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Mihara N, Imai K. Suppression of Krüppel-like factor 5 basal expression by CREB1 binding to far distal element. Tumour Biol 2023; 45:81-94. [PMID: 37694332 DOI: 10.3233/tub-230017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Krüppel-like factor 5 (KLF5) is a transcription factor regulating the proliferation and differentiation of epithelial cells, and its uncontrolled expression is closely associated with carcinoma progression. Sp3 binding to the minimal essential region (MER) of KLF5 gene is critical for KLF5 basal expression, but the expression control mechanism is unknown. OBJECTIVE This study aimed to identify a regulatory region for KLF5 basal expression and the binding protein in carcinoma cells by analyzing the promoter upstream region. METHODS Reporter assays determined the silencer region. The protein binding to the region was identified by database analysis and ChIP assay. The protein mediating the interaction between the region and the MER was confirmed through chromosome conformation capture (3 C) on ChIP assay. The effects of the protein on KLF5 expression were analyzed using qRT-PCR and western blot. RESULTS Reporter assay localized the 425-region from upstream KLF5 gene as the silencer. Database analysis and ChIP assay found CREB1 binding to the 425-region. CREB1 siRNA or mutation of CREB1-binding site in the 425-region increased luciferase activities and decreased the binding to 425-region. 3 C on ChIP assay showed that CREB1 mediated interaction of the 425-region and the MER. CREB1 overexpression decreased endogenous KLF5 expression and luciferase activity. CONCLUSIONS The 425-region is the silencer of KLF5 basal expression, and CREB1 binding suppresses the expression.
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Affiliation(s)
- Nozomi Mihara
- Department of Biochemistry, The Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan
| | - Kazushi Imai
- Department of Biochemistry, The Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan
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2
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Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells. BMC Genomics 2021; 22:901. [PMID: 34915843 PMCID: PMC8675486 DOI: 10.1186/s12864-021-08224-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Satellite cells are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify enhancers and transcription factors that regulate gene expression during the differentiation of bovine satellite cells into myotubes. RESULTS Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) was performed to identify genomic regions where lysine 27 of H3 histone is acetylated (H3K27ac), i.e., active enhancers, from bovine satellite cells before and during differentiation into myotubes. A total of 19,027 and 47,669 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively. Of these enhancers, 5882 were specific to before-differentiation, 35,723 to during-differentiation, and 13,199 common to before- and during-differentiation bovine satellite cells. Whereas most of the before- or during-differentiation-specific H3K27ac-marked enhancers were located distally to the transcription start site, the enhancers common to before- and during-differentiation were located both distally and proximally to the transcription start site. The three sets of H3K27ac-marked enhancers were associated with functionally different genes and enriched with different transcription factor binding sites. Specifically, many of the H3K27ac-marked enhancers specific to during-differentiation bovine satellite cells were associated with genes involved in muscle structure and development, and were enriched with binding sites for the MyoD, AP-1, KLF, TEAD, and MEF2 families of transcription factors. A positive role was validated for Fos and FosB, two AP-1 family transcription factors, in the differentiation of bovine satellite cells into myotubes by siRNA-mediated knockdown. CONCLUSIONS Tens of thousands of H3K27ac-marked active enhancers have been identified from bovine satellite cells before or during differentiation. These enhancers contain binding sites not only for transcription factors whose role in satellite cell differentiation is well known but also for transcription factors whose role in satellite cell differentiation is unknown. These enhancers and transcription factors are valuable resources for understanding the complex mechanism that mediates gene expression during satellite cell differentiation. Because satellite cell differentiation is a key step in skeletal muscle growth, the enhancers, the transcription factors, and their target genes identified in this study are also valuable resources for identifying and interpreting skeletal muscle trait-associated DNA variants in cattle.
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3
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Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin. Nat Genet 2021; 53:1177-1186. [PMID: 34341563 PMCID: PMC8610173 DOI: 10.1038/s41588-021-00904-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 06/25/2021] [Indexed: 11/30/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) ameliorates β-hemoglobinopathies by inhibiting the developmental switch from γ-globin (HBG1/HBG2) to β-globin (HBB) gene expression. Some forms of HPFH are associated with γ-globin promoter variants that either disrupt binding motifs for transcriptional repressors or create new motifs for transcriptional activators. How these variants sustain γ-globin gene expression postnatally remains undefined. We mapped γ-globin promoter sequences functionally in erythroid cells harboring different HPFH variants. Those that disrupt a BCL11A repressor binding element induce γ-globin expression by facilitating the recruitment of transcription factors NF-Y to a nearby proximal CCAAT box and GATA1 to an upstream motif. The proximal CCAAT element becomes dispensable for HPFH variants that generate new binding motifs for activators NF-Y or KLF1, but GATA1 recruitment remains essential. Our findings define distinct mechanisms through which transcription factors and their cis-regulatory elements activate γ-globin expression in different forms of HPFH, some of which are being recreated by therapeutic genome editing.
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4
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Folding Keratin Gene Clusters during Skin Regional Specification. Dev Cell 2021; 53:561-576.e9. [PMID: 32516596 DOI: 10.1016/j.devcel.2020.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023]
Abstract
Regional specification is critical for skin development, regeneration, and evolution. The contribution of epigenetics in this process remains unknown. Here, using avian epidermis, we find two major strategies regulate β-keratin gene clusters. (1) Over the body, macro-regional specificities (scales, feathers, claws, etc.) established by typical enhancers control five subclusters located within the epidermal differentiation complex on chromosome 25; (2) within a feather, micro-regional specificities are orchestrated by temporospatial chromatin looping of the feather β-keratin gene cluster on chromosome 27. Analyses suggest a three-factor model for regional specification: competence factors (e.g., AP1) make chromatin accessible, regional specifiers (e.g., Zic1) target specific genome regions, and chromatin regulators (e.g., CTCF and SATBs) establish looping configurations. Gene perturbations disrupt morphogenesis and histo-differentiation. This chicken skin paradigm advances our understanding of how regulation of big gene clusters can set up a two-dimensional body surface map.
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5
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Beekly BG, Frankel WC, Berg T, Allen SJ, Garcia-Galiano D, Vanini G, Elias CF. Dissociated Pmch and Cre Expression in Lactating Pmch-Cre BAC Transgenic Mice. Front Neuroanat 2020; 14:60. [PMID: 32982701 PMCID: PMC7475711 DOI: 10.3389/fnana.2020.00060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
The melanin-concentrating hormone (MCH) system plays a role in many physiological processes including reproduction and lactation. However, research regarding the function of MCH on different aspects of the reproductive function lags, due in part to a lack of validated genetic models with which to interrogate the system. This is particularly true in the case of female reproduction, as the anatomy and function of the MCH system is not well-characterized in the female mouse. We set out to determine whether the commercially available Pmch-Cre transgenic mouse line is a viable model to study the role of MCH neurons in distinct female reproductive states. We found that Pmch is transiently expressed in several nuclei of the rostral forebrain at the end of lactation. This includes the medial subdivision of the medial preoptic nucleus, the paraventricular nucleus of the hypothalamus, the ventral subdivision of the lateral septum, the anterodorsal preoptic nucleus and the anterodorsal nucleus of the thalamus. The Pmch expression in these sites, however, does not reliably induce Cre expression in the Pmch-Cre (BAC) transgenic mouse, making this line an inadequate model with which to study the role of MCH in behavioral and/or neuroendocrine adaptations of lactation. We also contribute to the general knowledge of the anatomy of the murine MCH system by showing that lactation-induced Pmch expression in the rostral forebrain is mostly observed in GABAergic (VGAT) neurons, in contrast to the typical MCH neurons of the tuberal and posterior hypothalamus which are glutamatergic (VGLUT2).
