1
|
Ou X, Yang J, Yang L, Zeng H, Shao L. Histone acetylation regulated by histone deacetylases during spermatogenesis. Andrology 2024. [PMID: 39132925 DOI: 10.1111/andr.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/03/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Physical, chemical, and biological factors in the environment constantly influence in vivo and in vitro biological processes, including diverse histone modifications involved in cancer and metabolism. However, the intricate mechanisms of acetylation regulation remain poorly elucidated. In mammalian spermatogenesis, acetylation plays a crucial role in repairing double-strand DNA breaks, regulating gene transcription, and modulating various signaling pathways. RESULTS This review summarizes the histone acetylation sites in the mouse testis and provides a comprehensive overview of how histone acetylation is involved in different stages of spermatogenesis under the regulation by histone deacetylases. The regulatory functions of various class histone deacetylases during spermatogenesis and the crossroad between histone acetylation and other histone modifications are highlighted. It is imperative to understand the mechanisms of histone acetylation regulated by histone deacetylases in spermatogenesis, which facilitates to prevent and treat infertility-related diseases.
Collapse
Affiliation(s)
- Xiangying Ou
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Juan Yang
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Linfeng Yang
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| |
Collapse
|
2
|
Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
Collapse
Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
| |
Collapse
|
3
|
Contreras‐Marciales ADP, López‐Guzmán SF, Benítez‐Hess ML, Oviedo N, Hernández‐Sánchez J. Characterization of the promoter region of the murine Catsper2 gene. FEBS Open Bio 2022; 12:2236-2249. [PMID: 36345591 PMCID: PMC9714369 DOI: 10.1002/2211-5463.13518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
CATSPER2 (Cation channel sperm-associated protein 2) protein, which is part of the calcium CATSPER channel located in the membrane of the flagellar principal piece of the sperm cell, is only expressed in the testis during spermatogenesis. Deletions or mutations in the Catsper2 gene are associated with the deafness-infertility syndrome (DIS) and non-syndromic male infertility. However, the mechanisms by which Catsper2 is regulated are unknown. Here, we report the characterization of the promoter region of murine Catsper2 and the role of CTCF and CREMτ in its transcription. We report that the promoter region has transcriptional activity in both directions, as determined by observing luciferase activity in mouse Sertoli and GC-1 spg transfected cells. WGBS data analysis indicated that a CpG island identified in silico is non-methylated; Chromatin immunoprecipitation (ChIP)-seq data analysis revealed that histone marks H3K4me3 and H3K36me3 are present in the promoter and body of the Catsper2 gene respectively, indicating that Catsper2 is subject to epigenetic regulation. In addition, the murine Catsper2 core promoter was delimited to a region between -54/+189 relative to the transcription start site (TSS), where three CTCF and one CRE binding site were predicted. The functionality of these sites was determined by mutation of the CTCF sites and deletion of the CRE site. Finally, ChIP assays confirmed that CREMτ and CTCF bind to the Catsper2 minimal promoter region. This study represents the first functional analysis of the murine Catsper2 promoter region and the mechanisms that regulate its expression.
Collapse
Affiliation(s)
- Andrea del Pilar Contreras‐Marciales
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - Sergio Federico López‐Guzmán
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - María Luisa Benítez‐Hess
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| | - Norma Oviedo
- Unidad de Investigación Médica en Inmunología e Infectología, Centro Médico Nacional, La RazaInstituto Mexicano del Seguro SocialCiudad de MéxicoMexico
| | - Javier Hernández‐Sánchez
- Departamento de Genética y Biología MolecularCentro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV)Ciudad de MéxicoMexico
| |
Collapse
|
4
|
Ji X, Meng W, Liu Z, Mu X. Emerging Roles of lncRNAs Regulating RNA-Mediated Type-I Interferon Signaling Pathway. Front Immunol 2022; 13:811122. [PMID: 35280983 PMCID: PMC8914027 DOI: 10.3389/fimmu.2022.811122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The type-I interferon (IFN-I) signaling pathway plays pivot roles in defending against pathogen invasion. Exogenous ssRNA and dsRNA could be immunogenic. RNA-mediated IFN signaling is extensively studied in the field. The incorrect functioning of this pathway leads to either autoimmune diseases or suffering from microorganism invasion. From the discrimination of “self” and “non-self” molecules by receptors to the fine-tune modulations in downstream cascades, all steps are under the surveillance featured by complex feedbacks and regulators. Studies in recent years highlighted the emerging roles of long noncoding RNAs (lncRNAs) as a reservoir for signaling regulation. LncRNAs bind to targets through the structure and sequence, and thus the mechanisms of action can be complex and specific. Here, we summarized lncRNAs modulating the RNA-activated IFN-I signaling pathway according to the event order during the signaling. We hope this review help understand how lncRNAs are participating in the regulation of IFN-I signaling.
Collapse
Affiliation(s)
- Xiaoxin Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Wei Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
- *Correspondence: Zichuan Liu, ; Xin Mu,
| |
Collapse
|
5
|
Coexpression Network Analysis of lncRNA Associated with Overexpression of DNMT1 in Esophageal Epithelial Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7162270. [PMID: 34660799 PMCID: PMC8519683 DOI: 10.1155/2021/7162270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
Screening and preliminary identification of high DNMT1 expression-related lncRNA, which is involved in various interrelated signaling pathways, has led to the development of a theoretical basis for various types of disease mechanisms. Differential expression profiles of lncRNA and mRNA were identified in a microarray. Ten lncRNAs with high levels of variation were identified by qRT-PCR. KEGG and GO analyses were used to identify differentially expressed mRNAs. Six signaling pathways were selected based on the KEGG results of the lncRNA-mRNA expression network analysis. From the microarrays in the experimental and control groups, we found a total of 6987 differentially expressed lncRNAs, and 7421 differentially expressed mRNAs were obtained (P < 0.05; fold change > 2.0x). GO analysis and KEGG pathway analysis showed high expression of DNMT1 in esophageal epithelial cells. Nine pathways were involved in mRNA upregulation, including natural killer cell-mediated cytotoxicity and many other prominent biochemical pathways. Forty-six pathways were associated with downregulated mRNAs and ribosomes involving multiple biological pathways. Coexpression network analysis showed that 8 mRNAs and 16 lncRNAs were linked to the p53 signaling pathway. In Helicobacter pylori infections, interactions occurred between 22 lncRNAs and 11 mRNAs in the ErbB signaling pathway and between 19 lncRNAs and 8 mRNAs in epithelial cell signal transduction. Interactions were present between 19 lncRNAs and 5 mRNAs in the sphingolipid signaling pathway, along with interactions between 21 lncRNAs and 12 mRNAs in the PI3K-Akt signaling pathway. Cytotoxicity interactions occurred between 22 lncRNAs and 9 mRNAs in natural killer cells.
Collapse
|
6
|
Burgos M, Hurtado A, Jiménez R, Barrionuevo FJ. Non-Coding RNAs: lncRNAs, miRNAs, and piRNAs in Sexual Development. Sex Dev 2021; 15:335-350. [PMID: 34614501 DOI: 10.1159/000519237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a group of RNAs that do not encode functional proteins, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and short interfering RNAs (siRNAs). In the last 2 decades an effort has been made to uncover the role of ncRNAs during development and disease, and nowadays it is clear that these molecules have a regulatory function in many of the developmental and physiological processes where they have been studied. In this review, we provide an overview of the role of ncRNAs during gonad determination and development, focusing mainly on mammals, although we also provide information from other species, in particular when there is not much information on the function of particular types of ncRNAs during mammalian sexual development.
