10.3389/fgene.2012.00017] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 01/28/2012] [Indexed: 01/29/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) have been shown to regulate important biological processes that support normal cellular functions. Aberrant regulation of these essential functions can promote tumor development. In this review, we underscore the importance of the regulatory role played by this distinct class of ncRNAs in cancer-associated pathways that govern mechanisms such as cell growth, invasion, and metastasis. We also highlight the possibility of using these unique RNAs as diagnostic and prognostic biomarkers in malignancies.
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Affiliation(s)
- Sheetal A Mitra
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles Los Angeles, CA, USA
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cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression. J Neurosci 2012; 31:18237-50. [PMID: 22171029 DOI: 10.1523/jneurosci.4554-11.2011] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Long-lasting forms of neuronal plasticity require de novo gene expression, but relatively little is known about the events that occur genome-wide in response to activity in a neuronal network. Here, we unveil the gene expression programs initiated in mouse hippocampal neurons in response to different stimuli and explore the contribution of four prominent plasticity-related transcription factors (CREB, SRF, EGR1, and FOS) to these programs. Our study provides a comprehensive view of the intricate genetic networks and interactions elicited by neuronal stimulation identifying hundreds of novel downstream targets, including novel stimulus-associated miRNAs and candidate genes that may be differentially regulated at the exon/promoter level. Our analyses indicate that these four transcription factors impinge on similar biological processes through primarily non-overlapping gene-expression programs. Meta-analysis of the datasets generated in our study and comparison with publicly available transcriptomics data revealed the individual and collective contribution of these transcription factors to different activity-driven genetic programs. In addition, both gain- and loss-of-function experiments support a pivotal role for CREB in membrane-to-nucleus signal transduction in neurons. Our data provide a novel resource for researchers wanting to explore the genetic pathways associated with activity-regulated neuronal functions.
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Gade P, Kalvakolanu DV. Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity. Methods Mol Biol 2012; 809:85-104. [PMID: 22113270 DOI: 10.1007/978-1-61779-376-9_6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Differential gene expression is facilitated by transcriptional regulatory mechanisms and chromatin modifications through DNA-protein interactions. One of the widely used assays to study this is chromatin immunoprecipitation (ChIP) assay, which enables analysis of association of regulatory molecules to specific promoters and histone modifications in vivo. This is of immense value as ChIP assays can provide glimpse of the regulatory mechanisms involved in gene expression in vivo. This article outlines the general strategies and protocols to study ChIP assays in differential recruitment of transcriptional factors (TFs) and also global analysis of transcription factor recruitment is discussed. Further, the applications of ChIP assays for discovering novel genes that are dependent on specific transcription factors were addressed.
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Affiliation(s)
- Padmaja Gade
- Department of Microbiology & Immunology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
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AMBATI S, DUAN J, HARTZELL DL, CHOI YH, DELLA-FERA MA, BAILE CA. GIP-Dependent Expression of Hypothalamic Genes. Physiol Res 2011; 60:941-50. [DOI: 10.33549/physiolres.932151] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
GIP (glucose dependent insulinotrophic polypeptide), originally identified as an incretin peptide synthesized in the gut, has recently been identified, along with its receptors (GIPR), in the brain. Our objective was to investigate the role of GIP in hypothalamic gene expression of biomarkers linked to regulating energy balance and feeding behavior related neurocircuitry. Rats with lateral cerebroventricular cannulas were administered 10 μg GIP or 10 μl artificial cerebrospinal fluid (aCSF) daily for 4 days, after which whole hypothalami were collected. Real time Taqman™ RT-PCR was used to quantitatively compare the mRNA expression levels of a set of genes in the hypothalamus. Administration of GIP resulted in up-regulation of hypothalamic mRNA levels of AVP (46.9±4.5 %), CART (25.9±2.7 %), CREB1 (38.5±4.5 %), GABRD (67.1±11 %), JAK2 (22.1±3.6 %), MAPK1 (33.8±7.8 %), NPY (25.3±5.3 %), OXT (49.1±5.1 %), STAT3 (21.6±3.8 %), and TH (33.9±8.5 %). In a second experiment the same set of genes was evaluated in GIPR-/- and GIPR+/? mice to determine the effect of lack of GIP stimulation on gene expression. In GIPR-/- mice expressions of the following genes were down-regulated: AVP (27.1±7.5 %), CART (28.3±3.7 %), OXT (25.2±5.8 %), PTGES (23.9±4.5 %), and STAT3 (8.8±2.3 %). These results suggest that AVP, CART, OXT and STAT3 may be involved in energy balance-related hypothalamic circuits affected by GIP.