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Affiliation(s)
- Bethany G Beekly
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
| | - William C Frankel
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States.,Baylor College of Medicine, Houston, TX, United States
| | - Tova Berg
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Susan J Allen
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - David Garcia-Galiano
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Giancarlo Vanini
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States.,Department of Anesthesiology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Carol F Elias
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States.,Department of Obstetrics and Gynecology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
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6
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Karim MM, Dakouri A, Zhang Y, Chen Q, Peng G, Strelkov SE, Gossen BD, Yu F. Two Clubroot-Resistance Genes, Rcr3 and Rcr9wa, Mapped in Brassica rapa Using Bulk Segregant RNA Sequencing. Int J Mol Sci 2020; 21:ijms21145033. [PMID: 32708772 PMCID: PMC7404267 DOI: 10.3390/ijms21145033] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/24/2022] Open
Abstract
Genetic resistance is widely used to manage clubroot (Plasmodiophora brassicae) in brassica crops, but new pathotypes have recently been identified on canola (Brassica napus) on the Canadian prairies. Resistance effective against both the most prevalent pathotype (3H, based on the Canadian Clubroot Differential system) and the new pathotypes is needed. BC1 plants of Brassica rapa from a cross of line 96-6990-2 (clubroot resistance originating from turnip cultivar ‘Waaslander’) and a susceptible doubled-haploid line, ACDC, exhibited a 1:1 segregation for resistance against pathotypes 3H and 5X. A resistance gene designated as Rcr3 was mapped initially based on the percentage of polymorphic variants using bulked segregant RNA sequencing (BSR-Seq) and further mapped using Kompetitive Allele Specific PCR. DNA variants were identified by assembling short reads against a reference genome of B. rapa. Rcr3 was mapped into chromosome A08. It was flanked by single nucleotide polymorphisms (SNP) markers (A90_A08_SNP_M12 and M16) between 10.00 and 10.23 Mb, in an interval of 231.6 Kb. There were 32 genes in the Rcr3 interval. Three genes (Bra020951, Bra020974, and Bra020979) were annotated with disease resistance mechanisms, which are potential candidates for Rcr3. Another resistance gene, designated as Rcr9wa, for resistance to pathotype 5X was mapped, with the flanking markers (A90_A08_SNP_M28 and M79) between 10.85 and 11.17 Mb using the SNP sites identified through BSR-Seq for Rcr3. There were 44 genes in the Rcr9wa interval, three of which (Bra020827, Bra020828, Bra020814) were annotated as immune-system-process related genes, which are potential candidates for Rcr9wa.
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Affiliation(s)
- Md. Masud Karim
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Abdulsalam Dakouri
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Yan Zhang
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Qilin Chen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Gary Peng
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Bruce D. Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
- Correspondence:
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7
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Pascual-Garcia P, Capelson M. Nuclear pores in genome architecture and enhancer function. Curr Opin Cell Biol 2019; 58:126-133. [PMID: 31063899 DOI: 10.1016/j.ceb.2019.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 01/28/2023]
Abstract
Nuclear genome architecture relies on interactions between the genome and various nuclear scaffolds. One such a nuclear scaffold is the nuclear pore complex (NPC), which in addition to its nuclear transport function, can interact with underlying chromatin. In particular, NPCs have been recently reported to associate with a number of enhancers and superenhancers in metazoan genomes, and select NPC components have been shown to promote the formation of specific genomic loops. Here, we provide a brief overview of current models of enhancer function, and discuss recent evidence that NPCs bind enhancers and contribute to topological genome organization. We also examine possible models of how gene and enhancer targeting to NPCs may contribute to tissue-specific genome architecture and expression programs, including the possibility that NPCs may promote phase separation of transcriptional compartments.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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8
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Application of droplet digital PCR in the analysis of genome integration and organization of the transgene in BAC transgenic mice. Sci Rep 2018; 8:6638. [PMID: 29703985 PMCID: PMC5923295 DOI: 10.1038/s41598-018-25001-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 04/13/2018] [Indexed: 12/16/2022] Open
Abstract
Transgenic (Tg) mice containing bacterial artificial chromosome (BAC) DNA are widely used for gene expression analysis and gene therapy models because BAC transgenes provide gene expression at physiological levels with the same developmental timing as endogenous genes. To ensure correct interpretation of transgene functions, investigation of the genomic organisation and integration of the BAC transgene is required. Here, we describe a reliable method based on droplet digital PCR (ddPCR) and inverse PCR to estimate copy number, genomic organisation and insertion sites of BAC transgenes in the mouse genome. We generated BAC Tg mice containing fragments of BAC clone RP23-59P20. ddPCR and iPCR analysis showed that the transgene consisted of five fragments of the BAC clone containing the Mkrn3 gene region, and that the transgene was inserted into Bckdhb, homozygous deletion of which causes the maple syrup urine disease phenotype. The ddPCR method described here should prove useful for analysis of genomic organisation and integration of BAC transgenes.
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9
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Messemaker TC, van Leeuwen SM, van den Berg PR, 't Jong AEJ, Palstra RJ, Hoeben RC, Semrau S, Mikkers HMM. Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot. Sci Rep 2018; 8:386. [PMID: 29321583 PMCID: PMC5762901 DOI: 10.1038/s41598-017-18649-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. This gatekeeper function requires well-regulated Sox2 levels. We postulated that Sox2 regulation is partially controlled by the Sox2 overlapping long non-coding RNA (lncRNA) gene Sox2ot. Here we show that the RNA levels of Sox2ot and Sox2 are inversely correlated during neural differentiation of mouse embryonic stem cells (ESCs). Through allele-specific enhanced transcription of Sox2ot in mouse Sox2eGFP knockin ESCs we demonstrate that increased Sox2ot transcriptional activity reduces Sox2 RNA levels in an allele-specific manner. Enhanced Sox2ot transcription, yielding lower Sox2 RNA levels, correlates with a decreased chromatin interaction of the upstream regulatory sequence of Sox2 and the ESC-specific Sox2 super enhancer. Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development.
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Affiliation(s)
- Tobias C Messemaker
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Selina M van Leeuwen
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | | | - Anke E J 't Jong
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee634, 3000CA, Rotterdam, The Netherlands
| | - Rob C Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, 2333 RA, Leiden, The Netherlands
| | - Harald M M Mikkers
- Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.
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10
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Huang L, Liu P, Yuan Z, Zhou T, Yu J. The free-energy cost of interaction between DNA loops. Sci Rep 2017; 7:12610. [PMID: 28974770 PMCID: PMC5626758 DOI: 10.1038/s41598-017-12765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
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Affiliation(s)
- Lifang Huang
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Peijiang Liu
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Zhanjiang Yuan
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China.
| | - Jianshe Yu
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China.