Collapse
Affiliation(s)
- Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Alicia Hurtado
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| |
Collapse
|
7
|
Tian H, Pan J, Fang S, Zhou C, Tian H, He J, Shen W, Meng X, Jin X, Gong Z. LncRNA DPP10-AS1 promotes malignant processes through epigenetically activating its cognate gene DPP10 and predicts poor prognosis in lung cancer patients. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0136. [PMID: 34106559 PMCID: PMC8330531 DOI: 10.20892/j.issn.2095-3941.2020.0136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE The purpose of this study was to explore the function and gene expression regulation of the newly identified lncRNA DPP10-AS1 in lung cancer, and its potential value as a prognostic biomarker. METHODS qRT-PCR and Western blot were conducted to detect the expression of DDP10-AS1 and DPP10 in lung cancer cell lines and tissues. The effects of DDP10-AS1 on DPP10 expression, cell growth, invasion, apoptosis, and in vivo tumor growth were investigated in lung cancer cells by Western blot, rescue experiments, colony formation, flow cytometry, and xenograft animal experiments. RESULTS The novel antisense lncRNA DPP10-AS1 was found to be highly expressed in cancer tissues (P < 0.0001), and its upregulation predicted poor prognosis in patients with lung cancer (P = 0.0025). Notably, DPP10-AS1 promoted lung cancer cell growth, colony formation, and cell cycle progression, and repressed apoptosis in lung cancer cells by upregulating DPP10 expression. Additionally, DPP10-AS1 facilitated lung tumor growth via upregulation of DPP10 protein in a xenograft mouse model. Importantly, DPP10-AS1 positively regulated DPP10 gene expression, and both were coordinately upregulated in lung cancer tissues. Mechanically, DPP10-AS1 was found to associate with DPP10 mRNA but did not enhance DPP10 mRNA stability. Hypomethylation of DPP10-AS1 and DPP10 contributed to their coordinate upregulation in lung cancer. CONCLUSIONS These findings indicated that the upregulation of the antisense lncRNA DPP10-AS1 promotes lung cancer malignant processes and facilitates tumorigenesis by epigenetically regulating its cognate sense gene DPP10. DPP10-AS1 may serve as a candidate prognostic biomarker and a potential therapeutic target in lung cancer.
Collapse
Affiliation(s)
- Haihua Tian
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Jinchang Pan
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Shuai Fang
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Chengwei Zhou
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Department of Thoracic Surgery, The Affiliated Hospital of Ningbo University School of Medicine, Ningbo 315020, China
| | - Hui Tian
- Department of Thoracic Surgery, The Affiliated Lihuili Hospital of Ningbo University, Ningbo 315048, China
| | - Jinxian He
- Department of Thoracic Surgery, The Affiliated Lihuili Hospital of Ningbo University, Ningbo 315048, China
| | - Weiyu Shen
- Department of Thoracic Surgery, The Affiliated Lihuili Hospital of Ningbo University, Ningbo 315048, China
| | - Xiaodan Meng
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Zhaohui Gong
- Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine, Ningbo 315211, China
- Zhejiang Province Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| |
Collapse
|
8
|
Otsuka K, Matsubara S, Shiraishi A, Takei N, Satoh Y, Terao M, Takada S, Kotani T, Satake H, Kimura AP. A Testis-Specific Long Noncoding RNA, Start, Is a Regulator of Steroidogenesis in Mouse Leydig Cells. Front Endocrinol (Lausanne) 2021; 12:665874. [PMID: 33897623 PMCID: PMC8061315 DOI: 10.3389/fendo.2021.665874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022] Open
Abstract
The testis expresses many long noncoding RNAs (lncRNAs), but their functions and overview of lncRNA variety are not well understood. The mouse Prss/Tessp locus contains six serine protease genes and two lncRNAs that have been suggested to play important roles in spermatogenesis. Here, we found a novel testis-specific lncRNA, Start (Steroidogenesis activating lncRNA in testis), in this locus. Start is 1822 nucleotides in length and was found to be localized mostly in the cytosol of germ cells and Leydig cells, although nuclear localization was also observed. Start-knockout (KO) mice generated by the CRISPR/Cas9 system were fertile and showed no morphological abnormality in adults. However, in adult Start-KO testes, RNA-seq and qRT-PCR analyses revealed an increase in the expression of steroidogenic genes such as Star and Hsd3b1, while ELISA analysis revealed that the testosterone levels in serum and testis were significantly low. Interestingly, at 8 days postpartum, both steroidogenic gene expression and testosterone level were decreased in Start-KO mice. Since overexpression of Start in two Leydig-derived cell lines resulted in elevation of the expression of steroidogenic genes including Star and Hsd3b1, Start is likely to be involved in their upregulation. The increase in expression of steroidogenic genes in adult Start-KO testes might be caused by a secondary effect via the androgen receptor autocrine pathway or the hypothalamus-pituitary-gonadal axis. Additionally, we observed a reduced number of Leydig cells at 8 days postpartum. Collectively, our results strongly suggest that Start is a regulator of steroidogenesis in Leydig cells. The current study provides an insight into the overall picture of the function of testis lncRNAs.
Collapse
Affiliation(s)
- Kai Otsuka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Natsumi Takei
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of NCCHD Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoya Kotani
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P. Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
- *Correspondence: Atsushi P. Kimura,
| |
Collapse
|
9
|
Bandara TAMK, Otsuka K, Matsubara S, Shiraishi A, Satake H, Kimura AP. A dual enhancer-silencer element, DES-K16, in mouse spermatocyte-derived GC-2spd(ts) cells. Biochem Biophys Res Commun 2020; 534:1007-1012. [PMID: 33121685 DOI: 10.1016/j.bbrc.2020.10.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/18/2020] [Indexed: 12/23/2022]
Abstract
The multifunctionality of genome is suggested at some loci in different species but not well understood. Here we identified a DES-K16 region in an intron of the Kctd16 gene as the chromatin highly marked with epigenetic modifications of both enhancers (H3K4me1 and H3K27ac) and silencers (H3K27me3) in mouse spermatocytes. In vitro reporter gene assay demonstrated that DES-K16 exhibited significant enhancer activity in spermatocyte-derived GC-2spd(ts) and hepatic tumor-derived Hepa1-6 cells, and a deletion of this sequence in GC-2spd(ts) cells resulted in a decrease and increase of Yipf5 and Kctd16 expression, respectively. This was consistent with increased and decreased expression of Yipf5 and Kctd16, respectively, in primary spermatocytes during testis development. While known dual enhancer-silencers exert each activity in different tissues, our data suggest that DES-K16 functions as both enhancer and silencer in a single cell type, GC-2spd(ts) cells. This is the first report on a dual enhancer-silencer element which activates and suppresses gene expression in a single cell type.
Collapse
Affiliation(s)
| | - Kai Otsuka
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Sorakugun, Kyoto, 619-0284, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Sorakugun, Kyoto, 619-0284, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Sorakugun, Kyoto, 619-0284, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Wang Y, Li D, Lu J, Chen L, Zhang S, Qi W, Li W, Xu H. Long noncoding RNA TTN-AS1 facilitates tumorigenesis and metastasis by maintaining TTN expression in skin cutaneous melanoma. Cell Death Dis 2020; 11:664. [PMID: 32820147 PMCID: PMC7441063 DOI: 10.1038/s41419-020-02895-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 01/23/2023]
Abstract
The antisense transcript, emanating from the opposite strand to a protein-coding or sense strand, has been reported to have critical roles in gene regulation. The perturbation of an antisense RNA can alter the expression of sense messenger RNAs. In this study, a long noncoding RNA TTN-AS1 (lncRNA-TTN-AS1), which is transcribed in the opposite direction of the human titin (TTN) gene, has been identified and explored in skin cutaneous melanoma (SKCM). We found that the expression of TTN and lncRNA-TTN-AS1 had a significantly positive correlation in SKCM cells. Functionally, ectopic expression of TTN and lncRNA-TTN-AS1 promoted SKCM tumorigenesis and metastasis both in vitro and in vivo. Moreover, knockdown of TTN partially abrogated lncRNA-TTN-AS1 induced SKCM tumorigenesis. Mechanistically, hypomethylation of transcription initiation site was responsible for lncRNA-TTN-AS1 high expression levels. LncRNA-TTN-AS1 facilitated SKCM progression by promoting TTN expression at both transcriptional and posttranscriptional levels. As detailed, lncRNA-TTN-AS1 had a significant effect on the increase of TTN promoter activity. Besides, lncRNA-TTN-AS1 also induced the accumulation of TTN in cytoplasm by increasing the stability of TTN mRNA. Clinically, we found that high TTN and lncRNA-TTN-AS1 expression were positively correlated with poor overall survival of SKCM patients, and may be considered as novel biomarkers and drug targets for SKCM patients.
