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Ao X, Rong Y, Han M, Wang X, Xia Q, Shang F, Liu Y, Lv Q, Wang Z, Su R, Zhang Y, Wang R. Combined Genome-Wide Association Study and Haplotype Analysis Identifies Candidate Genes Affecting Growth Traits of Inner Mongolian Cashmere Goats. Vet Sci 2024; 11:428. [PMID: 39330807 DOI: 10.3390/vetsci11090428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 08/27/2024] [Accepted: 09/05/2024] [Indexed: 09/28/2024] Open
Abstract
In this study, genome-wide association analysis was performed on the growth traits (body height, body length, chest circumference, chest depth, chest width, tube circumference, and body weight) of Inner Mongolian cashmere goats (Erlangshan type) based on resequencing data. The population genetic parameters were estimated, haplotypes were constructed for the significant sites, and association analysis was conducted between the haplotypes and phenotypes. A total of two hundred and eighty-four SNPs and eight candidate genes were identified by genome-wide association analysis, gene annotation, and enrichment analysis. The phenotypes of 16 haplotype combinations were significantly different by haplotype analysis. Combined with the above results, the TGFB2, BAG3, ZEB2, KCNJ12, MIF, MAP2K3, HACD3, and MEGF11 functional candidate genes and the haplotype combinations A2A2, C2C2, E2E2, F2F2, I2I2, J2J2, K2K2, N2N2, O2O2, P2P2, R1R1, T1T1, W1W1, X1X1, Y1Y1, and Z1Z1 affected the growth traits of the cashmere goats and could be used as molecular markers to improve the accuracy of early selection and the economic benefits of breeding.
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Affiliation(s)
- Xiaofang Ao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Mingxuan Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xinle Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qincheng Xia
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yan Liu
- College of Vocational and Technical, Inner Mongolia Agricultural University, Baotou 014109, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot 010018, China
- Key Laboratory of Goat and Sheep Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot 010018, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
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Chen Y, Qiang R, Zhang Y, Cao W, Wu L, Jiang P, Ai J, Ma X, Dong Y, Gao X, Li H, Lu L, Zhang S, Chai R. The Expression and Roles of the Super Elongation Complex in Mouse Cochlear Lgr5+ Progenitor Cells. Front Cell Neurosci 2021; 15:735723. [PMID: 34658793 PMCID: PMC8519586 DOI: 10.3389/fncel.2021.735723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/14/2021] [Indexed: 12/04/2022] Open
Abstract
The super elongation complex (SEC) has been reported to play a key role in the proliferation and differentiation of mouse embryonic stem cells. However, the expression pattern and function of the SEC in the inner ear has not been investigated. Here, we studied the inner ear expression pattern of three key SEC components, AFF1, AFF4, and ELL3, and found that these three proteins are all expressed in both cochlear hair cells (HCs)and supporting cells (SCs). We also cultured Lgr5+ inner ear progenitors in vitro for sphere-forming assays and differentiation assays in the presence of the SEC inhibitor flavopiridol. We found that flavopiridol treatment decreased the proliferation ability of Lgr5+ progenitors, while the differentiation ability of Lgr5+ progenitors was not affected. Our results suggest that the SEC might play important roles in regulating inner ear progenitors and thus regulating HC regeneration. Therefore, it will be very meaningful to further investigate the detailed roles of the SEC signaling pathway in the inner ear in vivo in order to develop effective treatments for sensorineural hearing loss.
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Affiliation(s)
- Yin Chen
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Ruiying Qiang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Yuan Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Wei Cao
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Hospital of Anhui Medical University, Hefei, China
| | - Leilei Wu
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Pei Jiang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Jingru Ai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Xiangyu Ma
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Ying Dong
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Xia Gao
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - He Li
- Department of Otolaryngology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ling Lu
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Shasha Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
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3
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Zhang D, Zhang X, Li F, La Y, Li G, Zhang Y, Li X, Zhao Y, Song Q, Wang W. The association of polymorphisms in the ovine PPARGC1B and ZEB2 genes with body weight in Hu sheep. Anim Biotechnol 2020; 33:90-97. [PMID: 32496943 DOI: 10.1080/10495398.2020.1775626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aims of this study were to analyze the effects of PPARGC1B and ZEB2 polymorphisms on the body weight of Hu sheep. DNA sequencing and KASPar technologies were used to detect single nucleotide polymorphisms (SNPs) within the PPARGC1B and ZEB2 genes of Hu sheep (n = 207). Two synonymous mutations, g.300 G > A and g.645 C > T, were detected in PPARGC1B and ZEB2, respectively. The body weights of sheep were recorded at 80, 100, 120, 140, 160 and 180-days, and associations between these polymorphisms and body weight changes were analyzed. Association analysis demonstrated that the polymorphisms in PPARGC1B and ZEB2 significantly associated with body weight (p < 0.05). At the g.300 G > A locus, individuals with the GG genotype had significantly higher body weight than those with the AA genotype, and at the g.645 C > T locus, individuals with the TT genotype had significantly higher body weight than those with the TC genotype. Individuals with both polymorphisms exhibited significantly different growth (p < 0.05). These data suggest that polymorphisms in the PPARGC1B and ZEB2 genes can be used as candidate molecular markers for the breeding of desirable growth traits in Hu sheep.
