Table of Contents Author Guidelines Submit a Manuscript
TheScientificWorldJOURNAL
Volume 10, Pages 90-102
http://dx.doi.org/10.1100/tsw.2010.7
Review Article

Long Noncoding RNAs, Chromatin, and Development

1School of Life Sciences, Oxford Brookes University, UK
2Cranfield Health, Cranfield University, UK
3Genetic Causes of Disease Group, Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), Barcelona, Spain

Received 30 September 2009; Revised 15 December 2009; Accepted 15 December 2009

Academic Editor: David L. Tannahill

Copyright © 2010 Daniel P. Caley et al.

Citations to this Article [65 citations]

The following is the list of published articles that have cited the current article.

  • Robert J Marks II, Michael J Behe, William A Dembski, Bruce L Gordon, John C Sanford, and Jonathan Wells, “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information,” Biological Information, pp. 210–231, . View at Publisher · View at Google Scholar
  • Julie E. Horvath, Christina B. Sheedy, Stephanie L. Merrett, Abdoulaye Banire Diallo, David L. Swofford, Eric D. Green, and Huntington F. Willard, “Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus,” Genome Research, vol. 21, no. 6, pp. 850–862, 2011. View at Publisher · View at Google Scholar
  • Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Raul Francisco Carter, “Pseudogenes: Pseudo-functional or key regulators in health and disease?,” Rna-A Publication of The Rna Society, vol. 17, no. 5, pp. 792–798, 2011. View at Publisher · View at Google Scholar
  • Tony Gutschner, Marion Baas, and Sven Diederichs, “Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases,” Genome Research, vol. 21, no. 11, pp. 1944–1954, 2011. View at Publisher · View at Google Scholar
  • Ewan A. Gibb, Emily A. Vucic, Katey S. S. Enfield, Greg L. Stewart, Kim M. Lonergan, Jennifer Y. Kennett, Daiana D. Becker-Santos, Calum E. MacAulay, Stephen Lam, Carolyn J. Brown, and Wan L. Lam, “Human Cancer Long Non-Coding RNA Transcriptomes,” Plos One, vol. 6, no. 10, 2011. View at Publisher · View at Google Scholar
  • Ewan A. Gibb, Katey S. S. Enfield, Ivy F. L. Tsui, Raj Chari, Stephen Lam, Carlos E. Alvarez, and Wan L. Lam, “Deciphering Squamous Cell Carcinoma Using Multidimensional Genomic Approaches,” Journal of Skin Cancer, vol. 2011, pp. 1–16, 2011. View at Publisher · View at Google Scholar
  • Sofia Nolasco, Javier Bellido, Joao Goncalves, Alexandra Tavares, Juan Carlos Zabala, and Helena Soares, “The Expression of Tubulin Cofactor A (TBCA) Is Regulated by a Noncoding Antisense Tbca RNA during Testis Maturation,” Plos One, vol. 7, no. 8, 2012. View at Publisher · View at Google Scholar
  • Deeksha Bhartiya, Shruti Kapoor, Saakshi Jalali, Satish Sati, Kriti Kaushik, Chetana Sachidanandan, Sridhar Sivasubbu, and Vinod Scaria, “Conceptual approaches for lncRNA drug discovery and future strategies,” Expert Opinion on Drug Discovery, vol. 7, no. 6, pp. 503–513, 2012. View at Publisher · View at Google Scholar
  • Alayne L Brunner, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, and Thea Gilks, “Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers.,” Genome biology, vol. 13, no. 8, 2012. View at Publisher · View at Google Scholar
