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Mayama S, Hamazaki N, Maruyama Y, Matsubara S, Kimura AP. Transcriptional activation of the mouse Scd2 gene by interdependent enhancers and long noncoding RNAs in ovarian granulosa cells. J Reprod Dev 2020; 66:435-444. [PMID: 32507774 PMCID: PMC7593631 DOI: 10.1262/jrd.2019-161] [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] [Indexed: 01/12/2023] Open
Abstract
Specific gene expression in granulosa cells is key for the function of ovary, but the molecular mechanism of transcriptional activation is not well studied.
Here we investigated the regulatory mechanism of the mouse stearoyl-CoA desaturase 2 (Scd2) gene encoding an enzyme for lipid metabolism.
Northern blot and in situ hybridization indicated that the mouse Scd2 mRNA was highly expressed in ovarian granulosa cells. We
found four conserved noncoding sequences (CNSs) and two long noncoding RNAs (lncRNAs) transcribed from regions upstream of the Scd2 gene as
candidates of regulatory elements/factors. These lncRNAs were predominantly transcribed in the opposite direction to Scd2 and localized in
nuclei and showed the correlation with Scd2 expression, raising the possibility of their transcriptional regulatory roles. Indeed, knockdown of
both lncRNAs, lncRNA-sc1 and lncRNA-sc2, significantly decreased the Scd2 mRNA level in primary granulosa
cells. Then, we investigated the histone modification pattern at this locus by a chromatin immunoprecipitation assay, and two CNSs, CNS1 and CNS2, were found to
be marked with high levels of histone H3K9/K27 acetylation in primary granulosa cells. By a reporter gene assay, both CNS1 and CNS2 interdependently exhibited
enhancer activity for the Scd2 promoter in primary granulosa cells. These data suggest that the mouse Scd2 gene is activated
by two lncRNAs and interdependent enhancers in ovarian granulosa cells, which provides a new insight into transcriptional activation in granulosa cells.
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Affiliation(s)
- Shota Mayama
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuhiko Hamazaki
- Division of Biology, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo 060-0810, Japan.,Present: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yuki Maruyama
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shin Matsubara
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Present: Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Division of Biology, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo 060-0810, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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2
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Wang X, Ma Z, Kong X, Lv Z. Effects of RNAs on chromatin accessibility and gene expression suggest RNA-mediated activation. Int J Biochem Cell Biol 2016; 79:24-32. [PMID: 27497987 DOI: 10.1016/j.biocel.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/20/2023]
Abstract
The study of the interaction between RNA and DNA sequences in activating genes has important significance for understanding the mechanisms of RNA-mediated activation. Here, we used in vitro chromatin reconstitution approach to observe whether RNAs increase DNase I digestion, plasmid transfection to observe whether RNAs promote gene expression, and bioinformatics analysis to predict the binding ability of RNAs to centromere DNA (constitutive heterochromatin). Synthetic RNAs (23nt) that were complementary to mouse albumin gene and total liver RNA increased DNase I digestion sensitivity of mouse albumin gene, suggesting that RNAs can increase chromatin accessibility. Transcribed sense-antisense tandem Alu elements activated an enhanced green fluorescent protein reporter gene after stable transfection. Bioinformatics analysis showed that the binding strength of RNA population to centromere DNAs is significantly lower than that of their flanking sequences, which suggests that the centromere is not easily affected by RNAs produced from other transcribed regions and may be the reason why centromeres consist of constitutive heterochromatin. The results in this paper illustrate that RNAs complementary to DNA sequences play roles in activating genes. Since RNA is mainly produced from the cell's own DNA, the work presented in this paper suggests that RNAs transcribed from DNA create feedback that activates DNA transcription.
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Affiliation(s)
- Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
| | - Zhihong Ma
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, The Second Hospital of Tangshan, 21 North Jianshe Road, Tangshan, Hebei Province, China.
| | - Xianglong Kong
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, Hebei Chest Hospital, 372 Shengli North Street, Shijiazhuang, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
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Komura-Kawa T, Hirota K, Shimada-Niwa Y, Yamauchi R, Shimell M, Shinoda T, Fukamizu A, O’Connor MB, Niwa R. The Drosophila Zinc Finger Transcription Factor Ouija Board Controls Ecdysteroid Biosynthesis through Specific Regulation of spookier. PLoS Genet 2015; 11:e1005712. [PMID: 26658797 PMCID: PMC4684333 DOI: 10.1371/journal.pgen.1005712] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 11/08/2015] [Indexed: 01/01/2023] Open
Abstract
Steroid hormones are crucial for many biological events in multicellular organisms. In insects, the principal steroid hormones are ecdysteroids, which play essential roles in regulating molting and metamorphosis. During larval and pupal development, ecdysteroids are synthesized in the prothoracic gland (PG) from dietary cholesterol via a series of hydroxylation and oxidation steps. The expression of all but one of the known ecdysteroid biosynthetic enzymes is restricted to the PG, but the transcriptional regulatory networks responsible for generating such exquisite tissue-specific regulation is only beginning to be elucidated. Here, we report identification and characterization of the C2H2-type zinc finger transcription factor Ouija board (Ouib) necessary for ecdysteroid production in the PG in the fruit fly Drosophila melanogaster. Expression of ouib is predominantly limited to the PG, and genetic null mutants of ouib result in larval developmental arrest that can be rescued by administrating an active ecdysteroid. Interestingly, ouib mutant animals exhibit a strong reduction in the expression of one ecdysteroid biosynthetic enzyme, spookier. Using a cell culture-based luciferase reporter assay, Ouib protein stimulates transcription of spok by binding to a specific ~15 bp response element in the spok PG enhancer element. Most remarkable, the developmental arrest phenotype of ouib mutants is rescued by over-expression of a functionally-equivalent paralog of spookier. These observations imply that the main biological function of Ouib is to specifically regulate spookier transcription during Drosophila development. Steroid hormones are crucial for development and reproduction in multicellular organisms. The spatially-restricted expression of almost all steroid biosynthesis genes is key to the specialization of steroid producing cells. In the last decade, insects have become the focus for research on the biosynthesis of the principal steroid hormones, ecdysteroids. However, the transcriptional regulatory mechanisms controlling the ecdysteroid biosynthesis genes are largely unknown. Here we show that a novel zinc finger transcription factor Ouija board (Ouib) is essential for activating the expression of one ecdysteroid biosynthesis gene, spookier, in the ecdysteroid producing cells. Ouib is the first invertebrate transcription factor that is predominantly expressed in the steroidogenic organs and essential for development via inducing expression of the steroidogenic gene. In addition, this is the first report showing the catalytic step-specific control of steroid hormone biosynthesis through transcriptional regulation.