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11
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Affiliation(s)
- Frédéric B Piel
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
| | - Martin H Steinberg
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
| | - David C Rees
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
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12
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Vathipadiekal V, Alsultan A, Baltrusaitis K, Farrell JJ, Al-Rubaish AM, Al-Muhanna F, Naserullah Z, Suliman A, Patra P, Milton JN, Farrer LA, Chui DH, Al-Ali AK, Sebastiani P, Steinberg MH. Homozygosity for a haplotype in the HBG2-OR51B4 region is exclusive to Arab-Indian haplotype sickle cell anemia. Am J Hematol 2016; 91:E308-11. [PMID: 27185208 DOI: 10.1002/ajh.24368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Vinod Vathipadiekal
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics; College of Medicine, King Saud University; Riyadh Saudi Arabia
| | - Kristin Baltrusaitis
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - John J. Farrell
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdullah M. Al-Rubaish
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Zaki Naserullah
- Alomran Scientific Chair for Hematological Diseases, King Faisal University, King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
- Department of Pediatrics, Maternity & Child Hospital; Dammam Kingdom of Saudi Arabia
| | - Ahmed Suliman
- Alomran Scientific Chair; King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
| | - P.K. Patra
- Department of Biochemistry; Pt. J.N.M. Medical College; Raipur Chhattisgarh India
| | - Jacqueline N. Milton
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - David H.K. Chui
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Amein K. Al-Ali
- Center for Research & Medical Consultation; University of Dammam; Dammam Saudi Arabia
| | - Paola Sebastiani
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Martin. H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
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13
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Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
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Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
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Yoneda R, Satoh Y, Yoshida I, Kawamura S, Kotani T, Kimura AP. A genomic region transcribed into a long noncoding RNA interacts with thePrss42/Tessp-2promoter in spermatocytes during mouse spermatogenesis, and its flanking sequences can function as enhancers. Mol Reprod Dev 2016; 83:541-57. [DOI: 10.1002/mrd.22650] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 04/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Ryoma Yoneda
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
| | - Yui Satoh
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
| | - Ikuya Yoshida
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
- Faculty of Science; Department of Biological Sciences; Hokkaido University; Sapporo Japan
| | - Shohei Kawamura
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
| | - Tomoya Kotani
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
- Faculty of Science; Department of Biological Sciences; Hokkaido University; Sapporo Japan
| | - Atsushi P. Kimura
- Graduate School of Life Science; Hokkaido University; Sapporo Japan
- Faculty of Science; Department of Biological Sciences; Hokkaido University; Sapporo Japan
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15
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Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
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Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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16
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Betts Z, Dickson AJ. Ubiquitous Chromatin Opening Elements (UCOEs) effect on transgene position and expression stability in CHO cells following methotrexate (MTX) amplification. Biotechnol J 2016; 11:554-64. [DOI: 10.1002/biot.201500159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/30/2015] [Accepted: 12/02/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Zeynep Betts
- The University of Manchester, Faculty of Life Sciences, Michael Smith Building; Manchester United Kingdom
| | - Alan J. Dickson
- The University of Manchester, Faculty of Life Sciences, Michael Smith Building; Manchester United Kingdom
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17
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Barr CL, Misener VL. Decoding the non-coding genome: elucidating genetic risk outside the coding genome. GENES, BRAIN, AND BEHAVIOR 2016; 15:187-204. [PMID: 26515765 PMCID: PMC4833497 DOI: 10.1111/gbb.12269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders.
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Affiliation(s)
- C. L. Barr
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - V. L. Misener
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
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18
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Mora A, Sandve GK, Gabrielsen OS, Eskeland R. In the loop: promoter-enhancer interactions and bioinformatics. Brief Bioinform 2015; 17:980-995. [PMID: 26586731 PMCID: PMC5142009 DOI: 10.1093/bib/bbv097] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/26/2015] [Indexed: 12/17/2022] Open
Abstract
Enhancer-promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter-enhancer interactions (PEIs). In the recent years, genome-wide analyses have identified signatures and mapped novel enhancers; however, being able to precisely identify their target gene(s) requires massive biological and bioinformatics efforts. In this review, we give a short overview of the chromatin landscape and transcriptional regulation. We discuss some key concepts and problems related to chromatin interaction detection technologies, and emerging knowledge from genome-wide chromatin interaction data sets. Then, we critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction. Lastly, we provide specific examples of how PEIs have been used to elucidate a functional role of non-coding single-nucleotide polymorphisms. The topic is at the forefront of epigenetic research, and by highlighting some future bioinformatics challenges in the field, this review provides a comprehensive background for future PEI studies.
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19
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Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:169-85. [PMID: 26558551 DOI: 10.1002/wdev.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Abstract
During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Hörnblad
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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20
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Douglas AT, Hill RD. Variation in vertebrate cis-regulatory elements in evolution and disease. Transcription 2015; 5:e28848. [PMID: 25764334 DOI: 10.4161/trns.28848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. Recent advances support this notion and show that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease.
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Affiliation(s)
- Adam Thomas Douglas
- a MRC Human Genetics Unit; MRC Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh, UK
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21
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Patrushev LI, Kovalenko TF. Functions of noncoding sequences in mammalian genomes. BIOCHEMISTRY (MOSCOW) 2015; 79:1442-69. [PMID: 25749159 DOI: 10.1134/s0006297914130021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Most of the mammalian genome consists of nucleotide sequences not coding for proteins. Exons of genes make up only 3% of the human genome, while the significance of most other sequences remains unknown. Recent genome studies with high-throughput methods demonstrate that the so-called noncoding part of the genome may perform important functions. This hypothesis is supported by three groups of experimental data: 1) approximately 10% of the sequences, most of which are located in noncoding parts of the genome, is evolutionarily conserved and thus can be of functional importance; 2) up to 99% of the mammalian genome is being transcribed forming short and long noncoding RNAs in addition to common mRNA; and 3) mutations in noncoding parts of the genome can be accompanied by progression of pathological states of the organism. In the light of these data, in the review we consider the functional role of numerous known sequences of noncoding parts of the genome including introns, DNA methylation regions, enhancers and locus control regions, insulators, S/MAR sequences, pseudogenes, and genes of noncoding RNAs, as well as transposons and simple repeats of centromeric and telomeric regions of chromosomes. The assumption is made that the intergenic noncoding sequences without definite/clear functions can be involved in spatial organization of genetic loci in interphase nuclei.