  • Jin-hua He, and Yu-guang Li, “Characteristics of Antisense Non-coding RNA in the INK4 Locus and Its Roles in Disease,” Chinese Medical Sciences Journal, vol. 28, no. 2, pp. 122–123, 2013. View at Publisher · View at Google Scholar
  • Suman Ghosal, Shaoli Das, and Jayprokas Chakrabarti, “Long Noncoding RNAs: New Players in the Molecular Mechanism for Maintenance and Differentiation of Pluripotent Stem Cells,” Stem Cells and Development, pp. 130514060847009, 2013. View at Publisher · View at Google Scholar
  • Ryan C. Pink, and David R.F. Carter, “Pseudogenes as regulators of biological function,” Essays in Biochemistry, vol. 54, no. 1, pp. 103–112, 2013. View at Publisher · View at Google Scholar
  • Laura Ann Jacobs, Findlay Bewicke-Copley, Mark Graham Poolman, Ryan Charles Pink, Laura Ann Mulcahy, Isabel Baker, Ellie-May Beaman, Travis Brooks, Daniel Paul Caley, William Cowling, James Michael Stevenson Currie, Jessica Horsburgh, Lottie Kenehan, Emma Keyes, Daniel Leite, Davide Massa, Adam McDermott-Rouse, Priya Samuel, Hannah Wood, Munira Kadhim, and David Raul Francisco Carter, “Meta-Analysis Using a Novel Database, miRStress, Reveals miRNAs That Are Frequently Associated with the Radiation and Hypoxia Stress-Responses,” Plos One, vol. 8, no. 11, 2013. View at Publisher · View at Google Scholar
  • Fernanda C. Humann, Gustavo J. Tiberio, and Klaus Hartfelder, “Sequence and Expression Characteristics of Long Noncoding RNAs in Honey Bee Caste Development - Potential Novel Regulators for Transgressive Ovary Size,” Plos One, vol. 8, no. 10, 2013. View at Publisher · View at Google Scholar
  • Jin-Hua He, Ze-Ping Han, and Yu-Guang Li, “Association between long non-coding RNA and human rare diseases (Review),” Biomedical Reports, vol. 2, no. 1, pp. 19–23, 2013. View at Publisher · View at Google Scholar
  • Te Liu, Yongyi Huang, Jiulin Chen, Huiying Chi, Zhihua Yu, Jian Wang, and Chuan Chen, “Attenuated ability of BACE1 to cleave the amyloid precursor protein via silencing long noncoding RNA BACE1-AS expression,” Molecular Medicine Reports, vol. 10, no. 3, pp. 1275–1281, 2014. View at Publisher · View at Google Scholar
  • Jiaming Huang, Peiqi Ke, Luyan Guo, Wei Wang, Hao Tan, Yanchun Liang, and Shuzhong Yao, “Lentivirus-Mediated RNA Interference Targeting the Long Noncoding RNA HOTAIR Inhibits Proliferation and Invasion of Endometrial Carcinoma Cells In Vitro and In Vivo,” International Journal of Gynecological Cancer, vol. 24, no. 4, pp. 635–642, 2014. View at Publisher · View at Google Scholar
  • Xiaodong Song, Guohong Cao, Lili Jing, Shengcui Lin, Xiaozhi Wang, Jinjin Zhang, Meirong Wang, Weili Liu, and Changjun Lv, “Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis,” Journal of Cellular and Molecular Medicine, 2014. View at Publisher · View at Google Scholar
  • Tim Peters, and Blanche Schroen, “Missing links in cardiology: long non-coding RNAs enter the arena,” Pflügers Archiv - European Journal of Physiology, 2014. View at Publisher · View at Google Scholar