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Affiliation(s)
| | | | | | | | | | - C. A. BAILE
- Department of Animal and Dairy Science, University of Georgia, Athens, USA
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Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M. Regulatory Variation Within and Between Species. Annu Rev Genomics Hum Genet 2011; 12:327-46. [DOI: 10.1146/annurev-genom-082908-150139] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wei Zheng
- Department of Molecular, Cellular, and Developmental Biology, Biostatics Resources, Keck Laboratory, Yale University, New Haven, Connecticut 06520;
| | - Tara A. Gianoulis
- Department of Genetics and Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts 02115;
| | - Konrad J. Karczewski
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305; ,
| | - Hongyu Zhao
- Biostatistics Division, Yale School of Public Health, New Haven, Connecticut 06520;
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305; ,
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Ulupinar E, Yucel F, Erol K. Lesion-induced synaptic plasticity in the somatosensory cortex of prenatally stressed rats. Neurotoxicol Teratol 2011; 33:548-57. [PMID: 21839167 DOI: 10.1016/j.ntt.2011.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 07/25/2011] [Accepted: 07/25/2011] [Indexed: 01/19/2023]
Abstract
Prenatal stress exposure causes long-lasting impairments of the behavioral and neuroendocrine responses to later stressors of the offspring. Although mechanisms underlying these effects remain largely unknown, abnormalities in the neuronal plasticity might be responsible for neurobiological alterations. This study used the whisker-to-barrel pathway as a model system to investigate the effects of prenatal stress on lesion-induced plasticity of neurons. Pregnant rats were subjected to immobilization stress during the trigeminal neurogenesis period, corresponding to gestational days 12 to 17, for three hours a day. After birth, the middle row (C) whisker follicles of pups from the control and stressed groups were electrocauterized. Ten days later, tangentially sectioned cortical hemispheres were stained with cytochrome oxidase histochemistry to calculate the volumes of each barrel row (A-E) in both lesioned and intact sides of the cortex, using stereological methods. The adrenal to body weight ratios were significantly increased in stressed animals, when compared to the controls. The pattern and total volume of the barrel subfield remained unaltered, but the lesion-induced map plasticity index, calculated as the D/C ratio, decreased in stressed animals. In addition, the BDNF (Brain Derived Neurotrophic Factor), NT-3 (neurotrophin-3) and the cyclic AMP response element binding protein (CREB) phosphorylation levels in tissue homogenates of the barrel cortices were measured using the ELISA method. In prenatally stressed animals, the BDNF and NT-3 levels were reduced on the lesioned side, but significant CREB activation was observed on the intact side of the barrel cortex. Taken together, the results show that prenatal stress exposure negatively affects critical period plasticity by reducing the expansion of active barrels following peripheral whisker lesion. These changes arise independent of CREB phosphorylation and appear to be mediated by reduced levels of neurotrophins.
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Affiliation(s)
- Emel Ulupinar
- Department of Anatomy, Eskisehir Osmangazi University Faculty of Medicine, Eskişehir, 26480, Turkey.