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Affiliation(s)
- Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yongfu La
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Guoze Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Lee JY, Lee SH, Kim KS, Park KH, Park KS. Ell3 functions as a critical decision maker at the crossroad between stem cell senescence and apoptosis. Stem Cell Res Ther 2019; 10:32. [PMID: 30654843 PMCID: PMC6335702 DOI: 10.1186/s13287-019-1137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/16/2018] [Accepted: 01/07/2019] [Indexed: 11/23/2022] Open
Abstract
Background Ell3 is a RNA polymerase II elongation factor that has various cell type-dependent functions, such as regulating the differentiation efficiency of embryonic stem cells and sensitizing cancer cells to anticancer drugs. However, there has been little research on the role of Ell3 on the regulation of senescence and apoptosis of stem cells. Methods We analyzed the senescence of Ell3-suppressed stem cells by mitochondrial activity, β-gal (+) cells, and lineage differentiation efficiency. The apoptosis of Ell3-overexpressing stem cells was analyzed by Annexin V staining, Immunoblot, and Live&dead assay. In addition, chromatin immunoprecipitation and luciferase assays were used to demonstrate p53 functions as a direct transcriptional activator of Ell3. Results Suppression of Ell3 expression induced senescence in stem cells by increasing Bcl-2 expression. Unlike the effect of Ell3 suppression, the ectopic expression of Ell3 induces apoptosis of stem cells and induces apoptosis of adjacent cells. In addition, p53 functions as a direct transcriptional activator of Ell3 during the stem cell apoptosis. Conclusions We suggest that the function of Ell3 is associated with the p53-Bcl2 axis in both senescent and apoptotic ADSCs. Electronic supplementary material The online version of this article (10.1186/s13287-019-1137-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jae-Yong Lee
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Korea
| | - Soo-Hong Lee
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Korea
| | - Kwang-Soo Kim
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Korea
| | - Keun-Hong Park
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Korea.
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5
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Lee JY, Park YJ, Oh N, Kwack KB, Park KS. A transcriptional complex composed of ER(α), GATA3, FOXA1 and ELL3 regulates IL-20 expression in breast cancer cells. Oncotarget 2018; 8:42752-42760. [PMID: 28514748 PMCID: PMC5522103 DOI: 10.18632/oncotarget.17459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/15/2017] [Indexed: 11/25/2022] Open
Abstract
Interleukin-20 (IL-20) is a member of the IL-10 family. IL-20 expression is regulated by a transcription elongation factor, Ell3, in estrogen receptor-positive (ER(+)) breast cancer cells. In this study, we demonstrated that ER(α), GATA3 and FOXA1 form a transcriptional complex with Ell3 to regulate IL-20 expression in ER(+) breast cancer cells. We also determined that GATA3 and FOXA1 share a binding site with ER(α) in the interleukin-20 promoter. Furthermore, we found that FOXA1 represses IL-20 expression, whereas GATA3 and ER(α) activate it. In addition, we demonstrated that Ell3 associates with ER(α) to increase its binding affinity to the IL-20 promoter, which may prevent FOXA1 binding to the same region of this promoter. Our results expand upon the current understanding of the regulatory mechanism of IL-20 in cancer.
