Table of Contents Author Guidelines Submit a Manuscript
The Scientific World Journal
Volume 2012, Article ID 541786, 11 pages
http://dx.doi.org/10.1100/2012/541786
Review Article

Molecular Mechanisms and Function Prediction of Long Noncoding RNA

Institute of Biostatistics, School of Life Science, Fudan University, 220 Handan Road, Shanghai 2004333, China

Received 30 October 2012; Accepted 21 November 2012

Academic Editors: G. P. Chrousos and T. Kino

Copyright © 2012 Handong Ma et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [41 citations]

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

  • Manu Madhavan, and Gopakumar G, “A tf-idf based topic model for identifying lncRNAs from genomic background,” Proceedings of the 33rd Annual ACM Symposium on Applied Computing - SAC '18, pp. 40–46, . View at Publisher · View at Google Scholar
  • Wang He, Qingqing Cai, Fenyong Sun, Guangzheng Zhong, Pei Wang, Hongyan Liu, Junhua Luo, Hao Yu, Jian Huang, and Tianxin Lin, “linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer,” Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2013. View at Publisher · View at Google Scholar
  • Yong He, Xiao-Ming Meng, Cheng Huang, Bao-Ming Wu, Lei Zhang, Xiong-Wen Lv, and Jun Li, “Long noncoding RNAs: Novel insights into hepatocelluar carcinoma,” Cancer Letters, 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
  • Jen-Yang Tang, Jin-Ching Lee, Yung-Ting Chang, Ming-Feng Hou, Hurng-Wern Huang, Chih-Chuang Liaw, and Hsueh-Wei Chang, “Long Noncoding RNAs-Related Diseases, Cancers, and Drugs,” The Scientific World Journal, vol. 2013, pp. 1–7, 2013. View at Publisher · View at Google Scholar
  • Xiao-Cong Lin, Ying Zhu, Wen-Biao Chen, Lie-Wen Lin, De-Heng Chen, Jian-Rong Huang, Kai Pan, Yan Lin, Bi-Tao Wu, Yong Dai, and Zhi-Guang Tu, “Integrated analysis of long non-coding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in gastric cancer pathogenesis,” International Journal of Oncology, vol. 45, no. 2, pp. 619–628, 2014. View at Publisher · View at Google Scholar
  • Maria Toto, and Giulia D'Angelo, “Regulation of ISWI chromatin remodelling activity,” Chromosoma, vol. 123, no. 1-2, pp. 91–102, 2014. View at Publisher · View at Google Scholar
  • Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, and Runsheng Chen, “NONCODEv4: exploring the world of long non-coding RNA genes,” Nucleic Acids Research, vol. 42, no. D1, pp. D98–D103, 2014. View at Publisher · View at Google Scholar
  • Rui Dong, Juan Du, Liping Wang, Jinsong Wang, Gang Ding, Songlin Wang, and Zhipeng Fan, “Comparison of Long Noncoding RNA and mRNA Expression Profiles in Mesenchymal Stem Cells Derived from Human Periodontal Ligament and Bone Marrow,” BioMed Research International, vol. 2014, pp. 1–12, 2014. View at Publisher · View at Google Scholar
  • Jiang-Hua Liu, Gang Chen, Yi-Wu Dang, Chun-Jun Li, and Dian-Zhong Luo, “Expression and Prognostic Significance of lncRNA MALAT1 in Pancreatic Cancer Tissues,” Asian Pacific Journal of Cancer Prevention, vol. 15, no. 7, pp. 2971–2977, 2014. View at Publisher · View at Google Scholar
  • Wenzhuo Zhuang, Xueping Ge, Sijun Yang, Moli Huang, Wenyue Zhuang, Ping Chen, Xiaohui Zhang, Jinxiang Fu, Jing Qu, and Bingzong Li, “Upregulation of lncRNA MEG3 Promotes Osteogenic Differentiation of Mesenchymal Stem Cells From Multiple Myeloma Patients By Targeting BMP4 Transcription,” Stem Cells, vol. 33, no. 6, pp. 1985–1997, 2015. View at Publisher · View at Google Scholar
  • Roy Blum, “Stepping inside the realm of epigenetic modifiers,” Biomolecular Concepts, vol. 6, no. 2, pp. 119–136, 2015. View at Publisher · View at Google Scholar
  • Travers Ching, Jayson Masaki, Jason Weirather, and Lana X. Garmire, “Non-coding yet non-trivial: a review on the computational genomics of lincRNAs,” Biodata Mining, vol. 8, 2015. View at Publisher · View at Google Scholar