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Pei DS, Yang XJ, Liu W, Guikema JEJ, Schrader CE, Strauss PR. A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase beta. Nucleic Acids Res 2010; 39:3156-65. [PMID: 21172930 PMCID: PMC3082881 DOI: 10.1093/nar/gkq1142] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though there is ample polb mRNA. Here, we report that Polb protein fails to appear at the appropriate time in development when AP endonuclease 1 (Apex), the upstream protein in BER, is knocked down. Because polb contains a Creb1 binding site, we examined whether knockdown of Apex affects creb1. Apex knockdown results in loss of Creb1 and Creb complex members but not Creb1 phosphorylation. This effect is independent of p53. Although both apex and creb1 mRNA rescue Creb1 and Polb after Apex knockdown, Apex is not a co-activator of creb1 transcription. This observation has broad significance, as similar results occur when Apex is inhibited in B cells from apex+/− mice. These results describe a novel regulatory circuit involving Apex, Creb1 and Polb and provide a mechanism for lethality of Apex loss in higher eukaryotes.
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Affiliation(s)
- De-Sheng Pei
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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Sakamoto K, Karelina K, Obrietan K. CREB: a multifaceted regulator of neuronal plasticity and protection. J Neurochem 2010; 116:1-9. [PMID: 21044077 DOI: 10.1111/j.1471-4159.2010.07080.x] [Citation(s) in RCA: 358] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since its initial characterization over 20 years ago, there has been intense and unwavering interest in understanding the role of the transcription factor cAMP-responsive element binding protein (CREB) in nervous system physiology. Through an array of experimental approaches and model systems, researchers have begun to unravel the complex and multifaceted role of this transcription factor in such diverse processes as neurodevelopment, synaptic plasticity, and neuroprotection. Here we discuss current insights into the molecular mechanisms by which CREB couples synaptic activity to long-term changes in neuronal plasticity, which is thought to underlie learning and memory. We also discuss work showing that CREB is a critical component of the neuroprotective transcriptional network, and data indicating that CREB dysregulation contributes to an array of neuropathological conditions.
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Affiliation(s)
- Kensuke Sakamoto
- Department of Neuroscience, Ohio State University, Columbus, Ohio 43210, USA
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36
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Martianov I, Choukrallah MA, Krebs A, Ye T, Legras S, Rijkers E, Van Ijcken W, Jost B, Sassone-Corsi P, Davidson I. Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells. BMC Genomics 2010; 11:530. [PMID: 20920259 PMCID: PMC3091680 DOI: 10.1186/1471-2164-11-530] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 09/29/2010] [Indexed: 11/16/2022] Open
Abstract
Background CREB and CREM are closely related factors that regulate transcription in response to various stress, metabolic and developmental signals. The CREMτ activator isoform is selectively expressed in haploid spermatids and plays an essential role in murine spermiogenesis. Results We have used chromatin immunoprecipitation coupled to sequencing (ChIP-seq) to map CREM and CREB target loci in round spermatids from adult mouse testis and spermatogonia derived GC1-spg cells respectively. We identify more than 9000 genomic loci most of which are cell-specifically occupied. Despite the fact that round spermatids correspond to a highly specialised differentiated state, our results show that they have a remarkably accessible chromatin environment as CREM occupies more than 6700 target loci corresponding not only to the promoters of genes selectively expressed in spermiogenesis, but also of genes involved in functions specific to other cell types. The expression of only a small subset of these target genes are affected in the round spermatids of CREM knockout animals. We also identify a set of intergenic binding loci some of which are associated with H3K4 trimethylation and elongating RNA polymerase II suggesting the existence of novel CREB and CREM regulated transcripts. Conclusions We demonstrate that CREM and CREB occupy a large number of promoters in highly cell specific manner. This is the first study of CREM target promoters directly in a physiologically relevant tissue in vivo and represents the most comprehensive experimental analysis of CREB/CREM regulatory potential to date.
