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Zhang Y, Zhang J, Wang C, Dai H, Du X, Li Q, Pan Z. The super-enhancer repertoire in porcine liver. J Anim Sci 2023; 101:skad056. [PMID: 36800318 PMCID: PMC10024791 DOI: 10.1093/jas/skad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 02/18/2023] Open
Abstract
The transcriptional initiation of genes is inextricably bound with the functions of cis-regulatory sequences. The pig is one of the most important livestock species and an ideal animal model for biomedical studies. At the same time, the liver is a critical organ with diverse and complex metabolic functions. Here, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with high-throughput sequencing to profile the chromatin landscape of histone H3 lysine 27 acetylation (H3K27ac), histone H3 lysine 4 monomethylation (H3K4me1), and CCAAT enhancer-binding protein β (C-EBPβ) in the 70-d-old porcine liver, compared the different profiles among the three markers and their associated stitched-enhancers by stitching and sorting the peaks within 12.5 kb (Pott and Lieb, 2015) and generated the porcine liver-specific super-enhancers (SEs) by the combination of three markers. Compared to typical enhancers (TEs) and other stitched-enhancers, liver-specific SEs showed a higher density of cis-motifs and SNPs, which may recruit more tissue-specific vital TFs. The expression profiles in fetal and 70-d-old pigs proved that a large proportion of SE-associated genes were up-regulated and were more related to hepatic metabolisms and detoxification pathways. Our results illustrated the difference and connection among promoter and enhancer markers, identified the features of liver SEs and their associated genes, and provided novel insight into cis-element identification, function, and liver transcriptional regulation.
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Affiliation(s)
- Yi Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinbi Zhang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Caixia Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjian Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Nizovtseva EV, Polikanov YS, Kulaeva OI, Clauvelin N, Postnikov YV, Olson WK, Studitsky VM. [Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin]. Mol Biol (Mosk) 2020; 53:1038-1048. [PMID: 31876282 DOI: 10.1134/s0026898419060132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/14/2019] [Indexed: 11/23/2022]
Abstract
Transcriptional enhancers in the cell nuclei typically interact with the target promoters in cis over long stretches of chromatin, but the mechanism of this communication remains unknown. Previously we have developed a defined in vitro system for quantitative analysis of the rate of distant enhancer-promoter communication (EPC) and have shown that the chromatin fibers maintain efficient distant EPC in cis. Here we investigate the roles of linker histone H1 and HMGN5 protein in EPC. A considerable negative effect of histone H1 on EPC depending on its C- and N-tails was shown. Protein HMGN5 that affects chromatin compaction and is associated with active chromatin counteracts EPC inhibition by H1. The data suggest that the efficiency of the interaction between the enhancer and the promoter depends on the structure and dynamics of the chromatin fiber localized between them and can be regulated by proteins associated with chromatin.