  • Xiao-Jun Liu, Xu-Dong Yao, and Ding-Wei Ye, “Advances in long non-coding RNA in prostate cancer,” Tumor, vol. 34, no. 2, pp. 187–190, 2014. View at Publisher · View at Google Scholar
  • Joseph Autuoro, Stephan Pirnie, and Gordon Carmichael, “Long Noncoding RNAs in Imprinting and X Chromosome Inactivation,” Biomolecules, vol. 4, no. 1, pp. 76–100, 2014. View at Publisher · View at Google Scholar
  • Marvin Natowicz, and Matthew Ginsbergpp. 279–302, 2014. View at Publisher · View at Google Scholar
  • Xiaofeng Lai, Suning Chen, Tian Xiao, Xingmei Zhu, Aidong Wen, and Jian Zhang, “Combined cancer therapy with non-conventional drugs: All roads lead to AMPK,” Mini-Reviews in Medicinal Chemistry, vol. 14, no. 8, pp. 642–654, 2014. View at Publisher · View at Google Scholar
  • Dan Qin, and Cunshuan Xu, “Study Strategies For Long Non-Coding Rnas And Their Roles In Regulating Gene Expression,” Cellular & Molecular Biology Letters, vol. 20, no. 2, pp. 323–349, 2015. View at Publisher · View at Google Scholar
  • Jun Wang, Yong-Xi Song, and Zhen-Ning Wang, “Non-coding RNAs in gastric cancer,” Gene, 2015. View at Publisher · View at Google Scholar
  • Juanjuan Zhu, Shanshan Liu, Fuqiang Ye, Yuan Shen, Yi Tie, Jie Zhu, Lixin Wei, Yinghua Jin, Hanjiang Fu, Yongge Wu, and Xiaofei Zheng, “Long Noncoding RNA MEG3 Interacts with p53 Protein and Regulates Partial p53 Target Genes in Hepatoma Cells,” Plos One, vol. 10, no. 10, 2015. View at Publisher · View at Google Scholar
  • Diego Franco, and Amelia E. Aranegapp. 153–172, 2015. View at Publisher · View at Google Scholar
  • Yaguang Zou, Chun Li, Fangpeng Shu, Zhihui Tian, Wenan Xu, Huiyong Xu, Hua Tian, Rong Shi, and Xiangming Mao, “lncRNA Expression Signatures in Periodontitis Revealed by Microarray: The Potential Role of lncRNAs in Periodontitis Pathogenesis,” Journal of Cellular Biochemistry, vol. 116, no. 4, pp. 640–647, 2015. View at Publisher · View at Google Scholar
  • Ryan Charles Pink, Priya Samuel, Davide Massa, Daniel Paul Caley, Susan Ann Brooks, and David Raul Francisco Carter, “The passenger strand, miR-21-3p, plays a role in mediating cisplatin resistance in ovarian cancer cells,” Gynecologic Oncology, 2015. View at Publisher · View at Google Scholar
  • Shafagh A. Waters, and Paul D. Waters, “Imprinted X chromosome inactivation: evolution of mechanisms in distantly related mammals,” AIMS Genetics, vol. 2, no. 2, pp. 110–126, 2015. View at Publisher · View at Google Scholar
  • Polly P. Huang, Nicholas J. G. Webster, Liza E. Brusman, Anita K. Iyer, and Pamela L. Mellon, “A novel gonadotropin-releasing hormone 1 (Gnrh1) enhancer-derived noncoding RNA regulates Gnrh1 gene expression in GnRH neuronal cell models,” PLoS ONE, vol. 11, no. 7, 2016. View at Publisher · View at Google Scholar
  • Juan Yao, Jun-Xing Huang, Mei Lin, Zheng-Dong Wu, Hong Yu, Peng-Cheng Wang, Jun Ye, Ping Chen, Jing Wu, and Guo-Jun Zhao, “Microarray expression profile analysis of aberrant long non-coding RNAs in esophageal squamous cell carcinoma,” International Journal Of Oncology, vol. 48, no. 6, pp. 2543–2557, 2016. View at Publisher · View at Google Scholar