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Affiliation(s)
- Igor Martianov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, Illkirch, France
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Inhibition of heat shock protein 90 attenuates adenylate cyclase sensitization after chronic morphine treatment. Biochem Biophys Res Commun 2010; 392:603-7. [PMID: 20100459 DOI: 10.1016/j.bbrc.2010.01.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 01/18/2010] [Indexed: 01/10/2023]
Abstract
Cellular adaptations to chronic opioid treatment result in enhanced responsiveness of adenylate cyclase and an increase in forskolin- or agonist-stimulated cAMP production. It is, however, not known whether chaperone molecules such as heat shock proteins contribute to this adenylate cyclase sensitization. Here, we report that treatment of cells with geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), led to effective attenuation of morphine-induced adenylate cyclase sensitization. In SK-N-SH human neuroblastoma cells, morphine significantly increased RNA transcript and protein levels of type I adenylate cyclase, leading to sensitization. Whole-genome tiling array analysis revealed that cAMP response element-binding protein, an important mediator for cellular adaptation to morphine, associated with the proximal promoter of Hsp90AB1 not only in SK-N-SH cells but also in rat PC12 and human embryonic kidney cells. Hsp90AB1 transcript and protein levels increased significantly during morphine treatment, and co-application of geldanamycin (0.1-10 nM) effectively suppressed the increase in forskolin-activated adenylate cyclase activation by 56%. Type I adenylate cyclase, but not Hsp90AB1, underwent significant degradation during geldanamycin treatment. These results indicate that Hsp90 is a new pharmacological target for the suppression of adenylate cyclase sensitization induced by chronic morphine treatment.
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Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq. Methods Mol Biol 2010; 674:161-77. [PMID: 20827591 DOI: 10.1007/978-1-60761-854-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Localizing the binding sites of regulatory proteins is becoming increasingly feasible and accurate. This is due to dramatic progress not only in chromatin immunoprecipitation combined by next-generation sequencing (ChIP-seq) but also in advanced statistical analyses. A fundamental issue, however, is the alarming number of false positive predictions. This problem can be remedied by improved peak calling methods of twin peaks, one at each strand of the DNA, kernel density estimators, and false discovery rate estimations based on control libraries. Predictions are filtered by de novo motif discovery in the peak environments. These methods have been implemented in, among others, Valouev et al.'s Quantitative Enrichment of Sequence Tags (QuEST) software tool. We demonstrate the prediction of the human growth-associated binding protein (GABPalpha) based on ChIP-seq observations.
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Briand LA, Blendy JA. Molecular and genetic substrates linking stress and addiction. Brain Res 2009; 1314:219-34. [PMID: 19900417 DOI: 10.1016/j.brainres.2009.11.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 12/19/2022]
Abstract
Drug addiction is one of the top three health concerns in the United States in terms of economic and health care costs. Despite this, there are very few effective treatment options available. Therefore, understanding the causes and molecular mechanisms underlying the transition from casual drug use to compulsive drug addiction could aid in the development of treatment options. Studies in humans and animal models indicate that stress can lead to both vulnerability to develop addiction, and increased drug taking and relapse in addicted individuals. Exposure to stress or drugs of abuse results in long-term adaptations in the brain that are likely to involve persistent alterations in gene expression or activation of transcription factors, such as the cAMP Response Element Binding (CREB) protein. The signaling pathways controlled by CREB have been strongly implicated in drug addiction and stress. Many potential CREB target genes have been identified based on the presence of a CRE element in promoter DNA sequences. These include, but are not limited to CRF, BDNF, and dynorphin. These genes have been associated with initiation or reinstatement of drug reward and are altered in one direction or the other following stress. While many reviews have examined the interactions between stress and addiction, the goal of this review was to focus on specific molecules that play key roles in both stress and addiction and are therefore posed to mediate the interaction between the two. Focus on these molecules could provide us with new targets for pharmacological treatments for addiction.
