1
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Peng F, Yan S, Liu H, Liu Z, Jiang F, Cao P, Fu R. Roles of LINC01473 and CD74 in osteoblasts in multiple myeloma bone disease. J Investig Med 2022; 70:1301-1307. [PMID: 35145037 PMCID: PMC9240337 DOI: 10.1136/jim-2021-002192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 11/22/2022]
Abstract
The suppression of osteoblast (OB) activity is partially responsible for multiple myeloma (MM) bone disease. Long non-coding RNAs (lncRNAs) play a vital role in bone formation and resorption. However, their functions in OBs from patients with MM have rarely been reported. Through high-throughput sequencing of OBs from patients with MM and healthy controls, we identified several lncRNAs and messenger RNAs (mRNAs) with different expression profile and validated them using quantitative real-time PCR. In total, 22 upregulated and 21 downregulated lncRNAs were found in OBs from patients with MM. Moreover, 18 upregulated protein-coding mRNAs were identified. The expression levels of LINC01473 and its associated co-expression mRNA, CD74, were higher in patients with MM than in healthy controls (p=0.047 and p=0.016, respectively). LINC01473 expression demonstrated a negative correlation with serum interleukin-2 and tumor necrosis factor α levels, whereas the expression of mRNA CD74 was positively associated with serum lactic dehydrogenase in patients with MM. Aberrant expression of lncRNAs and mRNAs was observed in OBs from patients with MM. This study identifies new promising targets for further research on imbalanced bone formation and resorption and MM immune escape.
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Affiliation(s)
- Fengping Peng
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Siyang Yan
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhaoyun Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Fengjuan Jiang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Panpan Cao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
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2
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Song J, Che J, You Z, Ye X, Li J, Ye L, Zhang Y, Qian Q, Zhong B. The clustered regularly interspaced short palindromic repeats/associated proteins system for the induction of gene mutations and phenotypic changes in Bombyx mori. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1112-1119. [PMID: 27827797 DOI: 10.1093/abbs/gmw106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/23/2016] [Accepted: 08/31/2016] [Indexed: 02/07/2023] Open
Abstract
To probe the general phenomena of gene mutations, Bombyx mori, the lepidopterous model organism, was chosen as the experimental model. To easily detect phenotypic variations, the piggyBac system was utilized to introduce two marker genes into the silkworm, and 23.4% transposition efficiency aided in easily breeding a new strain for the entire experiment. Then, the clustered regularly interspaced short palindromic repeats/an associated protein (Cas9) system was utilized. The results showed that the Cas9 system can induce efficient gene mutations and the base changes could be detected since the G0 individuals in B. mori; and that the mutation rates on different target sites were diverse. Next, the gRNA2-targeted site that generated higher mutation rate was chosen, and the experimental results were enumerated. First, the mutation proportion in G1 generation was 30.1%, and some gene mutations were not inherited from the G0 generation; second, occasionally, base substitutions did not lead to variation in the amino-acid sequence, which decreased the efficiency of phenotypic changes compared with that of genotypic changes. These results laid the foundation for better use of the Cas9 system in silkworm gene editing.
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Affiliation(s)
- Jia Song
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiaqian Che
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhengying You
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaogang Ye
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jisheng Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lupeng Ye
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuyu Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiujie Qian
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Boxiong Zhong
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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3
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Kalwa M, Hänzelmann S, Otto S, Kuo CC, Franzen J, Joussen S, Fernandez-Rebollo E, Rath B, Koch C, Hofmann A, Lee SH, Teschendorff AE, Denecke B, Lin Q, Widschwendter M, Weinhold E, Costa IG, Wagner W. The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation. Nucleic Acids Res 2016; 44:10631-10643. [PMID: 27634931 PMCID: PMC5159544 DOI: 10.1093/nar/gkw802] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023] Open
Abstract
There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm changes at HOTAIR binding sites. Five potential triple helix forming domains were predicted within the HOTAIR sequence based on reverse Hoogsteen hydrogen bonds. Notably, the predicted triple helix target sites for these HOTAIR domains were also enriched in differentially expressed genes and close to DNAm changes upon modulation of HOTAIR Electrophoretic mobility shift assays provided further evidence that HOTAIR domains form RNA-DNA-DNA triplexes with predicted target sites. Our results demonstrate that HOTAIR impacts on differentiation of MSCs and that it is associated with senescence-associated DNAm. Targeting of epigenetic modifiers to relevant loci in the genome may involve triple helix formation with HOTAIR.