  • Chan Liu, Hong-Tao Wu, Neng Zhu, Ya-Ning Shi, Zheng Liu, Bao-Xue Ao, Duan-Fang Liao, Xi-Long Zheng, and Li Qin, “Steroid receptor RNA activator: Biologic function and role in disease,” Clinica Chimica Acta, 2016. View at Publisher · View at Google Scholar
  • Min Wang, Di Yao, Suyu Wang, Qin Yan, and Weiping Lu, “Long non-coding RNA ENSMUST00000147869 protects mesangial cells from proliferation and fibrosis induced by diabetic nephropathy,” Endocrine, 2016. View at Publisher · View at Google Scholar
  • Bin He, Xiaobo Gu, and Wei Cong, “Long non-coding RNAs and esophageal cancer,” Chinese Journal of Cancer Biotherapy, vol. 23, no. 2, pp. 297–302, 2016. View at Publisher · View at Google Scholar
  • Jing Xu, Fang Zhang, Chao Gao, Xiaofeng Ma, Xiaolin Peng, Dexin Kong, and Junwei Hao, “Microarray Analysis of lncRNA and mRNA Expression Profiles in Patients with Neuromyelitis Optica,” Molecular Neurobiology, 2016. View at Publisher · View at Google Scholar
  • Chun-Li Da, Yao Tan, Yi-Yi Zhan, Ya-Wei Li, Ruo-Zheng Wang, and Kai Liu, “Radiation-induced expression of HOTAIR, snail and e-cadherin in esophageal squamous cell carcinoma cells,” World Chinese Journal of Digestology, vol. 24, no. 8, pp. 1227–1232, 2016. View at Publisher · View at Google Scholar
  • Ying Li, and Xin Wang, “Role of long noncoding RNAs in malignant disease (Review),” Molecular Medicine Reports, vol. 13, no. 2, pp. 1463–1469, 2016. View at Publisher · View at Google Scholar
  • Ying Gu, Fan Yang, Ru-ming Xu, Yun-yan Zhang, Yang Li, Su-xuan Liu, Guan-xin Zhang, Guo-kun Wang, and Li-ping Ma, “Differential expression profile of long non-coding RNA in cardiomyocytes autophagy induced by angiotensin II,” Cell Biology International, 2017. View at Publisher · View at Google Scholar
  • Yingwei Yue, Congfei Jin, Mingming Chen, Linlin Zhang, Xinfeng Liu, Wenzhi Ma, and Hong Guo, “A lncRNA promotes myoblast proliferation by up-regulating GH1,” In Vitro Cellular & Developmental Biology - Animal, 2017. View at Publisher · View at Google Scholar
  • Anna Grimaldi, Mayra Rachele Zarone, Carlo Irace, Silvia Zappavigna, Angela Lombardi, Hiromichi Kawasaki, Michele Caraglia, and Gabriella Misso, “Non-coding RNAs as a new dawn in tumor diagnosis,” Seminars in Cell & Developmental Biology, 2017. View at Publisher · View at Google Scholar
  • Tian An, Hui Fan, Yu F. Liu, Yan Y. Pan, Ying K. Liu, Fang F. Mo, Yu J. Gu, Ya L. Sun, Dan D. Zhao, Na Yu, Yue Ma, Chen Y. Liu, Qiu L. Wang, Zheng Y. Li, Fei Teng, Si Hua Gao, and Guang J. Jiang, “The difference in expression of long noncoding RNAs in rat semen induced by high-fat diet was associated with metabolic pathways,” PeerJ, vol. 5, pp. e3518, 2017. View at Publisher · View at Google Scholar
  • Modjtaba Emadi-Baygi, Rina Sedighi, Nooshin Nourbakhsh, and Parvaneh Nikpour, “Pseudogenes in gastric cancer pathogenesis: a review article,” Briefings in Functional Genomics, 2017. View at Publisher · View at Google Scholar
  • Fangzhou Hu, Kang Xu, Yunfan Zhou, Chang Wu, Shi Wang, Jun Xiao, Min Wen, Rurong Zhao, Kaikun Luo, Min Tao, Wei Duan, and Shaojun Liu, “Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†,” Biology of Reproduction, 2017. View at Publisher · View at Google Scholar