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Affiliation(s)
- Lisa A Briand
- Department of Pharmacology, The University of Pennsylvania School of Medicine, TRL, 125 South 31(st) Street, USA
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Murakami M, Ito H, Hagiwara K, Yoshida K, Sobue S, Ichihara M, Takagi A, Kojima T, Tanaka K, Tamiya-Koizumi K, Kyogashima M, Suzuki M, Banno Y, Nozawa Y, Murate T. ATRA inhibits ceramide kinase transcription in a human neuroblastoma cell line, SH-SY5Y cells: the role of COUP-TFI. J Neurochem 2009; 112:511-20. [PMID: 19903244 DOI: 10.1111/j.1471-4159.2009.06486.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ceramide is the central lipid in the sphingolipid metabolism. Ceramide kinase (CERK) and its product, ceramide 1-phosphate, have been implicated in various cellular functions. However, the regulatory mechanism of CERK gene expression remains to be determined. Here, we examined CERK mRNA level during all-trans retinoic acid (ATRA)-induced differentiation of a human neuroblastoma cell line, SH-SY5Y. ATRA reduced CERK mRNA and protein levels. Over-expression and small interfering RNA (siRNA) of CERK revealed that CERK is inhibitory against ATRA-induced neuronal differentiation and cell growth arrest. ATRA inhibited the transcriptional activity of 5'-promoter of CERK. Truncation and mutation study suggests that ATRA-responsible region was mainly located in the tandem retinoic acid responsive elements (RARE) between -40 bp and the first exon. The electrophoresis mobility shift assay revealed that ATRA produced two retarded bands, which were erased by antibody against chicken ovalbumin upstream promoter transcription factor I (COUP-TFI), RARalpha, and RXRalpha, respectively. DNA pull-down assay confirmed increased binding of these transcription factors to RARE. Transient expression of RAR, RXR, and COUP-TFI and siRNA transfection of these genes revealed that COUP-TFI inhibited CERK mRNA. Furthermore, chromatin immunoprecipitation assay showed the recruitment of co-repressors as well as three transcription factors. These results suggest that COUP-TFI was the ATRA-responsive suppressive transcription factor of CERK gene transcription.
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Affiliation(s)
- Masashi Murakami
- Research Fellow of the Japanese Society for the Promotion of Sciences, Nagoya, Japan
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Hartzell DD, Trinklein ND, Mendez J, Murphy N, Aldred SF, Wood K, Urh M. A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays. BMC Genomics 2009; 10:497. [PMID: 19860899 PMCID: PMC2774331 DOI: 10.1186/1471-2164-10-497] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 10/27/2009] [Indexed: 01/30/2023] Open
Abstract
Background Regulation of gene expression is essential for normal development and cellular growth. Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays. To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells. Results In analysis of CREB genome-wide binding events using a comprehensive DNA microarray of human promoters, we observe for the first time that CREB has a strong preference for binding at bidirectional promoters and unlike unidirectional promoters, these binding events often occur downstream of transcription start sites. Comparison between HaloCHIP-chip and ChIP-chip data reveal this to be true for both methodologies, indicating it is not a bias of the technology chosen. Transcriptional data obtained from promoter-luciferase reporter arrays also show an unprecedented, high level of activation of CREB-bound promoters in the presence of the co-activator protein TORC1. Conclusion These data suggest for the first time that TORC1 provides directional information when CREB is bound at bidirectional promoters and possible pausing of the CREB protein after initial transcriptional activation. Also, this combined approach demonstrates the ability to more broadly characterize CREB protein-DNA interactions wherein not only DNA binding sites are discovered, but also the potential of the promoter sequence to respond to CREB is evaluated.
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Affiliation(s)
- Danette D Hartzell
- SwitchGear Genomics 1455 Adams Drive, Suite 1317, Menlo Park, CA 94025, USA.