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Affiliation(s)
- Jae Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Young Joon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Nuri Oh
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Kyu Bum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
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6
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Alexander LEMM, Watters J, Reusch JA, Maurin M, Nepon-Sixt BS, Vrzalikova K, Alexandrow MG, Murray PG, Wright KL. Selective expression of the transcription elongation factor ELL3 in B cells prior to ELL2 drives proliferation and survival. Mol Immunol 2017; 91:8-16. [PMID: 28858629 DOI: 10.1016/j.molimm.2017.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/07/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022]
Abstract
B cell activation is dependent on a large increase in transcriptional output followed by focused expression on secreted immunoglobulin as the cell transitions to an antibody producing plasma cell. The rapid transcriptional induction is facilitated by the release of poised RNA pol II into productive elongation through assembly of the super elongation complex (SEC). We report that a SEC component, the Eleven -nineteen Lysine-rich leukemia (ELL) family member 3 (ELL3) is dynamically up-regulated in mature and activated human B cells followed by suppression as B cells transition to plasma cells in part mediated by the transcription repressor PRDM1. Burkitt's lymphoma and a sub-set of Diffuse Large B cell lymphoma cell lines abundantly express ELL3. Depletion of ELL3 in the germinal center derived lymphomas results in severe disruption of DNA replication and cell division along with increased DNA damage and cell death. This restricted utilization and survival dependence reveal a key step in B cell activation and indicate a potential therapeutic target against B cell lymphoma's with a germinal center origin.
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Affiliation(s)
- Lou-Ella M M Alexander
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33612, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - January Watters
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33612, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - Jessica A Reusch
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - Michelle Maurin
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - Brook S Nepon-Sixt
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - Katerina Vrzalikova
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark G Alexandrow
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States
| | - Paul G Murray
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kenneth L Wright
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
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7
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Ahn HJ, Kim KS, Shin KW, Lim KH, Kim JO, Lee JY, Kim J, Park JH, Yang KM, Baek KH, Ko JJ, Park KS. Ell3 stabilizes p53 following CDDP treatment via its effects on ubiquitin-dependent and -independent proteasomal degradation pathways in breast cancer cells. Oncotarget 2016; 6:44523-37. [PMID: 26540344 PMCID: PMC4792573 DOI: 10.18632/oncotarget.5972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/09/2015] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor protein p53 is unstable in quiescent cells and undergoes proteosomal degradation. Under conditions of cellular stress, p53 is rapidly stabilized by post-translational modification, thereby escaping degradation and translocating to the nucleus where it activates genes related to cell cycle arrest or apoptosis. Here, we report that the transcription elongation factor Ell3 sensitizes luminal type-cancer cell line, MCF7, which have wild-type p53, to the chemotherapeutic agent cis-diamminedichloroplatinum(II) (CDDP) by stabilizing p53. Overexpression of Ell3 in MCF7 cells suppressed the MDM2-mediated ubiquitin-dependent degradation pathway. In addition, Ell3 promoted binding of p53 to NADH quinone oxidoreductase 1, which is linked to the ubiquitin-independent degradation of p53. We found that Ell3 activates interleukin-20 (IL20) expression, which is linked to the ERK1/2 signaling pathway. Chemical inhibition of ERK1/2 signaling or molecular suppression of IL20 revealed that the ERK1/2 signaling pathway and IL20 are the main causes of p53 stabilization in Ell3-overexpressing MCF7 cells. These findings suggest that the ERK1/2 pathway can be targeted in the rational development of therapies to induce chemosensitization of breast cancer cells.
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Affiliation(s)
- Hee-Jin Ahn
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Kwang-Soo Kim
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Kyung-Won Shin
- Graduate School of Biomedical Science, CHA University, Seoul, Korea
| | - Kee-Hwan Lim
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Jin-Ock Kim
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Je-Yong Lee
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Jiewan Kim
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Ji-Hoon Park
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Kyung-Min Yang
- Department of Biomedical Science, College of Life Science and CHA Cancer Institute, CHA University, Seoul, Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Jeong-Jae Ko
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, College of Life Science and CHA Stem Cell Institute, CHA University, Seoul, Korea
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Sharma N. Regulation of RNA polymerase II-mediated transcriptional elongation: Implications in human disease. IUBMB Life 2016; 68:709-16. [DOI: 10.1002/iub.1538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University; Dwarka New Delhi 110078 India
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Smith SM, Carew NT, Milcarek C. RNA polymerases in plasma cells trav-ELL2 the beat of a different drum. World J Immunol 2015; 5:99-112. [DOI: 10.5411/wji.v5.i3.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/19/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
There is a major transformation in gene expression between mature B cells (including follicular, marginal zone, and germinal center cells) and antibody secreting cells (ASCs), i.e., ASCs, (including plasma blasts, splenic plasma cells, and long-lived bone marrow plasma cells). This significant change-over occurs to accommodate the massive amount of secretory-specific immunoglobulin that ASCs make and the export processes itself. It is well known that there is an up-regulation of a small number of ASC-specific transcription factors Prdm1 (B-lymphocyte-induced maturation protein 1), interferon regulatory factor 4, and Xbp1, and the reciprocal down-regulation of Pax5, Bcl6 and Bach2, which maintain the B cell program. Less well appreciated are the major alterations in transcription elongation and RNA processing occurring between B cells and ASCs. The three ELL family members ELL1, 2 and 3 have different protein sequences and potentially distinct cellular roles in transcription elongation. ELL1 is involved in DNA repair and small RNAs while ELL3 was previously described as either testis or stem-cell specific. After B cell stimulation to ASCs, ELL3 levels fall precipitously while ELL1 falls off slightly. ELL2 is induced at least 10-fold in ASCs relative to B cells. All of these changes cause the RNA Polymerase II in ASCs to acquire different properties, leading to differences in RNA processing and histone modifications.