  • Yuanwei Luo, Min Liang, Wenxiao Yao, Jifang Liu, Qiuling Niu, Jitao Chen, Zhaoyu Liu, Ming Li, Boyun Shi, Jinhui Pan, Lin Zhou, and Xinke Zhou, “Functional role of lncRNA LOC101927497 in N -methyl- N ′-nitro- N -nitrosoguanidine-induced malignantly transformed human gastric epithelial cells,” Life Sciences, 2017. View at Publisher · View at Google Scholar
  • Junhua Luo, Yu Yang, Haichao Yun, Jing Chen, Hang Li, Shangqi Yang, and Xiangming Mao, “LncRNA UCA1 promotes the invasion and EMT of bladder cancer cells by regulating the miR-143/HMGB1 pathway,” Oncology Letters, vol. 14, no. 5, pp. 5556–5562, 2017. View at Publisher · View at Google Scholar
  • Xiang-Peng Wang, Xing-Li Deng, Li-Yan Li, Cai Shan, and Wei Ma, “Long non-coding RNA PAR5 inhibits the proliferation and progression of glioma through interaction with EZH2,” Oncology Reports, vol. 38, no. 5, pp. 3177–3186, 2017. View at Publisher · View at Google Scholar
  • Xing-Yu Meng, Yuzi Luo, Muhammad Naveed Anwar, Yuan Sun, Yao Gao, Huawei Zhang, Muhammad Munir, and Hua-Ji Qiu, “Long Non-Coding RNAs: Emerging and Versatile Regulators in Host–Virus Interactions,” Frontiers in Immunology, vol. 8, 2017. View at Publisher · View at Google Scholar
  • Ning-Ning Yan, Zhan-Qiang He, Feng-Chun Zhang, and Hai-Yan Xu, “Progress of research on long noncoding RNA in breast cancer,” Journal of Shanghai Jiaotong University (Medical Science), vol. 37, no. 1, pp. 122–127, 2017. View at Publisher · View at Google Scholar
  • Pei Li, Boyu Wu, Tao Jiang, Wei Jiang, and Weiguo Huang, “The Research Progress of Long Noncoding RNAs in Nasopharyngeal Carcinoma,” Journal of Cancer Therapy, vol. 08, no. 08, pp. 751–763, 2017. View at Publisher · View at Google Scholar
  • Qian Liu, Shengshun Que, Hongxia Fan, Min Liu, Xin Li, Hua Tang, Xu Guo, and Xi Yang, “LncRNA RSU1P2 contributes to tumorigenesis by acting as a ceRNA against let-7a in cervical cancer cells,” Oncotarget, vol. 8, no. 27, pp. 43768–43781, 2017. View at Publisher · View at Google Scholar
  • Linlin Chen, Yan Zhou, and Hongjun Li, “LncRNA, miRNA and lncRNA-miRNA interaction in viral infection,” Virus Research, vol. 257, pp. 25–32, 2018. View at Publisher · View at Google Scholar
  • Qian Hu, Xiao Lin, Linxiaoxiao Ding, Yinduo Zeng, Danmei Pang, Nengtai Ouyang, Yanqun Xiang, and Herui Yao, “ARHGAP42 promotes cell migration and invasion involving PI3K/Akt signaling pathway in nasopharyngeal carcinoma,” Cancer Medicine, 2018. View at Publisher · View at Google Scholar
  • Jukun Song, Aizhu Ye, Enli Jiang, Xinhai Yin, Zhu Chen, Guohui Bai, Yu Zhou, and Jianguo Liu, “Reconstruction and analysis of the aberrant lncRNA-miRNA-mRNA network based on competitive endogenous RNA in CESC,” Journal of Cellular Biochemistry, 2018. View at Publisher · View at Google Scholar
  • Ming-Rong Cao, Ji-Ming Liu, Ze-Ping Han, Yu-Guang Li, Jin-Hua He, Yu-Bing Lv, and Jia-Bin Zhou, “Bioinformatic analysis and prediction of the function and regulatory network of long non-coding RNAs in hepatocellular carcinoma,” Oncology Letters, vol. 15, no. 5, pp. 7783–7793, 2018. View at Publisher · View at Google Scholar