Collapse
Affiliation(s)
- Ying Wang
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Dongping Li
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Jiqiang Lu
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Lin Chen
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Shengnan Zhang
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Weiyan Qi
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Weiguang Li
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China
| | - Hanmei Xu
- The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province, China Pharmaceutical University, Nanjing, 210009, China. .,State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
12
|
Satoh Y, Takei N, Kawamura S, Takahashi N, Kotani T, Kimura AP. A novel testis-specific long noncoding RNA, Tesra, activates the Prss42/Tessp-2 gene during mouse spermatogenesis†. Biol Reprod 2020; 100:833-848. [PMID: 30379984 PMCID: PMC6437258 DOI: 10.1093/biolre/ioy230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/06/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023] Open
Abstract
The progression of spermatogenesis is precisely controlled by meiotic stage-specific genes, but the molecular mechanism for activation of such genes is still elusive. Here we found a novel testis-specific long noncoding RNA (lncRNA), Tesra, that was specifically expressed in the mouse testis at the Prss/Tessp gene cluster on chromosome 9. Tesra was transcribed downstream of Prss44/Tessp-4, starting within the gene, as a 4435-nucleotide transcript and developmentally activated at a stage similar to that for Prss/Tessp genes. By in situ hybridization, Tesra was found to be localized in and around germ cells and Leydig cells, being consistent with biochemical data showing its existence in cytoplasmic, nuclear, and extracellular fractions. Based on the finding of more signals in nuclei of pachytene spermatocytes, we explored the possibility that Tesra plays a role in transcriptional activation of Prss/Tessp genes. By a ChIRP assay, the Tesra transcript was found to bind to the Prss42/Tessp-2 promoter region in testicular germ cells, and transient overexpression of Tesra significantly activated endogenous Prss42/Tessp-2 expression and increased Prss42/Tessp-2 promoter activity in a reporter construct. These findings suggest that Tesra activates the Prss42/Tessp-2 gene by binding to the promoter. Finally, we investigated whether Tesra co-functioned with enhancers adjacent to another lncRNA, lncRNA-HSVIII. In the Tet-on system, Tesra transcription significantly increased activity of one enhancer, but Tesra and the enhancer were not interdependent. Collectively, our results proposed a potential function of an lncRNA, Tesra, in transcriptional activation and suggest a novel relationship between an lncRNA and an enhancer.
Collapse
Affiliation(s)
- Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Natsumi Takei
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shohei Kawamura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Nobuhiko Takahashi
- Department of Internal Medicine, School of Dentistry, Health Sciences University of Hokkaido, Kanazawa, Ishikari-Tobetsu, Japan
| | - Tomoya Kotani
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
13
|
Fu Y, Zhang Y, Cui J, Yang G, Peng S, Mi W, Yin X, Yu Y, Jiang J, Liu Q, Qin Y, Xu W. SNP rs12982687 affects binding capacity of lncRNA UCA1 with miR-873-5p: involvement in smoking-triggered colorectal cancer progression. Cell Commun Signal 2020; 18:37. [PMID: 32143722 PMCID: PMC7059387 DOI: 10.1186/s12964-020-0518-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND This investigation was arranged to elucidate whether single nucleotide polymorphisms (SNPs) of lncRNA UCA1 was implicated in elevating colorectal cancer (CRC) risk by interacting with environmental exposures. METHODS LncRNASNP database was firstly adopted to predict SNPs that possibly affected binding of UCA1 with miRNAs and then the interactive effect of SNPs and environmental exposure on CRC risk was evaluated by recurring to type 2 gene-environment interactions (GEI) model. Besides, MTT assay, colony formation assay, transwell assay and wound healing assay were performed to assess the activity of CRC cell lines which carried distinct genotypes of specific SNPs. The impact of nicotine on activity of CRC cells was also appraised. RESULTS SNP rs12982687 of UCA1 intervened in the binding capacity of UCA1 with several miRNAs, especially miR-873-5p. MiRNAs regulated by UCA1, as predicted by mirPath software, shared genes that were enriched in HIF1 signaling pathway. Moreover, homozygote TT of rs12982687 reduced CRC risk among smokers, and CRC cells that carried rs12982687 (CC) displayed strong migration and invasion. By contrast, miR-873-5p mimic, which reduced UCA1 expression, delayed metastasis of CRC cells (all P < 0.05). Additionally, nicotine not merely elevated UCA1 and HIF-1α expressions in CRC cells, but also facilitated proliferation and metastasis of CRC cells (P < 0.05). CONCLUSIONS SNP rs12982687 was involved in smoking-triggered CRC progression, given its influence on UCA1's binding with miR-873-5p and HIF-1 signaling.
Collapse
Affiliation(s)
- Yang Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China.
| | - Yizheng Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Jinyuan Cui
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Ge Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Sanfei Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Wunan Mi
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Xiangya Yin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Yang Yu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Jianwu Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Qi Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, 450052, Henan Province, China
| | - Yiyu Qin
- Research Centre of Biomedical Technology, Jiangsu Vocational College of Medicine, No. 283 Jianfang South Road, Yancheng City, Jiangsu Province, 224000, China.
| | - Wen Xu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai, 200237, China.
| |
Collapse
|
14
|
Cheng M, Huang X, Zhang M, Huang Q. Computational and functional analyses of T2D GWAS SNPs for transcription factor binding. Biochem Biophys Res Commun 2020; 523:658-665. [PMID: 31948755 DOI: 10.1016/j.bbrc.2019.12.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022]
Abstract
Genome-wide association studies (GWASs) have successfully identified numerous non-coding genetic variants for type 2 diabetes (T2D), but the functional roles underlying these non-coding variants remain largely unknown. The effects of T2D GWAS lead SNPs on transcriptional factors binding motifs were firstly analyzed via JASPAR, followed by functional validations including dual-luciferase reporter assays, biotin-based DNA pull-down assays, real-time quantitative PCR, and western blotting. The results showed that GWAS SNP rs4430796 conferred T allele specific transcriptional enhancer activity via a PAX6 binding element, and upregulated the expression of HNF1B. GWAS SNP rs4607103 showed a bidirectional modulation of ADAMTS9-AS2 and ADAMTS9 by TCF7L2 in a T allele-specific manner. GWAS SNP rs849135 conferred C allele-specific bidirectional transcriptional enhancer activity via a CREB1 binding element. Our findings have uncovered the functional mechanisms of three T2D GWAS SNPs via affecting the binding of transcription factors, providing new insights into the genetics and molecular pathogenesis of T2D.
Collapse
Affiliation(s)
- Mengrong Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China; College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, Hubei, PR China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Manling Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China.
| |
Collapse
|
15
|
Li C, Shen C, Shang X, Tang L, Xiong W, Ge H, Zhang H, Lu S, Shen Y, Wang J, Fei J, Wang Z. Two novel testis-specific long noncoding RNAs produced by <i>1700121C10Rik</i> are dispensable for male fertility in mice. J Reprod Dev 2019; 66:57-65. [PMID: 31801914 PMCID: PMC7040208 DOI: 10.1262/jrd.2019-104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Testis-specific genes are prone to affect spermatogenesis or sperm fertility, and thus may play pivotal roles in male reproduction. However, whether a gene really affects male reproduction
in vivo needs to be confirmed using a gene knock-out (KO) model, a ‘gold standard’ method. Increasing studies have found that some of the evolutionarily conserved
testis-enriched genes are not essential for male fertility. In this study, we report that 1700121C10Rik, a previously uncharacterized gene, is specifically expressed in the
testis and produces two long noncoding RNAs (lncRNAs) in mouse: Transcript 1 and Transcript 2. qRT-PCR, northern blotting, and in situ hybridization revealed that expression
of both the lncRNAs commenced at the onset of sexual maturity and was predominant in round and elongating spermatids during spermiogenesis. Moreover, we found different subcellular
localization of Transcript 1 and Transcript 2 that was predominant in the cytoplasm and nucleus, respectively. 1700121C10Rik-KO mouse model disrupting Transcript 1 and
Transcript 2 expression was generated by CRISPR/Cas9 to determine their role in male reproduction. Results showed that 1700121C10Rik-KO male mice were fully fertile with
approximately standard testis size, testicular histology, sperm production, sperm morphology, sperm motility, and induction of acrosome reaction. Thus, we conclude that both the
testis-specific 1700121C10Rik-produced lncRNAs are dispensable for male fertility in mice under standard laboratory conditions.