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Affiliation(s)
- Marie Kalwa
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Sonja Hänzelmann
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Sabrina Otto
- Institute of Organic Chemistry, RWTH Aachen University, Aachen 52056, Germany
| | - Chao-Chung Kuo
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen 52074, Germany
| | - Carmen Koch
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Shih-Han Lee
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew E Teschendorff
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.,CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bernd Denecke
- Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Martin Widschwendter
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Aachen 52056, Germany
| | - Ivan G Costa
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany .,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany .,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
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4
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Meredith EK, Balas MM, Sindy K, Haislop K, Johnson AM. An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR. RNA (NEW YORK, N.Y.) 2016; 22:995-1010. [PMID: 27146324 PMCID: PMC4911922 DOI: 10.1261/rna.055830.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/06/2016] [Indexed: 05/19/2023]
Abstract
The human long noncoding RNA (lncRNA) HOTAIR acts in trans to recruit the Polycomb repressive complex 2 (PRC2) to the HOXD gene cluster and to promote gene silencing during development. In breast cancers, overexpression of HOTAIR increases metastatic potential via the repression of many additional genes. It has remained unclear what factors determine HOTAIR-dependent PRC2 activity at specific genomic loci, particularly when high levels of HOTAIR result in aberrant gene silencing. To identify additional proteins that contribute to the specific action of HOTAIR, we performed a quantitative proteomic analysis of the HOTAIR interactome. We found that the most specific interaction was between HOTAIR and the heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1, a member of a family of proteins involved in nascent mRNA processing and RNA matchmaking. Our data suggest that A2/B1 are key contributors to HOTAIR-mediated chromatin regulation in breast cancer cells: A2/B1 knockdown reduces HOTAIR-dependent breast cancer cell invasion and decreases PRC2 activity at the majority of HOTAIR-dependent loci. We found that the B1 isoform, which differs from A2 by 12 additional amino acids, binds with highest specificity to HOTAIR. B1 also binds chromatin and associates preferentially with RNA transcripts of HOTAIR gene targets. We furthermore demonstrate a direct RNA-RNA interaction between HOTAIR and a target transcript that is enhanced by B1 binding. Together, these results suggest a model in which B1 matches HOTAIR with transcripts of target genes on chromatin, leading to repression by PRC2.
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Affiliation(s)
- Emily K Meredith
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Maggie M Balas
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Karla Sindy
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Krystal Haislop
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Aaron M Johnson
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado 80045, USA
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5
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Cui L, Liu D, Shi W, Pan J, Qi X, Li X, Guo X, Zhou M, Li W, Li J, Haywood J, Xiao H, Yu X, Pu X, Wu Y, Yu H, Zhao K, Zhu Y, Wu B, Jin T, Shi Z, Tang F, Zhu F, Sun Q, Wu L, Yang R, Yan J, Lei F, Zhu B, Liu W, Ma J, Wang H, Gao GF. Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus. Nat Commun 2016; 5:3142. [PMID: 24457975 DOI: 10.1038/ncomms4142] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 12/18/2013] [Indexed: 12/25/2022] Open
Abstract
Influenza A (H7N9) virus has been causing human infections in China since February 2013, raising serious concerns of potential pandemics. Previous studies demonstrate that human infection is directly linked to live animal markets, and that the internal genes of the virus are derived from H9N2 viruses circulating in the Yangtze River Delta area in Eastern China. Here following analysis of 109 viruses, we show a much higher genetic heterogeneity of the H7N9 viruses than previously reported, with a total of 27 newly designated genotypes. Phylogenetic and genealogical inferences reveal that genotypes G0 and G2.6 dominantly co-circulate within poultry, with most human isolates belonging to the genotype G0. G0 viruses are also responsible for the inter- and intra-province transmissions, leading to the genesis of novel genotypes. These observations suggest the province-specific H9N2 virus gene pools increase the genetic diversity of H7N9 via dynamic reassortments and also imply that G0 has not gained overwhelming fitness and the virus continues to undergo reassortment.