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Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle. BMC Genomics 2015; 16:50. [PMID: 25651817 PMCID: PMC4328970 DOI: 10.1186/s12864-015-1238-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 01/12/2023] Open
Abstract
Background Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis. Results Our analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor. Conclusions Muscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1238-5) contains supplementary material, which is available to authorized users.
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11
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Kim YS, Yi BR, Kim NH, Choi KC. Role of the epithelial-mesenchymal transition and its effects on embryonic stem cells. Exp Mol Med 2014; 46:e108. [PMID: 25081188 PMCID: PMC4150931 DOI: 10.1038/emm.2014.44] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/04/2014] [Accepted: 04/10/2014] [Indexed: 01/02/2023] Open
Abstract
The epithelial–mesenchymal transition (EMT) is important for embryonic development and the formation of various tissues or organs. However, EMT dysfunction in normal cells leads to diseases, such as cancer or fibrosis. During the EMT, epithelial cells are converted into more invasive and active mesenchymal cells. E-box-binding proteins, including Snail, ZEB and helix–loop–helix family members, serve as EMT-activating transcription factors. These transcription factors repress the expression of epithelial markers, for example, E-cadherin, rearrange the cytoskeleton and promote the expression of mesenchymal markers, such as vimentin, fibronectin and other EMT-activating transcription factors. Signaling pathways that induce EMT, including transforming growth factor-β, Wnt/glycogen synthase kinase-3β, Notch and receptor tyrosine kinase signaling pathways, interact with each other for the regulation of this process. Although the mechanism(s) underlying EMT in cancer or embryonic development have been identified, the mechanism(s) in embryonic stem cells (ESCs) remain unclear. In this review, we describe the underlying mechanisms of important EMT factors, indicating a precise role for EMT in ESCs, and characterize the relationship between EMT and ESCs.
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Affiliation(s)
- Ye-Seul Kim
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Bo-Rim Yi
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Nam-Hyung Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Kyung-Chul Choi
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
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12
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Kohn KW, Zeeberg BM, Reinhold WC, Pommier Y. Gene expression correlations in human cancer cell lines define molecular interaction networks for epithelial phenotype. PLoS One 2014; 9:e99269. [PMID: 24940735 PMCID: PMC4062414 DOI: 10.1371/journal.pone.0099269] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/01/2014] [Indexed: 12/12/2022] Open
Abstract
Using gene expression data to enhance our knowledge of control networks relevant to cancer biology and therapy is a challenging but urgent task. Based on the premise that genes that are expressed together in a variety of cell types are likely to functions together, we derived mutually correlated genes that function together in various processes in epithelial-like tumor cells. Expression-correlated genes were derived from data for the NCI-60 human tumor cell lines, as well as data from the Broad Institute's CCLE cell lines. NCI-60 cell lines that selectively expressed a mutually correlated subset of tight junction genes served as a signature for epithelial-like cancer cells. Those signature cell lines served as a seed to derive other correlated genes, many of which had various other epithelial-related functions. Literature survey yielded molecular interaction and function information about those genes, from which molecular interaction maps were assembled. Many of the genes had epithelial functions unrelated to tight junctions, demonstrating that new function categories were elicited. The most highly correlated genes were implicated in the following epithelial functions: interactions at tight junctions (CLDN7, CLDN4, CLDN3, MARVELD3, MARVELD2, TJP3, CGN, CRB3, LLGL2, EPCAM, LNX1); interactions at adherens junctions (CDH1, ADAP1, CAMSAP3); interactions at desmosomes (PPL, PKP3, JUP); transcription regulation of cell-cell junction complexes (GRHL1 and 2); epithelial RNA splicing regulators (ESRP1 and 2); epithelial vesicle traffic (RAB25, EPN3, GRHL2, EHF, ADAP1, MYO5B); epithelial Ca(+2) signaling (ATP2C2, S100A14, BSPRY); terminal differentiation of epithelial cells (OVOL1 and 2, ST14, PRSS8, SPINT1 and 2); maintenance of apico-basal polarity (RAB25, LLGL2, EPN3). The findings provide a foundation for future studies to elucidate the functions of regulatory networks specific to epithelial-like cancer cells and to probe for anti-cancer drug targets.