Collapse
Affiliation(s)
- Chaojie Li
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chunling Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xuan Shang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingyun Tang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wenfeng Xiong
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haoyang Ge
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongxin Zhang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shunyuan Lu
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yan Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinjin Wang
- Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Jian Fei
- Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Zhugang Wang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Research Center for Model Organisms, Shanghai 201203, China
| |
Collapse
|
16
|
Sun L, Zhou R, Dong J, Liu S, Jiao Y, Wang L, Hu S, He P, Liu X, Zhao X, Jiang G, Zhao Y. Lnc-NA inhibits proliferation and metastasis in endometrioid endometrial carcinoma through regulation of NR4A1. J Cell Mol Med 2019; 23:4699-4710. [PMID: 31050196 PMCID: PMC6584524 DOI: 10.1111/jcmm.14345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 02/09/2019] [Accepted: 03/26/2019] [Indexed: 12/29/2022] Open
Abstract
Endometrioid endometrial carcinoma (EEC) is the most common gynaecologic malignancy worldwide. Long non-coding RNAs have previously been demonstrated to play important roles in regulating human diseases, particularly cancer. However, the biological functions and molecular mechanisms of long non-coding RNAs in EEC have not been extensively studied. Here, we describe the discovery of Lnc-NA from the promoter of the transcription factor nuclear receptor subfamily 4 group A member 1 (NR4A1) gene. The role and function of Lnc-NA in EEC remain unknown. In this study, we used quantitative real-time polymerase chain reactions to confirm that Lnc-NA expression was down-regulated in 30 EEC cases (90%) and in EEC cell lines compared with that in the paired adjacent tissues and normal endometrial cells. In vitro experiments further demonstrated that overexpressing Lnc-NA decreased EEC cell proliferation, migration and invasion and promoted apoptosis via inactivation of the apoptosis signalling pathway. Moreover, the results show that Lnc-NA expression was positively correlated with NR4A1. Furthermore, Lnc-NA regulated NR4A1 expression and activated the apoptosis signalling pathway to inhibit tumour progression. In summary, our results demonstrate that the Lnc-NA-NR4A1 axis could be a useful tumour suppressor and a promising therapeutic target for EEC.
Collapse
Affiliation(s)
- Linying Sun
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
- Institute of Public HealthTaishan Medical UniversityTaianChina
| | - Rongfang Zhou
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Jing Dong
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Shuang Liu
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Yulian Jiao
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Laicheng Wang
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Shengnan Hu
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Pengjuan He
- Department of Gynaecology and ObstetricsShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Xiaowen Liu
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Xingbo Zhao
- Department of Gynaecology and ObstetricsShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| | - Guosheng Jiang
- Department of ImmunologyBinzhou Medical UniversityYantaiChina
| | - Yueran Zhao
- Department of Central LabShandong Provincial Hospital affiliated with Shandong UniversityJinanChina
| |
Collapse
|
17
|
Dornelles-Wawruk H, Soledad Heredia R, de Paula-Junior MR, Cardoso MTO, Bonadio RS, Dos Reis BF, Pic-Taylor A, de Oliveira SF, Mazzeu JF. A Balanced Reciprocal Translocation t(2;9)(p25;q13) Disrupting the LINC00299 Gene in a Patient with Intellectual Disability. Mol Syndromol 2019; 10:234-238. [PMID: 31602198 DOI: 10.1159/000500397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a class of noncoding RNAs implicated in several biological processes. LincRNA 299 (LINC00299) maps to 2p25.1 and its function is still unknown. However, this gene has been proposed as a candidate for intellectual disability (ID) in a patient with a balanced translocation where the breakpoint disrupted its ORF. Here, we describe a new case of LINC00299 disruption associated with ID. The individual, a 42-year-old woman, was referred to the clinical geneticist because of her son who had severe syndromic ID. G-banding and chromosomal microarray analysis were performed. Karyotyping of the boy revealed an extranumerary derivative chromosome identified as an unbalanced translocation between chromosomes 2 and 9 of maternal origin. The mother's karyotype showed a balanced translocation 46,XX,t(2;9)(p25;q13). Chromosomal microarray indicated a disruption of LINC00299. These data corroborate the role of LINC00299 as a causative gene for ID and broadens the spectrum of LINC00299-related phenotypes.
Collapse
Affiliation(s)
| | - Romina Soledad Heredia
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil
| | | | | | - Raphael S Bonadio
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Bianca F Dos Reis
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Silviene F de Oliveira
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil
| |
Collapse
|
18
|
Wang P, Yang X, Zhao L, Liu D, Liu J, Ding Y. A novel long non-coding RNA TONSL-AS1 regulates progression of gastric cancer via activating TONSL. Exp Cell Res 2019; 382:111453. [PMID: 31158361 DOI: 10.1016/j.yexcr.2019.05.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 01/17/2023]
Abstract
Long non-coding RNAs (lncRNAs) are reported to play a significant role in various malignant tumors, yet their potential functions in gastric cancer are not clear. In this study, we found a novel lncRNA, named TONSL-AS1, was downregulated in gastric cancer tissues and cell lines compared with the normal. TONSL-AS1 inhibited cell migration, invasion and proliferation in SGC-7901, MGC-803 cells. Furthermore, TONSL-AS1 could suppress cell tumorigenesis in vivo. Mechanistically, TONSL-AS1's genomic neighboring gene TONSL, which was reported as a tumor suppress gene, was upregulated by TONSL. Additionally, the TONSL-AS1 was positively associated with TONSL in cancer tissues. Our study revealed that the tumor-inhibiting effect of TONSL-AS1 in gastric cancer cells was associated with TONSL. In general, our results indicated that TONSL-AS1 works as a tumor suppressor lncRNA, which may be a new therapeutic target for gastric cancer.
Collapse
Affiliation(s)
- Peng Wang
- Department of General Surgery, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No.1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China; Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Xi Yang
- Department of Gastroenterology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No. 1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China
| | - Liang Zhao
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Dongxiao Liu
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Junmao Liu
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Yongbin Ding
- Department of General Surgery, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No.1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China; Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University. No. 300, Guangzhou Road, Nanjing, Jiangsu, China.
| |
Collapse
|
19
|
LncRNA ZBTB40-IT1 modulated by osteoporosis GWAS risk SNPs suppresses osteogenesis. Hum Genet 2019; 138:151-166. [PMID: 30661131 DOI: 10.1007/s00439-019-01969-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Previous genome-wide linkage and association studies have identified an osteoporosis-associated locus at 1p36 that harbors SNPs rs34920465 and rs6426749. The 1p36 locus also comprises the WNT4 gene with known role in bone metabolism and functionally unknown ZBTB40/lncRNA ZBTB40-IT1 genes. How these might interact to contribute to osteoporosis susceptibility is not known. In this study, we show that lncRNA ZBTB40-IT1 is able to suppress osteogenesis and promote osteoclastogenesis by regulating the expression of WNT4, RUNX2, OSX, ALP, COL1A1, OPG and RANKL in U-2OS and hFOB1.19 cell lines, whereas ZBTB40 plays an opposite role in bone metabolism. Treatment with parathyroid hormone significantly downregulates the expression of ZBTB40-IT1 in U-2OS cell lines. ZBTB40 can suppress ZBTB40-IT1 expression but has no response to parathyroid hormone treatment. Dual-luciferase assay and biotin pull-down assay demonstrate that osteoporosis GWAS lead SNPs rs34920465-G and rs6426749-C alleles can respectively bind transcription factors JUN::FOS and CREB1, and upregulate ZBTB40 and ZBTB40-IT1 expression. Our study discovers the critical role of ZBTB40 and lncRNA ZBTB40-IT1 in bone metabolism, and provides a mechanistic basis for osteoporosis GWAS lead SNPs rs34920465 and rs6426749.