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Affiliation(s)
- Tatsuya Komura-Kawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiko Hirota
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuko Shimada-Niwa
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Rieko Yamauchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - MaryJane Shimell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Tetsuro Shinoda
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michael B. O’Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ryusuke Niwa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- * E-mail:
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Cohen H, Ben-Hamo R, Gidoni M, Yitzhaki I, Kozol R, Zilberberg A, Efroni S. Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. Breast Cancer Res 2014; 16:464. [PMID: 25410484 PMCID: PMC4303202 DOI: 10.1186/s13058-014-0464-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 10/14/2014] [Indexed: 02/03/2023] Open
Abstract
Introduction GATA binding protein 3 (GATA3) is a regulator of mammary luminal cell differentiation, and an estrogen receptor (ER) associated marker in breast cancer. Tumor suppressor functions of GATA3 have been demonstrated primarily in basal-like breast cancers. Here, we focused on its function in luminal breast cancer, where GATA3 is frequently mutated, and its levels are significantly elevated. Methods GATA3 target genes were identified in normal- and luminal cancer- mammary cells by ChIP-seq, followed by examination of the effects of GATA3 expressions and mutations on tumorigenesis-associated genes and processes. Additionally, mutations and expression data of luminal breast cancer patients from The Cancer Genome Atlas were analyzed to characterize genetic signatures associated with GATA3 mutations. Results We show that some GATA3 effects shift from tumor suppressing to tumor promoting during tumorigenesis, with deregulation of three genes, BCL2, DACH1, THSD4, representing major GATA3-controlled processes in cancer progression. In addition, we identify an altered activity of mutant GATA3, and distinct associated genetic signatures. These signatures depend on the functional domain mutated; and, for a specific subgroup, are shared with basal-like breast cancer patients, who are a clinical group with regard to considerations of mode of treatment. Conclusions The GATA3 dependent mechanisms may call for special considerations for proper prognosis and treatment of patients. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0464-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helit Cohen
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Moriah Gidoni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Ilana Yitzhaki
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Renana Kozol
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Alona Zilberberg
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
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Identifying and mapping cell-type-specific chromatin programming of gene expression. Proc Natl Acad Sci U S A 2014; 111:E645-54. [PMID: 24469817 DOI: 10.1073/pnas.1312523111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A problem of substantial interest is to systematically map variation in chromatin structure to gene-expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity and genome-wide gene-expression levels in 20 diverse human cell types. We show that ∼25% of genes show cell-type-specific expression explained by alterations in chromatin structure. We find that distal regions of chromatin structure (e.g., ±200 kb) capture more genes with this relationship than local regions (e.g., ±2.5 kb), yet the local regions show a more pronounced effect. By exploiting variation across cell types, we were capable of pinpointing the most likely hypersensitive sites related to cell-type-specific expression, which we show have a range of contextual uses. This quantitative framework is likely applicable to other settings aimed at relating continuous genomic measurements to gene-expression variation.
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Peterson KR, Fedosyuk H, Harju-Baker S. LCR 5' hypersensitive site specificity for globin gene activation within the active chromatin hub. Nucleic Acids Res 2012; 40:11256-69. [PMID: 23042246 PMCID: PMC3526258 DOI: 10.1093/nar/gks900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The DNaseI hypersensitive sites (HSs) of the human β-globin locus control region (LCR) may function as part of an LCR holocomplex within a larger active chromatin hub (ACH). Differential activation of the globin genes during development may be controlled in part by preferential interaction of each gene with specific individual HSs during globin gene switching, a change in conformation of the LCR holocomplex, or both. To distinguish between these possibilities, human β-globin locus yeast artificial chromosome (β-YAC) lines were produced in which the ε-globin gene was replaced with a second marked β-globin gene (βm), coupled to an intact LCR, a 5′HS3 complete deletion (5′ΔHS3) or a 5′HS3 core deletion (5′ΔHS3c). The 5′ΔHS3c mice expressed βm-globin throughout development; γ-globin was co-expressed in the embryonic yolk sac, but not in the fetal liver; and wild-type β-globin was co-expressed in adult mice. Although the 5′HS3 core was not required for βm-globin expression, previous work showed that the 5′HS3 core is necessary for ε-globin expression during embryonic erythropoiesis. A similar phenotype was observed in 5′HS complete deletion mice, except βm-globin expression was higher during primitive erythropoiesis and γ-globin expression continued into fetal definitive erythropoiesis. These data support a site specificity model of LCR HS-globin gene interaction.
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Affiliation(s)
- Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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