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Makkonen KM, Malinen M, Ropponen A, Väisänen S, Carlberg C. Cell cycle regulatory effects of retinoic Acid and forskolin are mediated by the cyclin C gene. J Mol Biol 2009; 393:261-71. [PMID: 19683536 DOI: 10.1016/j.jmb.2009.08.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 11/22/2022]
Abstract
As a partner of cyclin-dependent kinase (CDK) 3, Cyclin C controls cellular proliferation and, together with CDK8, represses gene transcription. In this study, we showed that the highly expressed Cyclin C gene is a direct target of the nuclear hormone all-trans retinoic acid (RA) in HEK293 human embryonal kidney cells. The RA receptor (RAR) gamma associates with a Cyclin C promoter region containing two RAR binding sites. The Cyclin C gene also directly responds to the cAMP activator Forskolin via the transcription factor CREB1 (cAMP response element-binding protein 1), for which we identified four binding sites within the first 2250 bp of its promoter. RARgamma and CREB1 show functional convergence via the corepressor NCoR1, which controls in particular the Forskolin response of Cyclin C. The histone deacetylases 1, 5, 6, 7 and 11 are involved in the basal expression of Cyclin C, but in HEK293 and MCF-7 human breast carcinoma cells the antiproliferative effects of the histone deacetylase inhibitor SAHA (suberoylanilide hydroxamic acid) are not mediated by Cyclin C. However, cell cycle progressing effects of all-trans RA and Forskolin are dependent on Cyclin C expression levels. This suggests that the primary regulation of Cyclin C by all-trans RA and Forskolin mediates some of the cell cycle control actions of these compounds.
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Peng G, Han M, Du Y, Lin A, Yu L, Zhang Y, Jing N. SIP30 is regulated by ERK in peripheral nerve injury-induced neuropathic pain. J Biol Chem 2009; 284:30138-47. [PMID: 19723624 DOI: 10.1074/jbc.m109.036756] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
ERK plays an important role in chronic neuropathic pain. However, the underlying mechanism is largely unknown. Here we show that in chronic constriction injury-treated rat spinal cords, up-regulation of SIP30 (SNAP25-interacting protein 30), which is involved in the development and maintenance of chronic constriction injury-induced neuropathic pain, correlates with ERK activation and that the up-regulation of SIP30 is suppressed by intrathecal delivery of the MEK inhibitor U0126. In PC12 cells, up-regulation of SIP30 by nerve growth factor is also dependent on ERK activation. We found that there is an ERK-responsive region in the rat sip30 promoter. Activation of ERK promotes the recruitment of the transcription factor cyclic AMP-response element-binding protein to the sip30 gene promoter. Taken together, our results provide a potential downstream target of ERK activation-mediated neuropathic pain.
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Affiliation(s)
- Guangdun Peng
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Makkonen KM, Pasonen-Seppänen S, Törrönen K, Tammi MI, Carlberg C. Regulation of the hyaluronan synthase 2 gene by convergence in cyclic AMP response element-binding protein and retinoid acid receptor signaling. J Biol Chem 2009; 284:18270-81. [PMID: 19416972 PMCID: PMC2709342 DOI: 10.1074/jbc.m109.012492] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/23/2009] [Indexed: 01/22/2023] Open
Abstract
The human hyaluronan synthase 2 (HAS2) gene encodes for an enzyme making hyaluronan, altered concentrations of which are associated with many pathological situations including wounding, several inflammatory conditions, and malignant tumors. In this study we showed that HAS2 is a primary target of the cAMP activator forskolin and the nuclear hormone all-trans-retinoic acid (RA). The first 2250 bp of the promoter contain three response elements (REs) for the transcription factor CREB1 as well as two REs for the nuclear receptor RAR. Chromatin immunoprecipitation and re-chromatin immunoprecipitation assays using selected fragments of the promoter containing the putative REs showed that forskolin and all-trans-RA modulate the formation of complexes between CREB1 and RAR with various co-regulators at the predicted sites. Interestingly, CREB1 complexes are regulated by all-trans-RA as are RAR complexes by forskolin. Reporter gene assays using nested promoter fragments supported these findings. Forskolin and all-trans-RA co-stimulation reduced the binding of CREB1, RAR, and the co-repressor nuclear receptor co-repressor 1 (NCoR1), but enhanced the association of co-activators MED1 and CREB-binding protein (CBP). RNA interference experiments suggested that MED1 and NCoR1 are central for the all-trans-RA induction of the HAS2 gene and CBP dominates its forskolin response. In general, our findings suggest a convergence of CREB1 and RAR signaling, and demonstrate the individual character of each RE in terms of co-regulator use.