Collapse
|
20
|
Jia J, Zhan D, Li J, Li Z, Li H, Qian J. The contrary functions of lncRNA HOTAIR/miR-17-5p/PTEN axis and Shenqifuzheng injection on chemosensitivity of gastric cancer cells. J Cell Mol Med 2018; 23:656-669. [PMID: 30338929 PMCID: PMC6307763 DOI: 10.1111/jcmm.13970] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/20/2018] [Accepted: 09/24/2018] [Indexed: 01/30/2023] Open
Abstract
This study was implemented to figure out whether lncRNA HOTAIR/miR‐17‐5p/PTEN axis played a role that was opposite to Shenqifuzheng (SQFZ) injection in regulating the chemosensitivity of gastric cancer cells. The gastric cancer tissues were gathered and four gastric cancer cell lines were prepared, including BGC‐823, MGC‐803, SGC‐7901, and MKN28. Moreover, cisplatin, adriamycin, mitomycin, and 5‐fluoroura were managed as the chemo‐therapeutics, and SQFZ was prepared as a Chinese medicine. Striking distinctions of HOTAIR, miR‐17‐5p, and PTEN expressions were observed between gastric cancer tissues and para‐carcinoma normal tissues (P < 0.05). MKN28 was associated with the highest resistance to cisplatin, adriamycin, mitomycin, and 5‐fluoroura among all the cell types, and SQFZ significantly improved the MKN28 cells’ sensitivity to the drugs (P < 0.05). The over‐expressed HOTAIR and miR‐17‐5p, as well as under‐expressed PTEN tended to significantly facilitate the viability, EMT process and proliferation of MKN28 cells that were subject to treatment of chemo‐therapies (P < 0.05). SQFZ could amplify the effects of si‐HOTAIR, miR‐17‐5p inhibitor, and pcDNA‐PTEN on boosting the chemosensitivity of gastric cancer cells (P < 0.05). In addition, HOTAIR was also found to directly target miR‐17‐5p, and PTEN appeared to be subject to the modification of HOTAIR and miR‐17‐5p in its acting on the viability, proliferation, EMT process, and apoptosis of gastric cancer cells. The HOTAIR/miR‐17‐5p/PTEN axis could be regarded as the potential treatment targets for gastric cancer, and adjuvant therapy of SQFZ injection could assist in further improving the treatment efficacy of chemo‐therapies for gastric cancer.
Collapse
Affiliation(s)
- Jianguang Jia
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| | - Dankai Zhan
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| | - Jing Li
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| | - Zhixiang Li
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| | - Hongbo Li
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| | - Jun Qian
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu City, China
| |
Collapse
|
21
|
Adetula AA, Gu L, Nwafor CC, Du X, Zhao S, Li S. Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens. Sci Rep 2018; 8:13185. [PMID: 30181614 PMCID: PMC6123486 DOI: 10.1038/s41598-018-31301-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.
Collapse
Affiliation(s)
- Adeyinka Abiola Adetula
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Lantao Gu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | | | - Xiaoyong Du
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
| |
Collapse
|
22
|
Takei N, Nakamura T, Kawamura S, Takada Y, Satoh Y, Kimura AP, Kotani T. High-Sensitivity and High-Resolution In Situ Hybridization of Coding and Long Non-coding RNAs in Vertebrate Ovaries and Testes. Biol Proced Online 2018; 20:6. [PMID: 29507535 PMCID: PMC5831722 DOI: 10.1186/s12575-018-0071-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/29/2018] [Indexed: 12/22/2022] Open
Abstract
Background Subcellular localization of coding and non-coding RNAs has emerged as major regulatory mechanisms of gene expression in various cell types and many organisms. However, techniques that enable detection of the subcellular distribution of these RNAs with high sensitivity and high resolution remain limited, particularly in vertebrate adult tissues and organs. In this study, we examined the expression and localization of mRNAs encoding Pou5f1/Oct4, Mos, Cyclin B1 and Deleted in Azoospermia-like (Dazl) in zebrafish and mouse ovaries by combining tyramide signal amplification (TSA)-based in situ hybridization with paraffin sections which can preserve cell morphology of tissues and organs at subcellular levels. In addition, the distribution of a long non-coding RNA (lncRNA), lncRNA-HSVIII, in mouse testes was examined by the same method. Results The mRNAs encoding Mos, Cyclin B1 and Dazl were found to assemble into distinct granules that were distributed in different subcellular regions of zebrafish and mouse oocytes, suggesting conserved and specific regulations of these mRNAs. The lncRNA-HSVIII was first detected in the nucleus of spermatocytes at prophase I of the meiotic cell cycle and was then found in the cytoplasm of round spermatids, revealing expression patterns of lncRNA during germ cell development. Collectively, the in situ hybridization method demonstrated in this study achieved the detection and comparison of precise distribution patterns of coding and non-coding RNAs at subcellular levels in single cells of adult tissues and organs. Conclusions This high-sensitivity and high-resolution in situ hybridization is applicable to many vertebrate species and to various tissues and organs and will be useful for studies on the subcellular regulation of gene expression at the level of RNA localization. Electronic supplementary material The online version of this article (10.1186/s12575-018-0071-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Natsumi Takei
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takuma Nakamura
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Shohei Kawamura
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yuki Takada
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Satoh
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Atsushi P Kimura
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan.,2Department of Biological Sciences, Faculty of Science, Hokkaido University, North 10 West 8, Sapporo, Hokkaido 060-0810 Japan
| | - Tomoya Kotani
- 1Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan.,2Department of Biological Sciences, Faculty of Science, Hokkaido University, North 10 West 8, Sapporo, Hokkaido 060-0810 Japan
| |
Collapse
|
23
|
Yang X, Wang CC, Lee WYW, Trovik J, Chung TKH, Kwong J. Long non-coding RNA HAND2-AS1 inhibits invasion and metastasis in endometrioid endometrial carcinoma through inactivating neuromedin U. Cancer Lett 2018; 413:23-34. [DOI: 10.1016/j.canlet.2017.10.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 11/17/2022]
|
24
|
Kimura AP, Yoneda R, Kurihara M, Mayama S, Matsubara S. A Long Noncoding RNA, lncRNA-Amhr2, Plays a Role in Amhr2 Gene Activation in Mouse Ovarian Granulosa Cells. Endocrinology 2017; 158:4105-4121. [PMID: 28938492 DOI: 10.1210/en.2017-00619] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023]
Abstract
Anti-Müllerian hormone (AMH) is critical to the regression of Müllerian ducts during mammalian male differentiation and targets ovarian granulosa cells and testicular Sertoli and Leydig cells of adults. Specific effects of AMH are exerted via its receptor, AMH type II receptor (Amhr2), but the mechanism by which the Amhr2 gene is specifically activated is not fully understood. To see whether a proximal promoter was sufficient for Amhr2 gene activation, we generated transgenic mice that bore the enhanced green fluorescent protein (EGFP) gene driven by a 500-bp mouse Amhr2 gene promoter. None of the established 10 lines, however, showed appropriate EGFP expression, indicating that the 500-bp promoter was insufficient for Amhr2 gene activation. As a regulatory element, we found a long noncoding RNA, lncRNA-Amhr2, transcribed from upstream of the Amhr2 gene in ovarian granulosa cells and testicular Sertoli cells. In primary granulosa cells, knockdown of lncRNA-Amhr2 resulted in a decrease of Amhr2 messnger RNA level, and a transient reporter gene assay showed that lncRNA-Amhr2 activation increased Amhr2 promoter activity. The activity was correlated with lncRNA-Amhr2 transcription in stably transfected OV3121 cells derived from mouse granulosa cells. Moreover, by the Tet-on system, the induction of lncRNA-Amhr2 transcription dramatically increased Amhr2 promoter activity in OV3121 cells. These results indicate that lncRNA-Amhr2 plays a role in Amhr2 gene activation in ovarian granulosa cells by enhancing promoter activity, providing insight into Amhr2 gene regulation underlying the AMH signaling in the female reproductive system.