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Affiliation(s)
- E V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA
| | - Y S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - O I Kulaeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA
| | - N Clauvelin
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Y V Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA
| | - W K Olson
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA
| | - V M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19422 USA.,Faculty of Biology, Moscow State University, Moscow, 119991 Russia.,
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3
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Nizovtseva EV, Polikanov YS, Kulaeva OI, Clauvelin N, Postnikov YV, Olson WK, Studitsky VM. Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin. Mol Biol 2019. [DOI: 10.1134/s002689331906013x] [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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4
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Nizovtseva EV, Clauvelin N, Todolli S, Polikanov YS, Kulaeva OI, Wengrzynek S, Olson WK, Studitsky VM. Nucleosome-free DNA regions differentially affect distant communication in chromatin. Nucleic Acids Res 2017; 45:3059-3067. [PMID: 27940560 PMCID: PMC5389534 DOI: 10.1093/nar/gkw1240] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/29/2016] [Indexed: 11/13/2022] Open
Abstract
Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chromatin structure/dynamics and, in turn, affect the rate of EPC in vitro and in silico. Increasing the length of internucleosomal linker DNA from 25 to 60 bp results in more efficient EPC. The presence of longer nucleosome-free DNA regions can positively or negatively affect the rate of EPC, depending upon the length and location of the DNA region within the chromatin fiber. Thus the presence of histone-free DNA regions can differentially affect the efficiency of EPC, suggesting that gene regulation over a distance could be modulated by changes in the length of internucleosomal DNA spacers.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Nicolas Clauvelin
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Stefjord Todolli
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Yury S Polikanov
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Olga I Kulaeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia
| | - Scott Wengrzynek
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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5
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Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Pedersen HL, Horvei KD, Thiyagarajan D, Seredkina N, Rekvig OP. Murine and Human Lupus Nephritis: Pathogenic Mechanisms and Theoretical Strategies for Therapy. Semin Nephrol 2016; 35:427-38. [PMID: 26573545 DOI: 10.1016/j.semnephrol.2015.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lupus nephritis is one of the most serious manifestations of systemic lupus erythematosus, and represents one of the criteria implemented to classify systemic lupus erythematosus. Although studied for decades, no consensus has been reached related to the basic cellular, molecular, and immunologic mechanism(s) responsible for lupus nephritis. No causal treatments have been developed; therapy is approached mainly with nonspecific immunosuppressive medications. More detailed insight into disease mechanisms therefore is indispensable to develop new therapeutic strategies. In this review, contemporary knowledge on the pathogenic mechanisms of lupus nephritis is discussed based on recent data in murine and human lupus nephritis. Specific focus is given to the effect of anti-double-stranded DNA/antinucleosome antibodies in the kidneys and whether they bind exposed chromatin fragments in glomeruli or whether they bind inherent glomerular structures by cross-recognition. Overall, the data presented here favor the exposed chromatin model because we did not find any indication to substantiate the anti-double-stranded DNA antibody cross-reacting model. At the end of this review we present data on why chromatin fragments are expressed in the glomeruli of patients with lupus nephritis, and discuss how this knowledge can be used to direct the development of future therapies.
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Affiliation(s)
- Hege Lynum Pedersen
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
| | - Kjersti Daae Horvei
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Dhivya Thiyagarajan
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Natalya Seredkina
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ole Petter Rekvig
- RNA and Molecular Pathology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway; Department of Radiology, University Hospital of North Norway, Tromsø, Norway
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Olson WK, Clauvelin N, Colasanti AV, Singh G, Zheng G. Insights into Gene Expression and Packaging from Computer Simulations. Biophys Rev 2012; 4:171-178. [PMID: 23139731 DOI: 10.1007/s12551-012-0093-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Within the nucleus of each cell lies DNA - an unfathomably long, twisted, and intricately coiled molecule - segments of which make up the genes that provide the instructions that a cell needs to operate. As we near the 60(th) anniversary of the discovery of the DNA double helix, crucial questions remain about how the physical arrangement of the DNA in cells affects how genes work. For example, how a cell stores the genetic information inside the nucleus is complicated by the necessity of maintaining accessibility to DNA for genetic processing. In order to gain insight into the roles played by various proteins in reading and compacting the genome, we have developed new methodologies to simulate the dynamic, three-dimensional structures of long, fluctuating, protein-decorated strands of DNA. Our a priori approach to the problem allows us to determine the effects of individual proteins and their chemical modifications on overall DNA structure and function. Here we present our recent treatment of the communication between regulatory proteins attached to precisely constructed stretches of chromatin. Our simulations account for the enhancement in communication detected experimentally on chromatin compared to protein-free DNA of the same chain length as well as the critical roles played by the cationic 'tails' of the histone proteins in this signaling. The states of chromatin captured in the simulations offer new insights into the ways that the DNA, histones, and regulatory proteins contribute to long-range communication along the genome.