  • Yunhe Zhao, Wei Wang, Jiaming Huang, Luyan Guo, Tianyu Liu, Chunliang Shang, Yanchun Liang, and Shuzhong Yao, “Identification of lncRNAs by microarray analysis reveals the potential role of lncrnas in cervical cancer pathogenesis,” Oncology Letters, vol. 15, no. 4, pp. 5584–5592, 2018. View at Publisher · View at Google Scholar
  • Ailing Li, Rui Peng, Yan Sun, Handeng Liu, Huimin Peng, and Zheng Zhang, “LincRNA 1700020I14Rik alleviates cell proliferation and fibrosis in diabetic nephropathy via miR-34a-5p/Sirt1/HIF-1α signaling,” Cell Death & Disease, vol. 9, no. 5, 2018. View at Publisher · View at Google Scholar
  • Hongbin Zhou, Yang Yang, Yuanshun Liu, Yaqing Li, Hua Jiang, Xiwang Ying, Zhehua Wang, Wulin Xu, and Xujun He, “Lentivirus-mediated silencing of HOTAIR lncRNA restores gefitinib sensitivity by activating bax/caspase-3 and suppressing TGF-α/EGFR signaling in lung adenocarcinoma,” Oncology Letters, vol. 15, no. 3, pp. 2829–2838, 2018. View at Publisher · View at Google Scholar
  • Fengxi Li, Qian Li, and Xianghua Wu, “Construction and analysis for differentially expressed long non-coding RNAs and MicroRNAs mediated competing endogenous RNA network in colon cancer,” Plos One, vol. 13, no. 2, pp. e0192494, 2018. View at Publisher · View at Google Scholar
  • Julien Bouckenheimer, Patricia Fauque, Charles-Henri Lecellier, Céline Bruno, Thérèse Commes, Jean-Marc Lemaître, John De Vos, and Said Assou, “Differential long non-coding RNA expression profiles in human oocytes and cumulus cells,” Scientific Reports, vol. 8, no. 1, 2018. View at Publisher · View at Google Scholar
  • Nurdjannah Hamid, “Factor analysis for balanced scorecard as measuring competitive advantage of infrastructure assets of owned-state ports in Indonesia: Pelindo IV, Makassar, Indonesia,” International Journal of Law and Management, pp. 00–00, 2018. View at Publisher · View at Google Scholar
  • Nurjannah Hamid, “Use balanced scorecard for measuring competitive advantage of infrastructure assets of owned-state ports in Indonesia: case in Pelindo IV, Indonesia,” Journal of Management Development, pp. 00–00, 2018. View at Publisher · View at Google Scholar
  • Jiawu Wang, Chengyao Zhang, Weiyang He, and Xin Gou, “Construction and comprehensive analysis of dysregulated long non-coding RNA-associated competing endogenous RNA network in clear cell renal cell carcinoma,” Journal of Cellular Biochemistry, 2018. View at Publisher · View at Google Scholar
  • Chuiguo Huang, Qian Li, Fengxi Li, and Xianghua Wu, “Construction and comprehensive analysis for dysregulated long non-coding RNA (LncRNA)-associated competing endogenous RNA (ceRNA) network in gastric cancer,” Medical Science Monitor, vol. 24, pp. 37–49, 2018. View at Publisher · View at Google Scholar
  • Wu, Sun, and Wu, “The association between LncRNA HOTAIR and cancer lymph node metastasis and distant metastasis: A meta-analysis,” Neoplasma, vol. 65, no. 2, pp. 178–184, 2018. View at Publisher · View at Google Scholar