Collapse
Affiliation(s)
- Atsushi P Kimura
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryoma Yoneda
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Misuzu Kurihara
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shota Mayama
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shin Matsubara
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|
25
|
Catsper1 promoter is bidirectional and regulates the expression of a novel lncRNA. Sci Rep 2017; 7:13351. [PMID: 29042633 PMCID: PMC5645346 DOI: 10.1038/s41598-017-13867-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/03/2017] [Indexed: 11/10/2022] Open
Abstract
The Catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. We previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. In the present study, we found that the Catsper1 promoter has in vitro transcriptional activity in either orientation in GC-1 spg mouse spermatogonial cells. The results also showed that this promoter regulates the expression of a new divergent Catsper1 gene named Catsper1au (Catsper1 antisense upstream transcript). Catsper1au is expressed in adult male mouse testis and liver tissues but not in female mouse liver or ovary tissues. In the testis, Catsper1au is expressed in embryos at 11.5 days post-coitum and from newborns to adults. This gene is also expressed in 1- to 3-week postnatal hearts and in 1-week to adult stage livers. The analysis of the 1402 bp whole genome sequence revealed that Catsper1au is an intronless and polyadenylated lncRNA, located in the nuclei of Sertoli and spermatogenic cells from adult testis. These data indicate that Catsper1au is divergently expressed from the Catsper1 promoter and could regulate gene expression during spermatogenesis.
Collapse
|
26
|
Peng B, Liu A, Yu X, Xu E, Dai J, Li M, Yang Q. Silencing of lncRNA AFAP1-AS1 suppressed lung cancer development by regulatory mechanism in cis and trans. Oncotarget 2017; 8:93608-93623. [PMID: 29212176 PMCID: PMC5706822 DOI: 10.18632/oncotarget.20549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Although the long noncoding RNA AFAP1-AS1 has been shown to be involved in various types of cancer, its involvement in lung cancer remains poorly understood. In the current study, we found that AFAP1-AS1 was substantially over expressed in lung cancer tissues and cell lines. In addition, AFAP1-AS1 expression level was proven to be associated with the malignant features of lung cancer. Knockdown of AFAP1-AS1 significantly suppressed cell proliferation by increasing cell apoptosis and G0/G1 phase retardation of cell cycle in lung cancer cells. Furthermore, AFAP1-AS1 knockdown could suppress tumor growth of lung cancer in BALB/c nude mice. We also identified that AFAP1-AS1 silencing could influence the expression of AFAP1 and KRT1 on mRNA and protein level by cis and trans regulatory mechanism. Moreover, the oncogenic activities of AFAP1-AS1 on cell proliferation are partially mediated by KRT1. In summary, these findings demonstrate that AFAP1-AS1 plays an essential role in promoting lung cancer development in vitro and vivo. It indicated that AFAP1-AS1 is a promising prognostic predictor for patients with lung cancer.
Collapse
Affiliation(s)
- Baoying Peng
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Anfei Liu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Xuanwei Yu
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Guangzhou Military Command of Chinese People's Liberation Army, Guangzhou 510010, China
| | - Jiabin Dai
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Mengcheng Li
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Yuexiu District, Guangzhou 510120, PR China.,The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| |
Collapse
|
27
|
Wichman L, Somasundaram S, Breindel C, Valerio DM, McCarrey JR, Hodges CA, Khalil AM. Dynamic expression of long noncoding RNAs reveals their potential roles in spermatogenesis and fertility†. Biol Reprod 2017; 97:313-323. [DOI: 10.1093/biolre/iox084] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022] Open
Abstract
Abstract
Mammalian reproduction requires that males and females produce functional haploid germ cells through complex cellular differentiation processes known as spermatogenesis and oogenesis, respectively. While numerous studies have functionally characterized protein-coding genes and small noncoding RNAs (microRNAs and piRNAs) that are essential for gametogenesis, the roles of regulatory long noncoding RNAs (lncRNAs) are yet to be fully characterized. Previously, we and others have demonstrated that intergenic regions of the mammalian genome encode thousands of long noncoding RNAs, and many studies have now demonstrated their critical roles in key biological processes. Thus, we postulated that some lncRNAs may also impact mammalian spermatogenesis and fertility. In this study, we identified a dynamic expression pattern of lncRNAs during murine spermatogenesis. Importantly, we identified a subset of lncRNAs and very few mRNAs that appear to escape meiotic sex chromosome inactivation, an epigenetic process that leads to the silencing of the X- and Y-chromosomes at the pachytene stage of meiosis. Further, some of these lncRNAs and mRNAs show a strong testis expression pattern suggesting that they may play key roles in spermatogenesis. Lastly, we generated a mouse knockout of one X-linked lncRNA, Tslrn1 (testis-specific long noncoding RNA 1), and found that males carrying a Tslrn1 deletion displayed normal fertility but a significant reduction in spermatozoa. Our findings demonstrate that dysregulation of specific mammalian lncRNAs is a novel mechanism of low sperm count or infertility, thus potentially providing new biomarkers and therapeutic strategies.
Collapse
Affiliation(s)
- Lauren Wichman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Saigopal Somasundaram
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Christine Breindel
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana M. Valerio
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - John R. McCarrey
- Department of Biology, The University of Texas at San Antonio, Texas, USA
| | - Craig A. Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ahmad M. Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Case Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, USA
| |
Collapse
|
28
|
Kurihara M, Otsuka K, Matsubara S, Shiraishi A, Satake H, Kimura AP. A Testis-Specific Long Non-Coding RNA, lncRNA-Tcam1, Regulates Immune-Related Genes in Mouse Male Germ Cells. Front Endocrinol (Lausanne) 2017; 8:299. [PMID: 29163367 PMCID: PMC5673629 DOI: 10.3389/fendo.2017.00299] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022] Open
Abstract
Spermatogenesis is precisely controlled by hormones from the hypothalamus-pituitary-gonadal axis and testis-specific genes, but the regulatory mechanism is not fully understood. Recently, a large number of long non-coding RNAs (lncRNAs) are found to be transcribed at each stage of meiosis of male germ cells, and their functions in spermatogenesis have yet to be fully investigated. lncRNA-testicular cell adhesion molecule 1 (lncRNA-Tcam1) is a nuclear lncRNA which is specifically expressed in mouse male germ cells and presumed to play a role in gene regulation during meiosis. Here, we present the identification of potential target genes of lncRNA-Tcam1 using spermatocyte-derived GC-2spd(ts) cells. Initially, 55 target gene candidates were detected by RNA-sequencing of two GC-2spd(ts) cell clones that were stably transfected with transgenes to express lncRNA-Tcam1 at different levels. Expression of 21 genes of the candidates was found to be correlated with lncRNA-Tcam1 at 7-14 postnatal days, when lncRNA-Tcam1 expression was elevated. Subsequently, we examined expression levels of the 21 genes in other two GC-2spd(ts) clones, and 11 genes exhibited the correlation with lncRNA-Tcam1. Induction of lncRNA-Tcam1 transcription using the Tet-off system verified that six genes, Trim30a, Ifit3, Tgtp2, Ifi47, Oas1g, and Gbp3, were upregulated in GC-2spd(ts) cells, indicating that lncRNA-Tcam1 is responsible for the regulation of gene expression of the six genes. In addition, five of the six genes, namely, Ifit3, Tgtp2, Ifi47, Oas1g, and Gbp3, are immune response genes, and Trim30a is a negative regulator of immune response. Altogether, the present study suggests that lncRNA-Tcam1 is responsible for gene regulation for the immune response during spermatogenesis.