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Affiliation(s)
- Wilma K Olson
- Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
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Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK. Internucleosomal interactions mediated by histone tails allow distant communication in chromatin. J Biol Chem 2012; 287:20248-57. [PMID: 22518845 DOI: 10.1074/jbc.m111.333104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Action across long distances on chromatin is a hallmark of eukaryotic transcriptional regulation. Although chromatin structure per se can support long-range interactions, the mechanisms of efficient communication between widely spaced DNA modules in chromatin remain a mystery. The molecular simulations described herein suggest that transient binary internucleosomal interactions can mediate distant communication in chromatin. Electrostatic interactions between the N-terminal tails of the core histones and DNA enhance the computed probability of juxtaposition of sites that lie far apart along the DNA sequence. Experimental analysis of the rates of communication in chromatin constructs confirms that long-distance communication occurs efficiently and independently of distance on tail-containing, but not on tailless, chromatin. Taken together, our data suggest that internucleosomal interactions involving the histone tails are essential for highly efficient, long-range communication between regulatory elements and their targets in eukaryotic genomes.
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Affiliation(s)
- Olga I Kulaeva
- Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854, USA
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9
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Hedberg A, Fismen S, Fenton KA, Fenton C, Osterud B, Mortensen ES, Rekvig OP. Heparin exerts a dual effect on murine lupus nephritis by enhancing enzymatic chromatin degradation and preventing chromatin binding in glomerular membranes. ACTA ACUST UNITED AC 2011; 63:1065-75. [PMID: 21190297 DOI: 10.1002/art.30211] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Association of nucleosome-IgG immune complexes with glomerular basement membranes (GBMs) is an important event in the development of lupus nephritis. Preventing this binding and/or increasing nuclease sensitivity of nucleosomes may be viable strategies for the prevention of the disease. Theoretically, heparin may alter nucleosomal structure and increase sensitivity to proteinases and nucleases, and may also inhibit binding of nucleosomes and nucleosome-IgG complexes to basement membrane structures. The aim of this study was to investigate whether and eventually how heparin prevents murine lupus nephritis. METHODS Surface plasmon resonance was used to analyze if heparin inhibits binding of nucleosomes to laminin and collagen. The effect of heparin on nuclease- and proteinase-mediated degradation of nucleosomes was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and agarose gel electrophoresis. In vitro results were compared with analyses in vivo in heparin-treated (NZB × NZW)F(1) mice. Anti-double-stranded DNA antibody production, deposition of nucleosome-IgG complexes in GBMs, and development of proteinuria were monitored, and circulating chromatin fragments were quantified using quantitative polymerase chain reaction. RESULTS In vitro studies demonstrated that heparin increased enzymatic degradation of nucleosomes and almost completely inhibited binding of nucleosomes to laminin and collagen. (NZB × NZW)F(1) mice treated with heparin demonstrated delayed or no antibody production and higher variation of circulating chromatin levels compared with untreated control mice. This effect was accompanied by highly reduced nucleosome-IgG complexes in GBMs and delayed development of nephritis. CONCLUSION Increasing the degradation of nucleosomes, reducing their immunogenicity, and preventing binding of nucleosome-IgG complexes in glomeruli together provide an alternative basis for the treatment of lupus nephritis.
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Hedberg A, Mortensen ES, Rekvig OP. Chromatin as a target antigen in human and murine lupus nephritis. Arthritis Res Ther 2011; 13:214. [PMID: 21542875 PMCID: PMC3132027 DOI: 10.1186/ar3281] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The present review focuses on pathogenic molecular and transcriptional events in patients with lupus nephritis. These factors are renal DNaseI, exposed chromatin fragments and the corresponding chromatin-reactive autoantibodies. Lupus nephritis is the most serious complication in human systemic lupus erythematosus, and is characterised by deposition of chromatin fragment-IgG complexes in the mesangial matrix and glomerular basement membranes. The latter deposition defines end-stage disease. This event is stringently linked to a renal-restricted shutdown of expression of the DNaseI gene, as determined by loss of DNaseI mRNA level and DNaseI enzyme activity. The major aim of the present review is to generate new therapeutic strategies based on new insight into the disease pathogenesis.