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Affiliation(s)
- Lunbiao Cui
- 1] Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China [2]
| | - Di Liu
- 1] CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China [2] Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China [3]
| | - Weifeng Shi
- 1] School of Basic Medical Sciences, Taishan Medical College, Shandong Province, China [2] CAS Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China [3]
| | - Jingcao Pan
- 1] Hangzhou Center for Disease Control and Prevention, Zhejiang Province, China [2]
| | - Xian Qi
- 1] Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China [2]
| | - Xianbin Li
- 1] Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, Guangdong Province, China [2] University of Chinese Academy of Sciences, Beijing, China
| | - Xiling Guo
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Minghao Zhou
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Wei Li
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Hangzhou Center for Disease Control and Prevention, Zhejiang Province, China
| | - Joel Haywood
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haixia Xiao
- Tianjin Institute of Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xinfen Yu
- Hangzhou Center for Disease Control and Prevention, Zhejiang Province, China
| | - Xiaoying Pu
- Hangzhou Center for Disease Control and Prevention, Zhejiang Province, China
| | - Ying Wu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huiyan Yu
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Kangchen Zhao
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Yefei Zhu
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Bin Wu
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Zhiyang Shi
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Fenyang Tang
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Fengcai Zhu
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - Qinglan Sun
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- CAS Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juncai Ma
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Wang
- Key Laboratory of Enteric Pathogenic Microbiology (Ministry of Health), Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, China
| | - George F Gao
- 1] CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China [2] University of Chinese Academy of Sciences, Beijing, China [3] Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China [4] Office of Director-General, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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6
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Li Q, Yan W, Chen H, Tan C, Han Z, Yao W, Li G, Yuan M, Xing Y. Duplication of OsHAP family genes and their association with heading date in rice. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1759-68. [PMID: 26798026 PMCID: PMC4783360 DOI: 10.1093/jxb/erv566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering in plants. It is not clear how many HAP genes regulate heading date in rice. In this study, we identified 35 HAP genes, including seven newly identified genes, and performed gene duplication and candidate gene-based association analyses. Analyses showed that segmental duplication and tandem duplication are the main mechanisms of HAP gene duplication. Expression profiling and functional identification indicated that duplication probably diversifies the functions of HAP genes. A nucleotide diversity analysis revealed that 13 HAP genes underwent selection. A candidate gene-based association analysis detected four HAP genes related to heading date. An investigation of transgenic plants or mutants of 23 HAP genes confirmed that overexpression of at least four genes delayed heading date under long-day conditions, including the previously cloned Ghd8/OsHAP3H. Our results indicate that the large number of HAP genes in rice was mainly produced by gene duplication, and a few HAP genes function to regulate heading date. Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading.
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Affiliation(s)
- Qiuping Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaxia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengqi Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Hubei Collaborative Innovation Center for Grain Industry , China
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7
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Qi W, Shi W, Li W, Huang L, Li H, Wu Y, Yan J, Jiao P, Zhu B, Ma J, Gao GF, Liao M, Liu D. Continuous reassortments with local chicken H9N2 virus underlie the human-infecting influenza A (H7N9) virus in the new influenza season, Guangdong, China. Protein Cell 2015; 5:878-82. [PMID: 25109943 PMCID: PMC4225483 DOI: 10.1007/s13238-014-0084-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Wenbao Qi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
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8
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Liu GY, Zhao GN, Chen XF, Hao DL, Zhao X, Lv X, Liu DP. The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster. Nucleic Acids Res 2015; 44:2613-27. [PMID: 26615201 PMCID: PMC4824075 DOI: 10.1093/nar/gkv1315] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 11/11/2015] [Indexed: 11/17/2022] Open
Abstract
The Hox genes encode transcription factors that determine embryonic pattern formation. In embryonic stem cells, the Hox genes are silenced by PRC2. Recent studies have reported a role for long noncoding RNAs in PRC2 recruitment in vertebrates. However, little is known about how PRC2 is recruited to the Hox genes in ESCs. Here, we used stable knockdown and knockout strategies to characterize the function of the long noncoding RNA Gm15055 in the regulation of Hoxa genes in mouse ESCs. We found that Gm15055 is highly expressed in mESCs and its expression is maintained by OCT4. Gm15055 represses Hoxa gene expression by recruiting PRC2 to the cluster and maintaining the H3K27me3 modification on Hoxa promoters. A chromosome conformation capture assay revealed the close physical association of the Gm15055 locus to multiple sites at the Hoxa gene cluster in mESCs, which may facilitate the in cis targeting of Gm15055 RNA to the Hoxa genes. Furthermore, an OCT4-responsive positive cis-regulatory element is found in the Gm15055 gene locus, which potentially regulates both Gm15055 itself and the Hoxa gene activation. This study suggests how PRC2 is recruited to the Hoxa locus in mESCs, and implies an elaborate mechanism for Hoxa gene regulation in mESCs.