Collapse
Affiliation(s)
- Misuzu Kurihara
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Kai Otsuka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P. Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
- *Correspondence: Atsushi P. Kimura,
| |
Collapse
|
29
|
Lan T, Chang L, Wu L, Yuan Y. Downregulation of ZEB2-AS1 decreased tumor growth and metastasis in hepatocellular carcinoma. Mol Med Rep 2016; 14:4606-4612. [PMID: 27748842 PMCID: PMC5102020 DOI: 10.3892/mmr.2016.5836] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/20/2016] [Indexed: 01/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the most common types of cancer worldwide and prognosis remains poor. Previous studies have suggested that long non-coding RNAs (lncRNAs) may be key regulators of tumor development and progression in HCC. It has been determined that 61–72% of transcribed regions contain lncRNAs in the antisense orientation (aslncRNAs). However, the function of aslncRNAs in HCC remains to be elucidated. The present study investigated the function of the aslncRNA zinc finger E-box binding homeobox 2 antisense RNA 1 (ZEB2-AS1) in 40 HCC tissues and 5 different human HCC cell lines using reverse transcription-quantitative polymerase chain reaction. Additionally, the expression levels of ZEB2-AS1 were downregulated by transfection of small interfering RNAs (siRNAs) to determine whether ZEB2-AS1 is capable of affecting cell proliferation, invasion and metastasis by regulating ZEB2, vimentin, fibronectin, E-cadherin and N-cadherin expression levels. The results of the present study demonstrated that the expression levels of ZEB2-AS1 were greater in HCC tissues when compared with the adjacent normal tissues. Furthermore, ZEB2-AS1 expression was significantly associated with the size of the primary tumor, intrahepatic metastasis and tumor-node-metastasis stage. The Kaplan-Meier survival curves suggested that patients with high ZEB2-AS1 expression levels experienced the lowest overall and recurrence-free survival rates compared with those that had low expression levels. In addition, the current study demonstrated that the downregulation of ZEB2-AS1 was associated with decreased tumor growth and metastasis in HCC by the regulation of the expression levels of epithelial mesenchymal transition-induced markers. In conclusion, lncRNA ZEB2-AS1 may be used as a valuable biomarker in patients with HCC.
Collapse
Affiliation(s)
- Tian Lan
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Lei Chang
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Long Wu
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yufeng Yuan
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| |
Collapse
|
30
|
Abstract
The last decade has been marked by an increased interest in relating epigenetic mechanisms to complex human behaviors, although this interest has not been balanced, accentuating various types of affective and primarily ignoring cognitive functioning. Recent animal model data support the view that epigenetic processes play a role in learning and memory consolidation and help transmit acquired memories even across generations. In this review, we provide an overview of various types of epigenetic mechanisms in the brain (DNA methylation, histone modification, and noncoding RNA action) and discuss their impact proximally on gene transcription, protein synthesis, and synaptic plasticity and distally on learning, memory, and other cognitive functions. Of particular importance are observations that neuronal activation regulates the dynamics of the epigenome's functioning under precise timing, with subsequent alterations in the gene expression profile. In turn, epigenetic regulation impacts neuronal action, closing the circle and substantiating the signaling pathways that underlie, at least partially, learning, memory, and other cognitive processes.
Collapse
|
31
|
Irano N, de Camargo GMF, Costa RB, Terakado APN, Magalhães AFB, Silva RMDO, Dias MM, Bignardi AB, Baldi F, Carvalheiro R, de Oliveira HN, de Albuquerque LG. Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle. PLoS One 2016; 11:e0159502. [PMID: 27494397 PMCID: PMC4975395 DOI: 10.1371/journal.pone.0159502] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/05/2016] [Indexed: 01/01/2023] Open
Abstract
The objective of this study was to perform a genome-wide association study (GWAS) to detect chromosome regions associated with indicator traits of sexual precocity in Nellore cattle. Data from Nellore animals belonging to farms which participate in the DeltaGen® and Paint® animal breeding programs, were used. The traits used in this study were the occurrence of early pregnancy (EP) and scrotal circumference (SC). Data from 72,675 females and 83,911 males with phenotypes were used; of these, 1,770 females and 1,680 males were genotyped. The SNP effects were estimated with a single-step procedure (WssGBLUP) and the observed phenotypes were used as dependent variables. All animals with available genotypes and phenotypes, in addition to those with only phenotypic information, were used. A single-trait animal model was applied to predict breeding values and the solutions of SNP effects were obtained from these breeding values. The results of GWAS are reported as the proportion of variance explained by windows with 150 adjacent SNPs. The 10 windows that explained the highest proportion of variance were identified. The results of this study indicate the polygenic nature of EP and SC, demonstrating that the indicator traits of sexual precocity studied here are probably controlled by many genes, including some of moderate effect. The 10 windows with large effects obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27, and together explained 7.91% of the total genetic variance. For SC, these windows are located on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of total variance. GWAS permitted to identify chromosome regions associated with EP and SC. The identification of these regions contributes to a better understanding and evaluation of these traits, and permits to indicate candidate genes for future investigation of causal mutations.
Collapse
Affiliation(s)
- Natalia Irano
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | | | - Raphael Bermal Costa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Ana Paula Nascimento Terakado
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Ana Fabrícia Braga Magalhães
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Rafael Medeiros de Oliveira Silva
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Marina Mortati Dias
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Annaiza Braga Bignardi
- Grupo de Melhoramento Animal de Mato Grosso, Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Mato Grosso, Rondonópolis, Mato Grosso, Brasil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Henrique Nunes de Oliveira
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
| | - Lucia Galvão de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brasil
- * E-mail:
| |
Collapse
|
32
|
LncRNA, a new component of expanding RNA-protein regulatory network important for animal sperm development. Semin Cell Dev Biol 2016; 59:110-117. [PMID: 27345292 DOI: 10.1016/j.semcdb.2016.06.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022]
Abstract
Spermatogenesis is one of the fundamental processes of sexual reproduction, present in almost all metazoan animals. Like many other reproductive traits, developmental features and traits of spermatogenesis are under strong selective pressure to change, both at morphological and underlying molecular levels. Yet evidence suggests that some fundamental features of spermatogenesis may be ancient and conserved among metazoan species. Identifying the underlying conserved molecular mechanisms could reveal core components of metazoan spermatogenic machinery and provide novel insight into causes of human infertility. Conserved RNA-binding proteins and their interacting RNA network emerge to be a common theme important for animal sperm development. We review research on the recent addition to the RNA family - Long non-coding RNA (lncRNA) and its roles in spermatogenesis in the context of the expanding RNA-protein network.
Collapse
|
33
|
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
| |
Collapse
|
34
|
A long non-coding RNA, BC048612 and a microRNA, miR-203 coordinate the gene expression of neuronal growth regulator 1 (NEGR1) adhesion protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:533-43. [DOI: 10.1016/j.bbamcr.2015.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 11/20/2015] [Accepted: 12/16/2015] [Indexed: 12/26/2022]
|
35
|
Tsai YC, Cooke NE, Liebhaber SA. Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster. Nucleic Acids Res 2016; 44:4651-64. [PMID: 26893355 PMCID: PMC4889918 DOI: 10.1093/nar/gkw090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/03/2016] [Indexed: 12/12/2022] Open
Abstract
The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR 'loops' over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed 'hCS chromatin hub'. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster.