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Affiliation(s)
- Annica Hedberg
- Molecular Pathology Research Group, Institute of Medical Biology, Faculty of Health Science, University of Tromsø, N-9037 Tromsø, Norway
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Nitsch R, Di Dato V, di Gennaro A, de Cristofaro T, Abbondante S, De Felice M, Zannini M, Di Lauro R. Comparative genomics reveals a functional thyroid-specific element in the far upstream region of the PAX8 gene. BMC Genomics 2010; 11:306. [PMID: 20470391 PMCID: PMC2996967 DOI: 10.1186/1471-2164-11-306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 05/14/2010] [Indexed: 12/01/2022] Open
Abstract
Background The molecular mechanisms leading to a fully differentiated thyrocite are still object of intense study even if it is well known that thyroglobulin, thyroperoxidase, NIS and TSHr are the marker genes of thyroid differentiation. It is also well known that Pax8, TTF-1, Foxe1 and Hhex are the thyroid-enriched transcription factors responsible for the expression of the above genes, thus are responsible for the differentiated thyroid phenotype. In particular, the role of Pax8 in the fully developed thyroid gland was studied in depth and it was established that it plays a key role in thyroid development and differentiation. However, to date the bases for the thyroid-enriched expression of this transcription factor have not been unraveled yet. Here, we report the identification and characterization of a functional thyroid-specific enhancer element located far upstream of the Pax8 gene. Results We hypothesized that regulatory cis-acting elements are conserved among mammalian genes. Comparison of a genomic region extending for about 100 kb at the 5'-flanking region of the mouse and human Pax8 gene revealed several conserved regions that were tested for enhancer activity in thyroid and non-thyroid cells. Using this approach we identified one putative thyroid-specific regulatory element located 84.6 kb upstream of the Pax8 transcription start site. The in silico data were verified by promoter-reporter assays in thyroid and non-thyroid cells. Interestingly, the identified far upstream element manifested a very high transcriptional activity in the thyroid cell line PC Cl3, but showed no activity in HeLa cells. In addition, the data here reported indicate that the thyroid-enriched transcription factor TTF-1 is able to bind in vitro and in vivo the Pax8 far upstream element, and is capable to activate transcription from it. Conclusions Results of this study reveal the presence of a thyroid-specific regulatory element in the 5' upstream region of the Pax8 gene. The identification of this regulatory element represents the first step in the investigation of upstream regulatory mechanisms that control Pax8 transcription during thyroid differentiation and are relevant to further studies on Pax8 as a candidate gene for thyroid dysgenesis.
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Affiliation(s)
- Roberto Nitsch
- Institute of Experimental Endocrinology and Oncology G. Salvatore, National Research Council, Naples, Italy
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Evidences for insulator activity of the 5′UTR of the Drosophila melanogaster LTR-retrotransposon ZAM. Mol Genet Genomics 2010; 283:503-9. [DOI: 10.1007/s00438-010-0529-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 02/28/2010] [Indexed: 10/19/2022]
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Studitsky VM. Mechanisms of distant enhancer action on DNA and in chromatin. Mol Biol 2009. [DOI: 10.1134/s0026893309020022] [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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Abstract
Regulation of many biological processes in eukaryotes involves distant communication between the regulatory DNA sequences (e.g., enhancers) and their targets over the DNA regions organized in chromatin. However previously developed methods for analysis of communication in chromatin in vitro are artifact-prone and/or do not allow analysis of communication on physiologically relevant, saturated arrays of nucleosomes. Here we describe a method for quantitative analysis of the rate of distant communication in cis on saturated arrays of nucleosomes capable of forming the 30-nm chromatin fibers in vitro.
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Affiliation(s)
- Yury S. Polikanov
- Department of Pharmacology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Vasily M. Studitsky
- Department of Pharmacology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA
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