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Affiliation(s)
- L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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22
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Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status. Biomaterials 2015; 70:12-22. [PMID: 26295435 DOI: 10.1016/j.biomaterials.2015.08.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/20/2022]
Abstract
Silver nanoparticles (nanosilver, AgNPs) have been shown to induce toxicity in vitro and in vivo; however, the molecular bases underlying the detrimental effects have not been thoroughly understood. Although there are numerous studies on its genotoxicity, only a few studies have investigated the epigenetic changes, even less on the changes of histone modifications by AgNPs. In the current study, we probed the AgNP-induced alterations to histone methylation that could be responsible for globin reduction in erythroid cells. AgNP treatment caused a significant reduction of global methylation level for histone 3 (H3) in erythroid MEL cells at sublethal concentrations, devoid of oxidative stress. The ChIP-PCR analyses demonstrated that methylation of H3 at lysine (Lys) 4 (H3K4) and Lys 79 (H3K79) on the β-globin locus was greatly reduced. The reduction in methylation could be attributed to decreased histone methyltransferase DOT-1L and MLL levels as well as the direct binding between AgNPs to H3/H4 that provide steric hindrance to prevent methylation as predicted by the all-atom molecular dynamics simulations. This direct interaction was further proved by AgNP-mediated pull-down assay and immunoprecipitation assay. These changes, together with decreased RNA polymerase II activity and chromatin binding at this locus, resulted in decreased hemoglobin production. By contrast, Ag ion-treated cells showed no alterations in histone methylation level. Taken together, these results showed a novel finding in which AgNPs could alter the methylation status of histone. Our study therefore opens a new avenue to study the biological effects of AgNPs at sublethal concentrations from the perspective of epigenetic mechanisms.
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23
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Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization. Mol Cell Biol 2015; 35:3504-16. [PMID: 26240285 DOI: 10.1128/mcb.00514-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/24/2015] [Indexed: 01/07/2023] Open
Abstract
Developmental stage-specific enhancer-promoter-insulator interactions regulate the chromatin configuration necessary for transcription at various loci and additionally for VDJ recombination at antigen receptor loci that encode immunoglobulins and T-cell receptors. To investigate these regulatory interactions, we analyzed the epigenetic landscape of the murine T-cell receptor β (TCRβ) locus in the presence and absence of an ectopic CTCF-dependent enhancer-blocking insulator, H19-ICR, in genetically manipulated mice. Our analysis demonstrated the ability of the H19-ICR insulator to restrict several aspects of enhancer-based chromatin alterations that are observed during activation of the TCRβ locus for transcription and recombination. The H19-ICR insulator abrogated enhancer-promoter contact-dependent chromatin alterations and additionally prevented Eβ-mediated histone modifications that have been suggested to be independent of enhancer-promoter interaction. Observed enhancer-promoter-insulator interactions, in conjunction with the chromatin structure of the Eβ-regulated domain at the nucleosomal level, provide useful insights regarding the activity of the regulatory elements in addition to supporting the accessibility hypothesis of VDJ recombination. Analysis of H19-ICR in the heterologous context of the developmentally regulated TCRβ locus suggests that different mechanisms proposed for CTCF-dependent insulator action might be manifested simultaneously or selectively depending on the genomic context and the nature of enhancer activity being curtailed.
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24
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Betts Z, Dickson AJ. Assessment of UCOE on Recombinant EPO Production and Expression Stability in Amplified Chinese Hamster Ovary Cells. Mol Biotechnol 2015; 57:846-58. [DOI: 10.1007/s12033-015-9877-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Res 2015; 43:W264-9. [PMID: 25916854 PMCID: PMC4489297 DOI: 10.1093/nar/gkv398] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/15/2015] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cis-regulatory elements form a complex gene transcription apparatus. Our previous work, ChIP-Array, combined TF binding and transcriptome data to construct gene regulatory networks (GRNs). Here we present an enhanced version, ChIP-Array 2, to integrate additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components. Moreover, we substantially extended our motif database for human, mouse, rat, fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select as input or backend support. With ChIP-Array 2, we compiled a library containing regulatory networks of 18 TFs/chromatin modifiers in mouse embryonic stem cell (mESC). The web server and the mESC library are publicly free and accessible athttp://jjwanglab.org/chip-array.
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Affiliation(s)
- Panwen Wang
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
| | - Jing Qin
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
| | - Yiming Qin
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yun Zhu
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
| | - Lily Yan Wang
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
| | - Mulin Jun Li
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
| | - Michael Q Zhang
- Bioinformatics Division, TNLIST, Tsinghua University, Beijing 100084, China Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Dallas, TX 75080, USA
| | - Junwen Wang
- Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, China
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26
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Moleirinho A, Lopes AM, Seixas S, Morales-Hojas R, Prata MJ, Amorim A. Distinctive patterns of evolution of the δ-globin gene (HBD) in primates. PLoS One 2015; 10:e0123365. [PMID: 25853817 PMCID: PMC4390247 DOI: 10.1371/journal.pone.0123365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
In most vertebrates, hemoglobin (Hb) is a heterotetramer composed of two dissimilar globin chains, which change during development according to the patterns of expression of α- and β-globin family members. In placental mammals, the β-globin cluster includes three early-expressed genes, ε(HBE)-γ(HBG)-ψβ(HBBP1), and the late expressed genes, δ (HBD) and β (HBB). While HBB encodes the major adult β-globin chain, HBD is weakly expressed or totally silent. Paradoxically, in human populations HBD shows high levels of conservation typical of genes under strong evolutionary constraints, possibly due to a regulatory role in the fetal-to-adult switch unique of Anthropoid primates. In this study, we have performed a comprehensive phylogenetic and comparative analysis of the two adult β-like globin genes in a set of diverse mammalian taxa, focusing on the evolution and functional divergence of HBD in primates. Our analysis revealed that anthropoids are an exception to a general pattern of concerted evolution in placental mammals, showing a high level of sequence conservation at HBD, less frequent and shorter gene conversion events. Moreover, this lineage is unique in the retention of a functional GATA-1 motif, known to be involved in the control of the developmental expression of the β-like globin genes. We further show that not only the mode but also the rate of evolution of the δ-globin gene in higher primates are strictly associated with the fetal/adult β-cluster developmental switch. To gain further insight into the possible functional constraints that have been shaping the evolutionary history of HBD in primates, we calculated dN/dS (ω) ratios under alternative models of gene evolution. Although our results indicate that HBD might have experienced different selective pressures throughout primate evolution, as shown by different ω values between apes and Old World Monkeys + New World Monkeys (0.06 versus 0.43, respectively), these estimates corroborated a constrained evolution for HBD in Anthropoid lineages, which is unlikely to be related to protein function. Collectively, these findings suggest that sequence change at the δ-globin gene has been under strong selective constraints over 65 Myr of primate evolution, likely due to a regulatory role in ontogenic switches of gene expression.