Collapse
Affiliation(s)
- Yu-Cheng Tsai
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
| | - Nancy E Cooke
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
| | - Stephen A Liebhaber
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
| |
Collapse
|
36
|
Long non-coding RNA LOC389641 promotes progression of pancreatic ductal adenocarcinoma and increases cell invasion by regulating E-cadherin in a TNFRSF10A-related manner. Cancer Lett 2015; 371:354-65. [PMID: 26708505 DOI: 10.1016/j.canlet.2015.12.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators in pathological processes, yet their potential roles in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we found that a novel lncRNA, LOC389641, was upregulated in PDAC tissues and cell lines. The expression of LOC389641 was significantly correlated with staging, lymph node metastasis and overall survival. Knockdown of LOC389641 impaired cell proliferation and invasion and induced cell apoptosis in vitro, whereas overexpression of LOC389641 had the opposite effect. The growth promoting effect of LOC389641 was also demonstrated in vivo. Further, a significant negative correlation was observed between E-cadherin levels and LOC389641 levels in vivo. Knockdown of LOC389641 upregulated E-cadherin expression, but knockdown of E-cadherin had a limited influence on LOC389641. Importantly, after E-cadherin was inhibited, the enhancement of LOC389641 on cell invasion was hindered. Moreover, the expression of LOC389641 was closely associated with its genomic neighboring gene TNFRSF10A. Lastly, knockdown experiments showed that TNFRSF10A might be a connection between LOC389641and E-cadherin. We conclude that LOC389641 promotes PDAC progression and increases cell invasion by regulating E-cadherin with the possible involvement of TNFRSF10A.
Collapse
|
37
|
Li T, Xie J, Shen C, Cheng D, Shi Y, Wu Z, Deng X, Chen H, Shen B, Peng C, Li H, Zhan Q, Zhu Z. Upregulation of long noncoding RNA ZEB1-AS1 promotes tumor metastasis and predicts poor prognosis in hepatocellular carcinoma. Oncogene 2015; 35:1575-84. [PMID: 26073087 DOI: 10.1038/onc.2015.223] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 03/10/2015] [Accepted: 03/30/2015] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. Despite progress in diagnostics and treatment of HCC, its prognosis remains poor. Emerging studies showed that long noncoding RNAs (lncRNAs) have crucial regulatory roles in cancer biology. In the current study, differentially expressed lncRNAs between HCC and paired non-tumor tissues were identified using microarrays. The effects of a specific differentially expressed lncRNA (termed ZEB1-AS1) on tumor progression were investigated in vitro and in vivo. We found that ZEB1-AS1 is frequently upregulated in HCC samples, especially in metastatic tumor tissues. DNA methylation analysis shows a tumor-specific ZEB1-AS1 promoter hypomethylation. Aberrant methylation is tightly correlated with overexpression of ZEB1-AS1 in HCC. Patients with ZEB1-AS1 hypomethylation or with high ZEB1-AS1 expression have poor recurrence-free survival. Functionally, ZEB1-AS1 promotes tumor growth and metastasis, acts as an oncogene in HCC. The ZEB1-AS1 gene is located in physical contiguity with ZEB1 and positively regulates the ZEB1 expression. ZEB1 inhibition partially abrogates ZEB1-AS1-induced epithelial to mesenchymal transition (EMT) and cancer metastasis. Our results provide novel insights into the function of lncRNA-driven hepatocarcinogenesis, highlight the important role of ZEB1-AS1 and ZEB1 in HCC progression, and indicate that ZEB1-AS1 may be served as a valuable prognostic biomarker for HCC.
Collapse
Affiliation(s)
- T Li
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - J Xie
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - C Shen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - D Cheng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Y Shi
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Z Wu
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - X Deng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - H Chen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - B Shen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - C Peng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - H Li
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Q Zhan
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Z Zhu
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, People's Republic of China
| |
Collapse
|
38
|
Li T, Xie J, Shen C, Cheng D, Shi Y, Wu Z, Deng X, Chen H, Shen B, Peng C, Li H, Zhan Q, Zhu Z. Amplification of Long Noncoding RNA ZFAS1 Promotes Metastasis in Hepatocellular Carcinoma. Cancer Res 2015; 75:3181-91. [PMID: 26069248 DOI: 10.1158/0008-5472.can-14-3721] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 06/02/2015] [Indexed: 12/17/2022]
Abstract
Despite progress in the diagnostics and treatment of hepatocellular carcinoma (HCC), its prognosis remains poor. In this study, we globally assessed long noncoding RNAs (lncRNA) for contributions to HCC using publicly available microarray data, in vitro and in vivo assays. Here, we report that ZFAS1, encoding a lncRNA that is frequently amplified in HCC, is associated with intrahepatic and extrahepatic metastasis and poor prognosis of HCC. ZFAS1 functions as an oncogene in HCC progression by binding miR-150 and abrogating its tumor-suppressive function in this setting. miR-150 repressed HCC cell invasion by inhibiting ZEB1 and the matrix metalloproteinases MMP14 and MMP16. Conversely, ZFAS1 activated ZEB1, MMP14, and MMP16 expression, inhibiting these effects of miR-150. Our results establish a function for ZFAS1 in metastatic progression and suggest its candidacy as a new prognostic biomarker and target for clinical management of HCC.
Collapse
Affiliation(s)
- Tao Li
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Junjie Xie
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Chuan Shen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Dongfeng Cheng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Yuan Shi
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Zhichong Wu
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Xiaxing Deng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Hao Chen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Baiyong Shen
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Chenghong Peng
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Hongwei Li
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Qian Zhan
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China
| | - Zhecheng Zhu
- Department of Hepato-Bilio-Pancreatic Surgery, Shanghai Institute of Digestive Surgery, Rui Jin Hospital affiliated with Shanghai Jiaotong University, Shanghai, China.
| |
Collapse
|
39
|
Kambara H, Gunawardane L, Zebrowski E, Kostadinova L, Jobava R, Krokowski D, Hatzoglou M, Anthony DD, Valadkhan S. Regulation of Interferon-Stimulated Gene BST2 by a lncRNA Transcribed from a Shared Bidirectional Promoter. Front Immunol 2015; 5:676. [PMID: 25688240 PMCID: PMC4311693 DOI: 10.3389/fimmu.2014.00676] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/15/2014] [Indexed: 01/30/2023] Open
Abstract
Recent genome-wide studies have revealed the presence of thousands of long non-protein-coding RNAs (lncRNAs), some of which may play critical roles in the cell. We have previously shown that a large number of lncRNAs show differential expression in response to interferon (IFN)α stimulation in primary human cells. Here, we show that a subset of IFN-induced lncRNAs are positioned in proximity of protein-coding IFN-stimulated genes (ISGs). The majority of gene pairs originated from bidirectional promoters and showed positively correlated expression. We focused our analysis on a pair consisting of the known protein-coding ISG, BST2, and an un-studied putative lncRNA originating from the promoter region of BST2 in a divergent orientation. We showed that this transcript was a multi-exonic, polyadenylated long RNA that lacked protein-coding capacity. BST2 and the lncRNA were both induced in response to IFNα in diverse cell types. The induction of both genes was mediated through the JAK-STAT pathway, suggesting that IFN-stimulated response elements within the shared promoter activated the transcription of both genes. RNAi-mediated knock-down of the lncRNA resulted in down-regulation of BST2, and we could show that this down-regulation occurred at the level of transcription. Forced overexpression of this lncRNA, which we named BST2 IFN-Stimulated Positive Regulator (BISPR), resulted in up-regulation of BST2, indicating that the regulation of expression of BST2 by BISPR is mediated through interactions involving BISPR RNA itself, rather than the impact of its transcription from an adjacent locus. Importantly, upon IFN stimulation, transcriptional activation of BISPR preceded the induction of BST2, suggesting that expression of BISPR facilitated the initiation of transcription in its paired protein-coding gene. The lncRNA-mediated transcriptional regulation described in this study may help govern the expression of additional protein-coding RNAs involved in IFN response and other cellular processes.
Collapse
Affiliation(s)
- Hiroto Kambara
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Lalith Gunawardane
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Elizabeth Zebrowski
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Lenche Kostadinova
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Raul Jobava
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Dawid Krokowski
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Maria Hatzoglou
- Department of Nutrition, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Donald D Anthony
- Divisions of Infectious and Rheumatic Diseases, Department of Medicine, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| | - Saba Valadkhan
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, OH , USA
| |
Collapse
|
40
|
Characterization of the humanTCAM1Ppseudogene and its activation by a potential dual promoter-enhancer: Comparison with a protein-coding mouse orthologue. FEBS Lett 2015; 589:540-7. [DOI: 10.1016/j.febslet.2015.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/14/2015] [Accepted: 01/15/2015] [Indexed: 11/17/2022]
|