  • Dhanya Ramachandran, Zhen Zeng, Adam E. Locke, Jennifer G. Mulle, Lora J. H. Bean, Tracie C. Rosser, Kenneth J. Dooley, Clifford L. Cua, George T. Capone, Roger H. Reeves, Cheryl L. Maslen, David J. Cutler, Eleanor Feingold, Stephanie L. Sherman, and Michael E. Zwick, “Genome-Wide Association Study of Down Syndrome-Associated Atrioventricular Septal Defects,” G3-Genes Genomes Genetics, vol. 5, no. 10, pp. 1961–1971, 2015. View at Publisher · View at Google Scholar
  • John M. Williams, Melanie Ball, Andrew Ward, and Tom Moore, “Psg22 expression in mouse trophoblast giant cells is associated with gene inversion and co-expression of antisense long non-coding RNAs,” Reproduction, vol. 149, no. 1, pp. 125–137, 2015. View at Publisher · View at Google Scholar
  • Nat N. V. Kav, Swati Megha, Urmila Basu, and Muhammad H. Rahmanpp. 93–106, 2015. View at Publisher · View at Google Scholar
  • Christopher R Cabanski, Nicole M White, Ha X Dang, Jessica M Silva-Fisher, Corinne E Rauck, Danielle Cicka, and Christopher A Maher, “Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function.,” RNA biology, vol. 12, no. 6, pp. 628–42, 2015. View at Publisher · View at Google Scholar
  • Lin-Jiang Pan, Teng-Fei Zhong, Rui-Xue Tang, Ping Li, Yi-Wu Dang, Su-Ning Huang, and Gang Chen, “Upregulation and clinicopathological significance of long non-coding NEAT1 RNA in NSCLC tissues,” Asian Pacific Journal of Cancer Prevention, vol. 16, no. 7, pp. 2851–2855, 2015. View at Publisher · View at Google Scholar
  • Juan Xu, Tingting Shao, Na Ding, Yongsheng Li, and Xia Li, “miRNA–miRNA crosstalk: from genomics to phenomics,” Briefings in Bioinformatics, pp. bbw073, 2016. View at Publisher · View at Google Scholar
  • Xing Chen, Chenggang Clarence Yan, Xu Zhang, and Zhu-Hong You, “Long non-coding RNAs and complex diseases: from experimental results to computational models,” Briefings in Bioinformatics, pp. bbw060, 2016. View at Publisher · View at Google Scholar
  • Hongbo Shi, Zhaoyue Zhang, Zhenzhen Wang, Jie Sun, Liang Cheng, Hengqiang Zhao, and Meng Zhou, “A potential panel of six-long non-coding RNA signature to improve survival prediction of diffuse large-B-cell lymphoma,” Scientific Reports, vol. 6, 2016. View at Publisher · View at Google Scholar
  • Ruifang Wu, Yuwen Su, Haijing Wu, Yong Dai, Ming Zhao, and Qianjin Lu, “Characters, functions and clinical perspectives of long non-coding RNAs,” Molecular Genetics And Genomics, vol. 291, no. 3, pp. 1013–1033, 2016. View at Publisher · View at Google Scholar
  • Meng Zhou, Yifan Sun, Hengqiang Zhao, Yanying Sun, Wanying Xu, Zhaoyue Zhang, Zhaohua Zhong, and Jie Sun, “Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer,” Oncotarget, vol. 7, no. 22, pp. 32433–32448, 2016. View at Publisher · View at Google Scholar
  • Zhang Haijun, Yu Yonghui, and Chai Jiake, “Expression signatures of lncRNAs in skeletal muscles at the early flow phase revealed by microarray in burned rats,” Ulusal Travma Ve Acil Cerrahi Dergisi-Turkish Journal Of Trauma & Emergency Surgery, vol. 22, no. 3, pp. 224–232, 2016. View at Publisher · View at Google Scholar
  • Meng Zhou, Hongbo Shi, Liang Cheng, Hengqiang Zhao, Jie Sun, Xiaojun Wang, Zhenzhen Wang, and Lei Yang, “Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer,” Oncotarget, vol. 7, no. 11, pp. 12598–12611, 2016. View at Publisher · View at Google Scholar
  • Travers Ching, Karolina Peplowska, Sijia Huang, Xun Zhu, Yi Shen, Janos Molnar, Herbert Yu, Maarit Tiirikainen, Ben Fogelgren, Rong Fan, and Lana X. Garmire, “Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis,” EBioMedicine, 2016. View at Publisher · View at Google Scholar
  • Pasi K. Korhonen, Neil D. Young, and Robin B. Gasser, “Making sense of genomes of parasitic worms: Tackling bioinformatic challenges,” Biotechnology Advances, 2016. View at Publisher · View at Google Scholar