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Affiliation(s)
- Ana Moleirinho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail:
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ramiro Morales-Hojas
- Genetics and Genomics Group, The Pirbright Institute, Compton Laboratory, Compton, Berkshire, United Kingdom
| | - Maria J. Prata
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Betts Z, Croxford AS, Dickson AJ. Evaluating the interaction between UCOE and DHFR-linked amplification and stability of recombinant protein expression. Biotechnol Prog 2015; 31:1014-25. [DOI: 10.1002/btpr.2083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/17/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Zeynep Betts
- Faculty of Life Sciences; University of Manchester; Michael Smith Building, Oxford Road Manchester M13 9PT UK
| | - Alexandra S Croxford
- Faculty of Life Sciences; University of Manchester; Michael Smith Building, Oxford Road Manchester M13 9PT UK
| | - Alan J Dickson
- Faculty of Life Sciences; University of Manchester; Michael Smith Building, Oxford Road Manchester M13 9PT UK
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28
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Acquired alterations of hypothalamic gene expression of insulin and leptin receptors and glucose transporters in prenatally high-glucose exposed three-week old chickens do not coincide with aberrant promoter DNA methylation. PLoS One 2015; 10:e0119213. [PMID: 25811618 PMCID: PMC4374847 DOI: 10.1371/journal.pone.0119213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/20/2015] [Indexed: 12/03/2022] Open
Abstract
Background Prenatal exposures may have a distinct impact for long-term health, one example being exposure to maternal ‘diabesity’ during pregnancy increasing offspring ‘diabesity’ risk. Malprogramming of the central nervous regulation of body weight, food intake and metabolism has been identified as a critical mechanism. While concrete disrupting factors still remain unclear, growing focus on acquired epigenomic alterations have been proposed. Due to the independent development from the mother, the chicken embryo provides a valuable model to distinctively establish causal factors and mechanisms. Aim The aim of this study was to determine the effects of prenatal hyperglycemia on postnatal hypothalamic gene expression and promoter DNA methylation in the chicken. Methods and Findings To temporarily induce high-glucose exposure in chicken embryos, 0.5 ml glucose solution (30 mmol/l) were administered daily via catheter into a vessel of the chorioallantoic egg membrane from days 14 to 17 of incubation. At three weeks of postnatal age, body weight, total body fat, blood glucose, mRNA expression (INSR, LEPR, GLUT1, GLUT3) as well as corresponding promoter DNA methylation were determined in mediobasal hypothalamic brain slices (Nucleus infundibuli hypothalami). Although no significant changes in morphometric and metabolic parameters were detected, strongly decreased mRNA expression occurred in all candidate genes. Surprisingly, however, no relevant alterations were observed in respective promoter methylation. Conclusion Prenatal hyperglycemia induces strong changes in later hypothalamic expression of INSR, LEPR, GLUT1, and GLUT3 mRNA. While the chicken provides an interesting approach for developmental malprogramming, the classical expression regulation via promoter methylation was not observed here. This may be due to alternative/interacting brain mechanisms or the thus far under-explored bird epigenome.
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29
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Wang D, Papp AC, Sun X. Functional characterization of CYP2D6 enhancer polymorphisms. Hum Mol Genet 2015; 24:1556-62. [PMID: 25381333 PMCID: PMC4381757 DOI: 10.1093/hmg/ddu566] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 11/15/2022] Open
Abstract
CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction.
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Affiliation(s)
- Danxin Wang
- Center for Pharmacogenomics, School of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Audrey C Papp
- Center for Pharmacogenomics, School of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaochun Sun
- Center for Pharmacogenomics, School of Medicine, The Ohio State University, Columbus, OH 43210, USA
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An autoregulatory pathway establishes the definitive chromatin conformation at the pit-1 locus. Mol Cell Biol 2015; 35:1523-32. [PMID: 25691665 DOI: 10.1128/mcb.01283-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
The transcription factor Pit-1 (POU1-F1) plays a dominant role in cell lineage expansion and differentiation in the anterior pituitary. Prior studies of the mouse Pit-1 (mPit-1) gene revealed that this master regulatory locus is activated at embryonic day 13.5 (E13.5) by an early enhancer (EE), whereas its subsequent expression throughout adult life is maintained by a more distal definitive enhancer (DE). Here, we demonstrate that the sequential actions of these two enhancers are linked to corresponding shifts in their proximities to the Pit-1 promoter. We further demonstrate that the looping of the definitive enhancer to the mPit-1 promoter is critically dependent on a self-sustaining autoregulatory mechanism mediated by the Pit-1 protein. These Pit-1-dependent actions are accompanied by localized recruitment of CBP and enrichment for H3K27 acetylation within the Pit-1 locus. These data support a model in which the sequential actions of two developmentally activated enhancers are linked to a corresponding shift in higher-order chromatin structures. This shift establishes an autoregulatory circuit that maintains durable expression of Pit-1 throughout adult life.
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Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest ARR, Drabløs F. Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics 2014; 15:120. [PMID: 24669905 PMCID: PMC3986914 DOI: 10.1186/1471-2164-15-120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 12/07/2013] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status and processes is an important task for improving our understanding of human cellular biology. The FANTOM5 and ENCODE projects represent two independent large scale efforts to map regulatory and transcriptional features to the human genome. Here we investigate chromatin features around a comprehensive set of transcription start sites in four cell lines by integrating data from these two projects. RESULTS Transcription start sites can be distinguished by chromatin states defined by specific combinations of both chromatin mark enrichment and the profile shapes of these chromatin marks. The observed patterns can be associated with cellular functions and processes, and they also show association with expression level, location relative to nearby genes, and CpG content. In particular we find a substantial number of repressed inter- and intra-genic transcription start sites enriched for active chromatin marks and Pol II, and these sites are strongly associated with immediate-early response processes and cell signaling. Associations between start sites with similar chromatin patterns are validated by significant correlations in their global expression profiles. CONCLUSIONS The results confirm the link between chromatin state and cellular function for expressed transcripts, and also indicate that active chromatin states at repressed transcripts may poise transcripts for rapid activation during immune response.
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Affiliation(s)
- Morten Rye
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, NO-7491 Trondheim, Norway
- St. Olavs Hospital, Postboks 3250, Sluppen 7006, Trondheim
| | | | - Carsten O Daub
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Piero Carninci
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair RR Forrest
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, NO-7491 Trondheim, Norway
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Antoniou MN, Skipper KA, Anakok O. Optimizing retroviral gene expression for effective therapies. Hum Gene Ther 2014; 24:363-74. [PMID: 23517535 DOI: 10.1089/hum.2013.062] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With their ability to integrate their genetic material into the target cell genome, retroviral vectors (RV) of both the gamma-retroviral (γ-RV) and lentiviral vector (LV) classes currently remain the most efficient and thus the system of choice for achieving transgene retention and therefore potentially long-term expression and therapeutic benefit. However, γ-RV and LV integration comes at a cost in that transcription units will be present within a native chromatin environment and thus be subject to epigenetic effects (DNA methylation, histone modifications) that can negatively impact on their function. Indeed, highly variable expression and silencing of γ-RV and LV transgenes especially resulting from promoter DNA methylation is well documented and was the cause of the failure of gene therapy in a clinical trial for X-linked chronic granulomatous disease. This review will critically explore the use of different classes of genetic control elements that can in principle reduce vector insertion site position effects and epigenetic-mediated silencing. These transcriptional regulatory elements broadly divide themselves into either those with a chromatin boundary or border function (scaffold/matrix attachment regions, insulators) or those with a dominant chromatin remodeling and transcriptional activating capability (locus control regions,, ubiquitous chromatin opening elements). All these types of elements have their strengths and weaknesses within the constraints of a γ-RV and LV backbone, showing varying degrees of efficacy in improving reproducibility and stability of transgene function. Combinations of boundary and chromatin remodeling; transcriptional activating elements, which do not impede vector production; transduction efficiency; and stability are most likely to meet the requirements within a gene therapy context especially when targeting a stem cell population.
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Affiliation(s)
- Michael N Antoniou
- Gene Expression and Therapy Group, King's College London School of Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, SE1 9RT, United Kingdom.