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Affiliation(s)
- Kurt W. Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
| | - Barry M. Zeeberg
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - William C. Reinhold
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
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Hu A, Shang C, Li Q, Sun N, Wu L, Ma Y, Jiao X, Min J, Zeng G, He X. Epithelial-mesenchymal transition delayed by E-cad to promote tissue formation in hepatic differentiation of mouse embryonic stem cells in vitro. Stem Cells Dev 2014; 23:877-87. [PMID: 24266635 DOI: 10.1089/scd.2013.0354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Hepatic differentiation of embryonic stem cells (ESCs) usually results in a single cell lineage, and the formation of liver tissues remains difficult. Here, we examine the role of epithelial-mesenchymal transition (EMT) that is regulated by epithelial cadherin (E-cad) expression in hepatic tissue formation from ESCs. E-cad was transfected into mouse ESCs to enable a stable expression of E-cad. Hepatic differentiation of ESCs was then induced by hepatic growth factors. Wnt/β-catenin signaling and EMT speed were examined to determine the differentiation process. Hepatic and angiogenesis markers, as well as differentiated cell-adhesive force were also examined to identify the hepatic tissue differentiation. In our results, E-cad expression gradually decreased in normal ESC (N-ESC) differentiation, but remained stable in the E-cad transfected ESC (EC-ESC) group. In EC-ESC differentiation, expressions of cytoplastic β-catenin and EMT were much lower and significantly prolonged. Angiogenesis markers vascular endothelial growth factor receptor-1 (VEGFR-1) and CD31/PECAM-1 were expressed only on day 5-13 in N-ESC differentiation, whereas VEGFR-1 and CD31/PECAM-1 were expressed prolonged on day 5-17 in the EC-ESC group and were coincident with the expression of hepatic markers. Finally, EC-ESC differentiation maintained multilayer-growth patterns, and abundant vascular network structures appeared and migrated in albumin-positive cell areas. The cellular adhesion forces between embryonic body cells in EC-ESC differentiation during day 13-17 were similar to those of mouse liver tissue. In conclusion, accelerated EMT due to the decreased E-cad expression may partially contribute to the failure of hepatic tissue formation in N-ESC differentiation. E-cad can act in synergy with hepatic growth factors and facilitate the early-stage formation of hepatic tissues through down-regulating Wnt/β-catenin signaling and delaying EMT. This work provides a new insight into hepatic tissue differentiation that is mediated by E-cad from ESC.
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Affiliation(s)
- Anbin Hu
- 1 Department of General Surgery, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, China
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Smith E, Shilatifard A. Transcriptional elongation checkpoint control in development and disease. Genes Dev 2013; 27:1079-88. [PMID: 23699407 DOI: 10.1101/gad.215137.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transcriptional elongation control by RNA polymerase II and its associated factors has taken center stage as a process essential for the regulation of gene expression throughout development. In this review, we analyze recent findings on the identification of factors functioning in the regulation of the transcriptional elongation checkpoint control (TECC) stage of gene expression and how the factors' misregulation is associated with disease pathogenesis, including cancer.