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Affiliation(s)
- Guo-You Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Guang-Nian Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiao-Feng Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - De-Long Hao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiang Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
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9
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Abstract
Recent years have witnessed the discovery of several classes of noncoding RNAs (ncRNAs), which are indispensable for the regulation of cellular processes. Many of these RNAs are regulatory in nature with functions in gene expression regulation such as piwi-interacting RNAs, small interfering RNAs and micro RNAs. Long noncoding RNAs (lncRNAs) comprise the most recently characterized class. LncRNAs are involved in transcriptional regulation, chromatin remodeling, imprinting, splicing, and translation, among other critical functions in the cell. Recent studies have elucidated the importance of lncRNAs in hematopoietic development. Dysregulation of lncRNA expression is a feature of various diseases and cancers, and is also seen in hematopoietic malignancies. This article focuses on lncRNAs that have been implicated in the pathogenesis of hematopoietic malignancies.
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Affiliation(s)
- Norma I Rodríguez-Malavé
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
| | - Dinesh S Rao
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
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10
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Phylogenetics of varied subtypes of avian influenza viruses in China: potential threat to humans. Protein Cell 2014; 5:253-7. [PMID: 24622845 PMCID: PMC3978160 DOI: 10.1007/s13238-014-0036-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Werber M, Wittler L, Timmermann B, Grote P, Herrmann BG. The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo. Development 2014; 141:2325-30. [PMID: 24803591 DOI: 10.1242/dev.105858] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Differential gene expression is a prerequisite for the formation of multiple cell types from the fertilized egg during embryogenesis. Understanding the gene regulatory networks controlling cellular differentiation requires the identification of crucial differentially expressed control genes and, ideally, the determination of the complete transcriptomes of each individual cell type. Here, we have analyzed the transcriptomes of six major tissues dissected from mid-gestational (TS12) mouse embryos. Approximately one billion reads derived by RNA-seq analysis provided extended transcript lengths, novel first exons and alternative transcripts of known genes. We have identified 1375 genes showing tissue-specific expression, providing gene signatures for each of the six tissues. In addition, we have identified 1403 novel putative long noncoding RNA gene loci, 439 of which show differential expression. Our analysis provides the first complete transcriptome data for the mouse embryo. It offers a rich data source for the analysis of individual genes and gene regulatory networks controlling mid-gestational development.
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Affiliation(s)
- Martin Werber
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Phillip Grote
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany Institute for Medical Genetics, Charité - University Medicine Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
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Demerdash Z, El Baz H, Mahmoud F, Mohamed S, Maher K, Gaafar T, Shawky S, Hassan M, Abdelhady D, Taha T. Enhancing ex vivo expansion of cord blood-derived unrestricted somatic stem cells for clinical applications. Cell Prolif 2014; 46:628-36. [PMID: 24460716 DOI: 10.1111/cpr.12070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To study effects of serum-containing medium (SCM) versus serum-free medium (SFM) and influence of seeding density, on rate of expansion of cord blood (CB) unrestricted somatic stem cells (USSCs), as a prerequisite for evaluating their therapeutic potential in ongoing clinical trials. MATERIAL AND METHODS Isolation, propagation and characterization of USSCs from CB samples were performed and followed by their passage 3 culture in SCM and SFM, at cell densities of 5, 50, 500 and 5000 cells/cm(2) . RESULTS The cells were CD44(+) , CD90(+) , CD73(+) , CD105(+) , CD34(-) , CD45(-) , and HLA-DR, with Oct4 & Sox2 gene expression; they were differentiated into osteoblasts and adipocytes. USSCs cultured in SCM had significantly higher population doubling levels (P < 0.01) than those cultured in SFM. Those cultured in SCM at 5 cells/cm(2) and those cultured in SFM at 50 cells/cm(2) had significantly higher population doubling (P < 0.01) levels than those cultured at higher cell densities. CONCLUSIONS For scaling up of USSCs from 106 (?) to 1012 (?) in 6 weeks, culturing of CB-derived cells of early passage (≤P3) in SCM at low cell seeding density (5 cells/cm(2) ) is suggested for increasing cell count with lower passaging frequency, followed by culture of expanded USSCs at 50 cells/cm(2) in SFM, to avoid undesirable effects of bovine serum in clinical applications.
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Affiliation(s)
- Z Demerdash
- Immunology, Theodor Bilharz Research Institute, Cairo, 12411, Egypt
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Abstract
The regulation of gene expression by non-coding RNAs (ncRNAs) has become a new paradigm in biology. RNA-mediated gene silencing pathways have been studied extensively, revealing diverse epigenetic and posttranscriptional mechanisms. In contrast, the roles of ncRNAs in activating gene expression remains poorly understood. In this review, we summarize the current knowledge of gene activation by small RNAs, long non-coding RNAs, and enhancer-derived RNAs, with an emphasis on epigenetic mechanisms.
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Affiliation(s)
- Alan L Jiao
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
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