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Integrated analysis of long noncoding RNA and coding RNA expression in esophageal squamous cell carcinoma. Int J Genomics 2013; 2013:480534. [PMID: 24222893 PMCID: PMC3814080 DOI: 10.1155/2013/480534] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/26/2013] [Indexed: 01/14/2023] Open
Abstract
Tumorigenesis is a complex dynamic biological process that includes multiple steps of genetic and epigenetic alterations, aberrant expression of noncoding RNA, and changes in the expression profiles of coding genes. We call the collection of those perturbations in genome space the “cancer initiatome.” Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and they have key regulatory functions in chromatin remodeling and gene expression. Spatiotemporal variation in the expression of lncRNAs has been observed in development and disease states, including cancer. A few dysregulated lncRNAs have been studied in cancers, but the role of lncRNAs in the cancer initiatome remains largely unknown, especially in esophageal squamous cell carcinoma (ESCC). We conducted a genome-wide screen of the expression of lncRNAs and coding RNAs from ESCC and matched adjacent nonneoplastic normal tissues. We identified differentially expressed lncRNAs and coding RNAs in ESCC relative to their matched normal tissue counterparts and validated the result using polymerase chain reaction analysis. Furthermore, we identified differentially expressed lncRNAs that are co-located and co-expressed with differentially expressed coding RNAs in ESCC and the results point to a potential interaction between lncRNAs and neighboring coding genes that affect ether lipid metabolism, and the interaction may contribute to the development of ESCC. These data provide compelling evidence for a potential novel genomic biomarker of esophageal squamous cell cancer.
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Ohno K, Sawada JI, Takiya S, Kimoto M, Matsumoto A, Tsubota T, Uchino K, Hui CC, Sezutsu H, Handa H, Suzuki Y. Silk gland factor-2, involved in fibroin gene transcription, consists of LIM homeodomain, LIM-interacting, and single-stranded DNA-binding proteins. J Biol Chem 2013; 288:31581-91. [PMID: 24022586 DOI: 10.1074/jbc.m113.514471] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SGF-2 binds to promoter elements governing posterior silk gland-specific expression of the fibroin gene in Bombyx mori. We purified SGF-2 and showed that SGF-2 contains at least four gene products: the silkworm orthologues of LIM homeodomain protein Awh, LIM domain-binding protein (Ldb), a sequence-specific single-stranded DNA-binding protein (Lcaf), and the silk protein P25/fibrohexamerin (fhx). Using co-expression of these factors in Sf9 cells, Awh, Ldb, and Lcaf proteins were co-purified as a ternary complex that bound to the enhancer sequence in vitro. Lcaf interacts with Ldb as well as Awh through the conserved regions to mediate transcriptional activation in yeast. Misexpression of Awh in transgenic silkworms induces ectopic expression of the fibroin gene in the middle silk glands, where Ldb and Lcaf are expressed. Taken together, this study demonstrates that SGF-2 is a multisubunit activator complex containing Awh. Moreover, our results suggest that the Ldb·Lcaf protein complex serves as a scaffold to facilitate communication between transcriptional control elements.
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Affiliation(s)
- Kaoru Ohno
- From the National Institute for Basic Biology, 38 Nishigonaka, Myodaiji-cho, Okazaki 444-8585
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36
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Mousavi K, Zare H, Dell'orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 2013; 51:606-17. [PMID: 23993744 DOI: 10.1016/j.molcel.2013.07.022] [Citation(s) in RCA: 372] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 06/06/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Transcription factors and DNA regulatory binding motifs are fundamental components of the gene regulatory network. Here, by using genome-wide binding profiling, we show extensive occupancy of transcription factors of myogenesis (MyoD and Myogenin) at extragenic enhancer regions coinciding with RNA synthesis (i.e., eRNA). In particular, multiple regions were transcribed to eRNA within the regulatory region of MYOD1, including previously characterized distal regulatory regions (DRR) and core enhancer (CE). While (CE)RNA enhanced RNA polymerase II (Pol II) occupancy and transcription at MYOD1, (DRR)RNA acted to activate the downstream myogenic genes. The deployment of transcriptional machinery to appropriate loci is contingent on chromatin accessibility, a rate-limiting step preceding Pol II assembly. By nuclease sensitivity assay, we found that eRNAs regulate genomic access of the transcriptional complex to defined regulatory regions. In conclusion, our data suggest that eRNAs contribute to establishing a cell-type-specific transcriptional circuitry by directing chromatin-remodeling events.
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Affiliation(s)
- Kambiz Mousavi
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA.
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37
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Distinct chromatin configurations regulate the initiation and the maintenance of hGH gene expression. Mol Cell Biol 2013; 33:1723-34. [PMID: 23428872 DOI: 10.1128/mcb.01166-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
For many mammalian genes, initiation of transcription during embryonic development must be subsequently sustained over extensive periods of adult life. It remains unclear whether maintenance of gene expression reflects the same set of pathways as are involved in initial gene activation. The human pituitary growth hormone (hGH-N) locus is activated in the differentiating somatotrope midway through embryogenesis by a multicomponent locus control region (LCR). DNase I-hypersensitive site I (HSI) of the LCR is essential to full developmental activation of the hGH-N locus. Here we demonstrate that conditional deletion of HSI from the active hGH locus in the adult pituitary effectively silences hGH-N expression. Analyses of chromatin structure and locus positioning demonstrate that a specific subset of the HSI functions active in the embryo retain their HSI dependence in the adult pituitary. These functions sustain engagement of the hGH locus with polymerase II (Pol II) factories, histone acetylation at the hGH-N promoter, and looping of the LCR to its target promoter. These data reveal that HSI is essential to both the maintenance and the initiation phases of gene expression. These observations contribute to our mechanistic understanding of how stable patterns of mammalian gene expression are established in a terminally differentiated cell.
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Regulatory elements associated with paternally-expressed genes in the imprinted murine Angelman/Prader-Willi syndrome domain. PLoS One 2013; 8:e52390. [PMID: 23390487 PMCID: PMC3563663 DOI: 10.1371/journal.pone.0052390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/13/2012] [Indexed: 11/19/2022] Open
Abstract
The Angelman/Prader-Willi syndrome (AS/PWS) domain contains at least 8 imprinted genes regulated by a bipartite imprinting center (IC) associated with the SNRPN gene. One component of the IC, the PWS-IC, governs the paternal epigenotype and expression of paternal genes. The mechanisms by which imprinting and expression of paternal genes within the AS/PWS domain – such as MKRN3 and NDN – are regulated by the PWS-IC are unclear. The syntenic region in the mouse is organized and imprinted similarly to the human domain with the murine PWS-IC defined by a 6 kb interval within the Snrpn locus that includes the promoter. To identify regulatory elements that may mediate PWS-IC function, we mapped the location and allele-specificity of DNase I hypersensitive (DH) sites within the PWS-IC in brain cells, then identified transcription factor binding sites within a subset of these DH sites. Six major paternal-specific DH sites were detected in the Snrpn gene, five of which map within the 6 kb PWS-IC. We postulate these five DH sites represent functional components of the murine PWS-IC. Analysis of transcription factor binding within multiple DH sites detected nuclear respiratory factors (NRF's) and YY1 specifically on the paternal allele. NRF's and YY1 were also detected in the paternal promoter region of the murine Mrkn3 and Ndn genes. These results suggest that NRF's and YY1 may facilitate PWS-IC function and coordinately regulate expression of paternal genes. The presence of NRF's also suggests a link between transcriptional regulation within the AS/PWS domain and regulation of respiration. 3C analyses indicated Mkrn3 lies in close proximity to the PWS-IC on the paternal chromosome, evidence that the PWS-IC functions by allele-specific interaction with its distal target genes. This could occur by allele-specific co-localization of the PWS-IC and its target genes to transcription factories containing NRF's and YY1.