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Affiliation(s)
| | | | - Kari Törrönen
- Biomedicine, University of Kuopio, FIN-70211 Kuopio, Finland and
| | - Markku I. Tammi
- Biomedicine, University of Kuopio, FIN-70211 Kuopio, Finland and
| | - Carsten Carlberg
- From the Departments of Bioscience and
- the Life Sciences Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
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Jancic D, Lopez de Armentia M, Valor LM, Olivares R, Barco A. Inhibition of cAMP response element-binding protein reduces neuronal excitability and plasticity, and triggers neurodegeneration. ACTA ACUST UNITED AC 2009; 19:2535-47. [PMID: 19213815 DOI: 10.1093/cercor/bhp004] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The cAMP-responsive element-binding protein (CREB) pathway has been involved in 2 major cascades of gene expression regulating neuronal function. The first one presents CREB as a critical component of the molecular switch that controls long-lasting forms of neuronal plasticity and learning. The second one relates CREB to neuronal survival and protection. To investigate the role of CREB-dependent gene expression in neuronal plasticity and survival in vivo, we generated bitransgenic mice expressing A-CREB, an artificial peptide with strong and broad inhibitory effect on the CREB family, in forebrain neurons in a regulatable manner. The expression of A-CREB in hippocampal neurons impaired L-LTP, reduced intrinsic excitability and the susceptibility to induced seizures, and altered both basal and activity-driven gene expression. In the long-term, the chronic inhibition of CREB function caused severe loss of neurons in the CA1 subfield as well as in other brain regions. Our experiments confirmed previous findings in CREB-deficient mutants and revealed new aspects of CREB-dependent gene expression in the hippocampus supporting a dual role for CREB-dependent gene expression regulating intrinsic and synaptic plasticity and promoting neuronal survival.
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Affiliation(s)
- Dragana Jancic
- Instituto de Neurociencias de Alicante (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Campus de Sant Joan, 03550 Alicante, Spain
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Affiliation(s)
- Sebastian J Maerkl
- Ecole Polytechnique Fédérale de Lausanne, Institute of Bioengineering, Switzerland.
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Louro R, Smirnova AS, Verjovski-Almeida S. Long intronic noncoding RNA transcription: expression noise or expression choice? Genomics 2008; 93:291-8. [PMID: 19071207 DOI: 10.1016/j.ygeno.2008.11.009] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 11/16/2008] [Indexed: 02/07/2023]
Abstract
Recently, it was discovered that non-protein-coding RNAs (ncRNAs) represent the majority of the human transcripts. Regulatory role of many classes of ncRNAs is broadly recognized; however, long intronic ncRNAs have received little attention. In the past few years, evidence that intronic regions are key sources of regulatory ncRNAs has first appeared. Here we present an updated vision of the intronic ncRNA world, giving special attention to the long intronic ncRNAs. We summarize aspects of their expression pattern, evolutionary constraints, biogenesis, and responsiveness to physiological stimuli, and postulate their mechanisms of action. Deciphering nature's choice of different types of messages conveyed by ncRNAs will shed light on the RNA-based layer of regulatory processes in eukaryotic cells.