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Affiliation(s)
- Edwin Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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Ahn HJ, Kim G, Park KS. Ell3 stimulates proliferation, drug resistance, and cancer stem cell properties of breast cancer cells via a MEK/ERK-dependent signaling pathway. Biochem Biophys Res Commun 2013; 437:557-64. [PMID: 23850691 DOI: 10.1016/j.bbrc.2013.06.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 01/16/2023]
Abstract
Ell3 is a RNA polymerase II transcription elongation factor that is enriched in testis. The C-terminal domain of Ell3 shows strong similarities to that of Ell (eleven-nineteen lysine-rich leukemia gene), which acts as a negative regulator of p53 and regulates cell proliferation and survival. Recent studies in our laboratory showed that Ell3 induces the differentiation of mouse embryonic stem cells by protecting differentiating cells from apoptosis via the promotion of p53 degradation. In this study, we evaluated the function of Ell3 in breast cancer cell lines. MCF-7 cell lines overexpressing Ell3 were used to examine cell proliferation and cancer stem cell properties. Ectopic expression of Ell3 in breast cancer cell lines induces proliferation and 5-FU resistance. In addition, Ell3 expression increases the cancer stem cell population, which is characterized by CD44 (+) or ALDH1 (+) cells. Mammosphere-forming potential and migration ability were also increased upon Ell3 expression in breast cancer cell lines. Through biochemical and molecular biological analyses, we showed that Ell3 regulates proliferation, cancer stem cell properties and drug resistance in breast cancer cell lines partly through the MEK-extracellular signal-regulated kinase signaling pathway. Murine xenograft experiments showed that Ell3 expression promotes tumorigenesis in vivo. These results suggest that Ell3 may play a critical role in promoting oncogenesis in breast cancer by regulating cell proliferation and cancer stem cell properties via the ERK1/2 signaling pathway.
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Affiliation(s)
- Hee-Jin Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Republic of Korea
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Arumemi F, Bayles I, Paul J, Milcarek C. Shared and discrete interacting partners of ELL1 and ELL2 by yeast two-hybrid assay. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.47101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Carpignano F, Silva G, Surdo S, Leva V, Montecucco A, Aredia F, Scovassi AI, Merlo S, Barillaro G, Mazzini G. A new cell-selective three-dimensional microincubator based on silicon photonic crystals. PLoS One 2012; 7:e48556. [PMID: 23139792 PMCID: PMC3490954 DOI: 10.1371/journal.pone.0048556] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/27/2012] [Indexed: 01/09/2023] Open
Abstract
In this work, we show that vertical, high aspect-ratio (HAR) photonic crystals (PhCs), consisting of periodic arrays of 5 µm wide gaps with depth of 50 µm separated by 3 µm thick silicon walls, fabricated by electrochemical micromachining, can be used as three-dimensional microincubators, allowing cell lines to be selectively grown into the gaps. Silicon micromachined dice incorporating regions with different surface profiles, namely flat silicon and deeply etched PhC, were used as microincubators for culturing adherent cell lines with different morphology and adhesion properties. We extensively investigated and compared the proliferative behavior on HAR PhCs of eight human cell models, with different origins, such as the epithelial (SW613-B3; HeLa; SW480; HCT116; HT29) and the mesenchymal (MRC-5V1; CF; HT1080). We also verified the contribution of cell sedimentation into the silicon gaps. Fluorescence microscopy analysis highlights that only cell lines that exhibit, in the tested culture condition, the behavior typical of the mesenchymal phenotype are able to penetrate into the gaps of the PhC, extending their body deeply in the narrow gaps between adjacent silicon walls, and to grow adherent to the vertical surfaces of silicon. Results reported in this work, confirmed in various experiments, strongly support our statement that such three-dimensional microstructures have selection capabilities with regard to the cell lines that can actively populate the narrow gaps. Cells with a mesenchymal phenotype could be exploited in the next future as bioreceptors, in combination with HAR PhC optical transducers, e.g., for label-free optical detection of cellular activities involving changes in cell adhesion and/or morphology (e.g., apoptosis) in a three-dimensional microenvironment.
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Affiliation(s)
- Francesca Carpignano
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università di Pavia, Pavia, Italy
| | - Gloria Silva
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università di Pavia, Pavia, Italy
| | - Salvatore Surdo
- Dipartimento di Ingegneria dell’Informazione, Elettronica, Informatica, Telecomunicazioni, Università di Pisa, Pisa, Italy
| | | | | | | | | | - Sabina Merlo
- Dipartimento di Ingegneria Industriale e dell’Informazione, Università di Pavia, Pavia, Italy
| | - Giuseppe Barillaro
- Dipartimento di Ingegneria dell’Informazione, Elettronica, Informatica, Telecomunicazioni, Università di Pisa, Pisa, Italy
| | - Giuliano Mazzini
- IGM-CNR, Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
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