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Bonham AJ, Wenta N, Osslund LM, Prussin AJ, Vinkemeier U, Reich NO. STAT1:DNA sequence-dependent binding modulation by phosphorylation, protein:protein interactions and small-molecule inhibition. Nucleic Acids Res 2012. [PMID: 23180800 PMCID: PMC3553987 DOI: 10.1093/nar/gks1085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The DNA-binding specificity and affinity of the dimeric human transcription factor (TF) STAT1, were assessed by total internal reflectance fluorescence protein-binding microarrays (TIRF-PBM) to evaluate the effects of protein phosphorylation, higher-order polymerization and small-molecule inhibition. Active, phosphorylated STAT1 showed binding preferences consistent with prior characterization, whereas unphosphorylated STAT1 showed a weak-binding preference for one-half of the GAS consensus site, consistent with recent models of STAT1 structure and function in response to phosphorylation. This altered-binding preference was further tested by use of the inhibitor LLL3, which we show to disrupt STAT1 binding in a sequence-dependent fashion. To determine if this sequence-dependence is specific to STAT1 and not a general feature of human TF biology, the TF Myc/Max was analysed and tested with the inhibitor Mycro3. Myc/Max inhibition by Mycro3 is sequence independent, suggesting that the sequence-dependent inhibition of STAT1 may be specific to this system and a useful target for future inhibitor design.
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Affiliation(s)
- Andrew J Bonham
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, USA
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40
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Sheffield NC, Furey TS. Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. Genes (Basel) 2012; 3:651-70. [PMID: 24705081 PMCID: PMC3899983 DOI: 10.3390/genes3040651] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/17/2012] [Accepted: 09/25/2012] [Indexed: 01/11/2023] Open
Abstract
After finishing a human genome reference sequence in 2002, the genomics community has turned to the task of interpreting it. A primary focus is to identify and characterize not only protein-coding genes, but all functional elements in the genome. The effort includes both individual investigators and large-scale projects like the Encyclopedia of DNA Elements (ENCODE) project. As part of the ENCODE project, several groups have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. ChIP-seq experiments have also been used to discover transcription factor binding sites and map histone modifications. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide an overview of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of regulatory elements distributed throughout the genome.
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Affiliation(s)
- Nathan C Sheffield
- Program in Computational Biology and Bioinformatics, Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA.
| | - Terrence S Furey
- Depts of Genetics and Biology, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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41
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Ulyanov SV, Gavrilov AA. Chicken β-globin genes: A model system to study the transcriptional regulation at the level of genome domains. Mol Biol 2012. [DOI: 10.1134/s0026893312040127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee YJ, Horie Y, Wallace GR, Choi YS, Park JA, Choi JY, Song R, Kang YM, Kang SW, Baek HJ, Kitaichi N, Meguro A, Mizuki N, Namba K, Ishida S, Kim J, Niemczyk E, Lee EY, Song YW, Ohno S, Lee EB. Genome-wide association study identifies GIMAP as a novel susceptibility locus for Behcet's disease. Ann Rheum Dis 2012; 72:1510-6. [PMID: 23041938 DOI: 10.1136/annrheumdis-2011-200288] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVES To identify non-major histocompatibility complex susceptible genes that might contribute to Behçet's disease (BD). METHODS We performed a genome-wide association study using DNA samples from a Korean population consisting of 379 BD patients and 800 controls. A replication study was performed in a Japanese population (363 BD patients and 272 controls). To evaluate the functional implication of the target single nucleotide polymorphisms (SNP), gene expression levels in peripheral T cells, allele-specific modulation of promoter activity and biological effect of mRNA knockdown were investigated. RESULTS We found a novel association of BD to the GIMAP locus, mapped to chromosome 7q36.1 (rs1608157, p=6.01×10(-8) in a minor allele dominant model; rs11769828, allele based p=1.60×10(-6)). A fine mapping study identified an association with four additional SNP: rs1522596 (OR=1.45, p=7.70×10(-6)) in GIMAP4; rs10266069 (OR=1.32, p=2.67×10(-4)) and rs10256482 (OR=1.27, p=5.27×10(-4)) in GIMAP2; and rs2286900 (OR=1.61, p=3.53×10(-5)) in GIMAP1 areas. Replication study using DNA samples from the Japanese population validated the significant association between BD and the GIMAP locus. The GIMAP4 promoter construct plasmid with the minor allele of rs1608157 displayed significantly lower activity than one with the major allele. Moreover, CD4 T cells from BD patients showed a lower level of GIMAP4 mRNA, and GIMAP4 knockdown was protective against Fas-mediated apoptosis. CONCLUSIONS These results suggest that a GIMAP cluster is a novel susceptibility locus for BD, which is involved in T-cell survival, and T-cell aberration can contribute to the development of BD.
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Affiliation(s)
- Yun Jong Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnamsi, Korea
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Natoli G, Andrau JC. Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 2012; 46:1-19. [PMID: 22905871 DOI: 10.1146/annurev-genet-110711-155459] [Citation(s) in RCA: 288] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mammalian genomes are extensively transcribed outside the borders of protein-coding genes. Genome-wide studies recently demonstrated that cis-regulatory genomic elements implicated in transcriptional control, such as enhancers and locus-control regions, represent major sites of extragenic noncoding transcription. Enhancer-templated transcripts provide a quantitatively small contribution to the total amount of cellular nonribosomal RNA; nevertheless, the possibility that enhancer transcription and the resulting enhancer RNAs may, in some cases, have functional roles, rather than represent mere transcriptional noise at accessible genomic regions, is supported by an increasing amount of experimental data. In this article we review the current knowledge on enhancer transcription and its functional implications.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), I-20139 Milan, Italy.
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44
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Kim A, Dean A. Chromatin loop formation in the β-globin locus and its role in globin gene transcription. Mol Cells 2012; 34:1-5. [PMID: 22610406 PMCID: PMC3887778 DOI: 10.1007/s10059-012-0048-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/16/2012] [Accepted: 04/18/2012] [Indexed: 01/13/2023] Open
Abstract
Although linearly distant along mouse chromosome 7 and human chromosome 11, the mammalian β-globin gene is located in close proximity to the upstream locus control region enhancer when it is actively transcribed in the nuclear chromatin environment of erythroid cells. This organization is thought to generate a chromatin loop between the LCR, a powerful enhancer, and active globin genes by extruding intervening regions containing inactive genes. Loop formation in the β-globin locus requires erythroid specific transcriptional activators, co-factors and insulator-related factors. Chromatin structural features such as histone modifications and DNase I hypersensitive site formation as well as nuclear localization are all involved in loop formation in the locus through diverse mechanisms. Current models envision the formation of the loop as a necessary step in globin gene transcription activation, but this has not been definitively established and many questions remain about what is necessary to achieve globin gene transcription activation.