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Affiliation(s)
- Rodrigo Louro
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
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Lalonde J, Lachance PED, Chaudhuri A. Developmental and activity-dependent genomic occupancy profiles of CREB in monkey area V1. GENES BRAIN AND BEHAVIOR 2008; 8:149-60. [PMID: 19016891 DOI: 10.1111/j.1601-183x.2008.00450.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mammalian neocortex displays significant plastic rearrangement in response to altered sensory input, especially during early postnatal development. It is believed that cyclic AMP-response element-binding (CREB) plays an important role in orchestrating the molecular events that guide neuroplastic change, although the details of its genomic targets during normal postnatal development or in response to sensory deprivation remain unknown. Here, we performed CREB chromatin immunoprecipitation (ChIP) from monkey area V1 tissue and hybridized enriched DNA fragments to promoter microarrays (ChIP chip analysis). Our goal was to determine and categorize the CREB regulon in monkey area V1 at two distinct developmental stages (peak of critical period vs. adulthood) and after 5 days of monocular enucleation (ME) at both ages. Classification of enriched candidates showed that the majority of isolated promoter loci (n = 795) were common to all four conditions. A particularly interesting group of candidates (n = 192) was specific to samples derived from enucleated infant area V1. Gene ontology analysis of CREB targets during early postnatal development showed a subgroup of genes implicated in cytoskeleton-based structural modification. Analysis of messenger RNA expression (quantitative real-time-polymerase chain reaction) of candidate genes showed striking differences in expression profiles between infant and adult area V1 after ME. Our study represents the first extensive genomic analysis of CREB DNA occupancy in monkey neocortex and provides new insight into the multifaceted transcriptional role of CREB in guiding neuroplastic change.
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Affiliation(s)
- J Lalonde
- Department of Psychology, McGill University, Québec, Canada.
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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Gaffney DJ, Blekhman R, Majewski J. Selective constraints in experimentally defined primate regulatory regions. PLoS Genet 2008; 4:e1000157. [PMID: 18704158 PMCID: PMC2490716 DOI: 10.1371/journal.pgen.1000157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 07/09/2008] [Indexed: 11/18/2022] Open
Abstract
Changes in gene regulation may be important in evolution. However, the evolutionary properties of regulatory mutations are currently poorly understood. This is partly the result of an incomplete annotation of functional regulatory DNA in many species. For example, transcription factor binding sites (TFBSs), a major component of eukaryotic regulatory architecture, are typically short, degenerate, and therefore difficult to differentiate from randomly occurring, nonfunctional sequences. Furthermore, although sites such as TFBSs can be computationally predicted using evolutionary conservation as a criterion, estimates of the true level of selective constraint (defined as the fraction of strongly deleterious mutations occurring at a locus) in regulatory regions will, by definition, be upwardly biased in datasets that are a priori evolutionarily conserved. Here we investigate the fitness effects of regulatory mutations using two complementary datasets of human TFBSs that are likely to be relatively free of ascertainment bias with respect to evolutionary conservation but, importantly, are supported by experimental data. The first is a collection of almost >2,100 human TFBSs drawn from the literature in the TRANSFAC database, and the second is derived from several recent high-throughput chromatin immunoprecipitation coupled with genomic microarray (ChIP-chip) analyses. We also define a set of putative cis-regulatory modules (pCRMs) by spatially clustering multiple TFBSs that regulate the same gene. We find that a relatively high proportion ( approximately 37%) of mutations at TFBSs are strongly deleterious, similar to that at a 2-fold degenerate protein-coding site. However, constraint is significantly reduced in human and chimpanzee pCRMS and ChIP-chip sequences, relative to macaques. We estimate that the fraction of regulatory mutations that have been driven to fixation by positive selection in humans is not significantly different from zero. We also find that the level of selective constraint in our TFBSs, pCRMs, and ChIP-chip sequences is negatively correlated with the expression breadth of the regulated gene, whereas the opposite relationship holds at that gene's nonsynonymous and synonymous sites. Finally, we find that the rate of protein evolution in a transcription factor appears to be positively correlated with the breadth of expression of the gene it regulates. Our study suggests that strongly deleterious regulatory mutations are considerably more likely (1.6-fold) to occur in tissue-specific than in housekeeping genes, implying that there is a fitness cost to increasing "complexity" of gene expression.
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