  • Tian Zhou, Jia-wang Ding, Xin-An Wang, and Xia-xia Zheng, “Long noncoding RNAs and atherosclerosis,” Atherosclerosis, 2016. View at Publisher · View at Google Scholar
  • Mohammad Reza Bakhtiarizadeh, Batool Hosseinpour, Babak Arefnezhad, Narges Shamabadi, Seyed Alireza Salami, and T.E. Bureau, “In silico prediction of long intergenic non-coding RNAs in sheep,” Genome, pp. 1–13, 2016. View at Publisher · View at Google Scholar
  • Tong Li, Meng Zhang, Feng Gao, Jialiang Gan, Chengfei Xu, and Bin Cai, “Expression and clinicopathological significance of the lncRNA HOXA11-AS in colorectal cancer,” Oncology Letters, vol. 12, no. 5, pp. 4155–4160, 2016. View at Publisher · View at Google Scholar
  • Wenjin Yang, Yijun Guo, Wei Chen, Jinsong Zeng, Wusong Tong, Lei Chen, and Ping Zheng, “Exosomal lncRNA GAS5 regulates the apoptosis of macrophages and vascular endothelial cells in atherosclerosis,” PLoS ONE, vol. 12, no. 9, 2017. View at Publisher · View at Google Scholar
  • Yanan Sun, Xiaoyan Zou, Jun He, and Yuqin Mao, “Identification of long non-coding RNAs biomarkers associated with progression of endometrial carcinoma and patient outcomes.,” Oncotarget, vol. 8, no. 32, pp. 52604–52613, 2017. View at Publisher · View at Google Scholar
  • Chen Li Chew, Stephanie Ana Conos, Bilal Unal, and Vinay Tergaonkar, “Noncoding RNAs: Master Regulators of Inflammatory Signaling,” Trends in Molecular Medicine, 2017. View at Publisher · View at Google Scholar
  • Ousheng Liu, Fei Yan, Liping Wang, Qiao Yi, Zhipeng Fan, Xiao Lin, Shu Diao, Luyuan Jin, Songlin Wang, and Yanqin Lu, “Analysis of senescence-related differentiation potentials and gene expression profiles in human dental pulp stem cells,” Cells Tissues Organs, vol. 203, no. 1, pp. 1–11, 2017. View at Publisher · View at Google Scholar
  • Xueqin Gao, Ling Li, Yingying Cong, Yini Wang, and Ping Lin, “Differential expression profiles of long non-coding RNAs as potential biomarkers for the early diagnosis of acute myocardial infarction,” Oncotarget, vol. 8, no. 51, pp. 88613–88621, 2017. View at Publisher · View at Google Scholar
  • Zhenyu Bao, Dong Dong, and Weitao Zhang, “A potential prognostic lncRNA signature for predicting survival in patients with bladder urothelial carcinoma,” Oncotarget, vol. 8, no. 6, pp. 10485–10497, 2017. View at Publisher · View at Google Scholar
  • Yuanxiu Lin, Leiyu Jiang, Qing Chen, Yali Li, Yunting Zhang, Ya Luo, Yong Zhang, Bo Sun, Xiaorong Wang, and Haoru Tang, “Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria×ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway,” Plant and Cell Physiology, 2018. View at Publisher · View at Google Scholar
  • Zhao-Hai Wang, Zhen-Yu Zhu, Pei-Rui Zhang, Na-Na Zhao, Si-Jie Cheng, Zhi-Xian Hong, Xi-Liang Wang, Shao-Geng Zhang, Jin Yan, Lin-Xiang Yu, Peng-Hui Yang, Cheng Wang, and Cheng-Cai Lai, “Downregulation of BRAF-activated non-protein coding RNA in patients with hepatitis B virus-associated hepatocellular carcinoma,” Oncology Letters, vol. 15, no. 5, pp. 7794–7798, 2018. View at Publisher · View at Google Scholar
  • Yi-Hao Lo, Hsuan Liu, Wei-Shone Chen, Jui-Ho Wang, Chung-Yu Yeh, Chao-Wen Hsu, Kuo-Wang Tsai, and You-Zuo Chen, “Linc00659, a long noncoding RNA, acts as novel oncogene in regulating cancer cell growth in colorectal cancer,” Molecular Cancer, vol. 17, no. 1, 2018. View at Publisher · View at Google Scholar
  • Yingjie Lu, Xiangwei Meng, Lifeng Wang, and Xiaoyun Wang, “Analysis of long non-coding RNA expression profiles identifies functional lncRNAs associated with the progression of acute coronary syndromes,” Experimental and Therapeutic Medicine, vol. 15, no. 2, pp. 1376–1384, 2018. View at Publisher · View at Google Scholar
  • Qiaowei Fan, and Bingrong Liu, “Discovery of a novel six-long non-coding RNA signature predicting survival of colorectal cancer patients,” Journal of Cellular Biochemistry, 2018. View at Publisher · View at Google Scholar