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Affiliation(s)
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, NIH, Bethesda, MD 20892,
USA
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45
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Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. Nucleic Acids Res 2012; 40:7858-69. [PMID: 22684627 PMCID: PMC3439890 DOI: 10.1093/nar/gks477] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
More than 98% of a typical vertebrate genome does not code for proteins. Although non-coding regions are sprinkled with short (<200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. One possibility is that unannotated conserved islands could encode non-coding RNAs (ncRNAs); alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. We define transcribed regions by applying a novel transcript-calling algorithm to RNA-Seq data obtained from total cellular RNA, and we define RFBSs using ChIP-Seq and DNAse-hypersensitivity assays. We find that unannotated conserved islands are four times more likely to coincide with RFBSs than with unannotated ncRNAs. Thousands of conserved RFBSs can be categorized as insulators based on the presence of CTCF or as enhancers based on the presence of p300/CBP and H3K4me1. While many unannotated conserved RFBSs are transcriptionally active to some extent, the transcripts produced tend to be unspliced, non-polyadenylated and expressed at levels 10 to 100-fold lower than annotated coding or ncRNAs. Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements.
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Affiliation(s)
- Martin Hemberg
- Department of Ophthalmology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02215, USA.
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46
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Fleetwood MR, Ho Y, Cooke NE, Liebhaber SA. DNase I hypersensitive site II of the human growth hormone locus control region mediates an essential and distinct long-range enhancer function. J Biol Chem 2012; 287:25454-65. [PMID: 22669946 DOI: 10.1074/jbc.m112.365825] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Locus control regions (LCRs) comprise sets of DNA elements capable of establishing autonomous chromatin domains that support robust and physiologically appropriate expression of target genes, often working over extensive distances. Human growth hormone (hGH-N) expression in the pituitary is under the regulation of a well characterized LCR containing four DNase I hypersensitive sites (HSs). The two pituitary-specific HS, HSI and HSII, are located 14.5 and 15.5 kb 5' to the hGH-N promoter. HSI is essential for activation of hGH-N during pituitary development and for sustaining robust activity in the adult. To determine whether the closely linked HSII has a role in hGH-N expression, it was deleted from a previously validated hGH/P1 transgene. Analysis of three independent hGH/P1(ΔHSII) transgenic mouse lines revealed that this deletion had no adverse effect on the formation of HSI, yet resulted in a substantial loss (70%) in hGH-N mRNA expression. This loss of expression was accompanied by a corresponding reduction in recruitment of the pituitary-specific transcription factor Pit-1 to the hGH-N promoter and a selective decrease in promoter occupancy of the elongation-linked isoform of RNA polymerase II. Sufficiency of HSI and HSII in LCR activity was explored by establishing two additional sets of mouse transgenic lines in which DNA segments containing these HS were positioned within the λ phage genome. In this "neutral" DNA context, HSII was required for the recruitment of HAT activity. These data establish HSII as a nonredundant component of the hGH LCR essential for establishment of robust levels of hGH-N gene expression.
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Affiliation(s)
- Margaret R Fleetwood
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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The long non-coding RNA, MHM, plays a role in chicken embryonic development, including gonadogenesis. Dev Biol 2012; 366:317-26. [PMID: 22546690 DOI: 10.1016/j.ydbio.2012.03.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 03/01/2012] [Accepted: 03/26/2012] [Indexed: 11/22/2022]
Abstract
MHM is a chicken Z chromosome-linked locus that is methylated and transcriptionally silent in male cells, but is hypomethylated and transcribed into a long non-coding RNA in female cells. MHM has been implicated in both localised dosage compensation and sex determination in the chicken embryo, but direct evidence is lacking. We investigated the potential role of MHM in chicken embryonic development, using expression analysis and retroviral-mediated mis-expression. At embryonic stages, MHM is only expressed in females. Northern blotting showed that both sense and antisense strands of the MHM locus are transcribed, with the sense strand being more abundant. Whole mount in situ hybridization confirmed that the sense RNA is present in developing female embryos, notably in gonads, limbs, heart, branchial arch and brain. Within these cells, the MHM RNA is localized to the nucleus. The antisense transcript is lowly expressed and has a cytoplasmic localization in cells. Mis-expression of MHM sense and antisense sequences results in overgrowth of tissues in which transcripts are predominantly expressed. This includes altered asymmetric ovarian development in females. In males, MHM mis-expression impairs gonadal expression of the testis gene, DMRT1. Both MHM sense and antisense mis-expression cause brain abnormalities, while MHM sense causes an increase in male-biased embryo mortality. These results indicate that MHM has a role in chicken normal embryonic development, including gonadal sex differentiation.
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48
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Krivega I, Dean A. Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev 2012; 22:79-85. [PMID: 22169023 PMCID: PMC3342482 DOI: 10.1016/j.gde.2011.11.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/09/2011] [Indexed: 12/23/2022]
Abstract
In metazoans, enhancers of gene transcription must often exert their effects over tens of kilobases of DNA. Over the past decade it has become clear that to do this, enhancers come into close proximity with target promoters with the looping away of intervening sequences. In a few cases proteins that are involved in the establishment or maintenance of these loops have been revealed but how the proper gene target is selected remains mysterious. Chromatin insulators had been appreciated as elements that play a role in enhancer fidelity through their enhancer blocking or barrier activity. However, recent work suggests more direct participation of insulators in enhancer-gene interactions. The emerging view begins to incorporate transcription activation by distant enhancers with large scale nuclear architecture and subnuclear movement.
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Affiliation(s)
- Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20982
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20982
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An RNA-independent linkage of noncoding transcription to long-range enhancer function. Mol Cell Biol 2012; 32:2020-9. [PMID: 22431516 DOI: 10.1128/mcb.06650-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The detection of noncoding transcription at multiple enhancers within the mammalian genome raises critical questions regarding whether and how this activity contributes to enhancer function. Here, using in vivo analysis of a human growth hormone (hGH) transgene locus, we report that activation of a domain of noncoding transcription adjacent to the long-range hGH-N enhancer, HSI, is established by the enhancer independent of any interactions with its target promoter. We further demonstrate that the appearance of this enhancer-linked noncoding transcription is temporally and spatially concordant with induction of hGH-N in the embryonic pituitary. Finally, we show that the level of transcriptional enhancement of hGH-N by HSI is directly related to the intensity of HSI-dependent noncoding transcription and is fully independent of the structure of the locally transcribed RNA. These data extend our understanding of the relationship of long-range enhancer activity to enhancer-dependent noncoding transcription and establish a model that may be of general relevance to additional mammalian loci.
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Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S. SNP markers and their impact on plant breeding. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:728398. [PMID: 23316221 PMCID: PMC3536327 DOI: 10.1155/2012/728398] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/14/2012] [Indexed: 05/19/2023]
Abstract
The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.
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Affiliation(s)
- Jafar Mammadov
- Department of Trait Genetics and Technologies, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
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