Visualizing the Structure and Motion of the Long Noncoding
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Long Non-Coding RNA HOTAIR Regulates Polycomb-Dependent Chromatin
Author Manuscript Published OnlineFirst on August 23, 2011; DOI: 10.1158/0008-5472.CAN-11-1021 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Kogo et al. 1 Long non-coding RNA HOTAIR regulates Polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Ryunosuke Kogo1, 4, 6, Teppei Shimamura2, 6, Koshi Mimori1, 6, Kohichi Kawahara3, Seiya Imoto2, Tomoya Sudo1, Fumiaki Tanaka1, Kohei Shibata1, Akira Suzuki3, Shizuo Komune4, Satoru Miyano2, and Masaki Mori5 Authors’ Affiliations 1 Department of Surgery, Medical Institute of Bioregulation, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan. 2 Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. 3 Division of Cancer Genetics, Medical Institute Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan. 4 Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan. 5 Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka Downloaded from cancerres.aacrjournals.org on September 28, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on August 23, 2011; DOI: 10.1158/0008-5472.CAN-11-1021 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Kogo et al. 2 University, 2-2 Yamadaoka, Suita, 565-0871, Japan 6) These authors contributed equally to this work. Running title: HOTAIR in colorectal cancer Key words: HOTAIR, ncRNA, colorectal cancer, PRC2, liver metastasis Disclosure: There are no potential conflicts of interest to disclose. -
Role of MALAT1 in Gynecological Cancers: Pathologic and Therapeutic Aspects (Review)
ONCOLOGY LETTERS 21: 333, 2021 Role of MALAT1 in gynecological cancers: Pathologic and therapeutic aspects (Review) FENG‑HUA QIAO1, MIN TU2 and HONG‑YAN LIU3 Departments of 1Gynecology and 2Orthopedics, Second People's Hospital of Jingmen; 3Department of Gynecology, Maternal and Child Health Hospital of Jingmen, Jingmen, Hubei 448000, P.R. China Received June 28, 2020; Accepted February 2, 2021 DOI: 10.3892/ol.2021.12594 Abstract. Gynecological cancers, including breast, ovarian, 5. Targeting MALAT1 in gynecological cancer therapeutics uterine, vaginal, cervical and vulvar cancers are among the 6. Future research major threats to modern life, particularly to female health. 7. Conclusions Long non‑coding RNAs (lncRNAs) play critical roles in normal development of organisms, as well as the tumorigenesis process, and metastasis‑associated lung adenocarcinoma tran‑ 1. Introduction script 1 (MALAT1) is a large infrequently spliced lncRNA, which have been implicated in different gynecological cancers. Gynecologic cancer is any cancer of the female reproduc‑ MALAT1 is overexpressed in breast, ovarian, cervical and tive organs, including ovarian, uterine, vaginal, cervical and endometrial cancers, which initiates cancer progression by vulvar cancers. Generally, all women are at risk of devel‑ inducing changes in the expression of several anti‑apoptotic oping gynecological cancers, and risk increases with age (1). and epithelial‑to‑mesenchymal transition‑related genes. Each gynecologic cancer is unique, with different signs and Targeting MALAT1 is an important strategy to combat symptoms, different risk factors and different therapeutic strat‑ gynecological cancers, and application of RNA‑interference egies (2,3). Gynecological cancers are associated with high technology and chemotherapeutic process are crucial to target mortality rates worldwide as it is difficult to detect the cancers and minimize MALAT1 activity. -
HOTAIR Launches Lncrnas
Annotated Classic HOTAIR Launches lncRNAs Irene Bozzoni1,* 1Department of Biology and Biotechnology, “Charles Darwin” Sapienza - University of Rome, P. le A. Moro 5, 00185 Rome, Italy *Correspondence: [email protected] We are pleased to present a series of Annotated Classics celebrating 40 years of exciting biology in the pages of Cell. This install- ment revisits “Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs” from Howard Chang’s lab. Here, Irene Bozzoni comments on how Rinn et al. ignited our appreciation for the ability of noncoding RNAs to regulate key cellular and developmental processes in trans. Each Annotated Classic offers a personal perspective on a groundbreaking Cell paper from leader in the field with notes on what stood out at the time of first reading and retrospective comments regarding the longer term influence of the work. To see Irene Bozzoni’s thoughts on different parts of the manuscript, just download the PDF and then hover over or double-click the highlighted text and comment boxes on the following pages. You can also view the annotations by opening the Comments navigation panel in Acrobat. Cell 159, November 20, 2014 ©2014 Elsevier Inc. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs John L. Rinn,1 Michael Kertesz,3,5 Jordon K. Wang,1,5 Sharon L. Squazzo,4 Xiao Xu,1 Samantha A. Brugmann,2 L. Henry Goodnough,2 Jill A. Helms,2 Peggy J. Farnham,4 Eran Segal,3,* and Howard Y. Chang1,* 1 Program in Epithelial Biology 2 Department of Surgery Stanford University School of Medicine, Stanford, CA 94305, USA 3 Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel 4 Department of Pharmacology and Genome Center, University of California, Davis, CA 95616, USA 5 These authors contributed equally to this work. -
Long Non-Coding RNA MALAT1 Drives Gastric Cancer Progression By
Li et al. Cancer Cell Int (2017) 17:44 DOI 10.1186/s12935-017-0408-8 Cancer Cell International PRIMARY RESEARCH Open Access Long non‑coding RNA MALAT1 drives gastric cancer progression by regulating HMGB2 modulating the miR‑1297 Jijun Li, Jinghua Gao*, Wen Tian, Yongsheng Li and Jinghua Zhang Abstract Background: Emerging evidences have verified that long non-coding RNAs (lncRNAs) play important regulatory roles in the pathogenesis and progression of cancers. lncRNAs metastasis associated lung adenocarcinoma transcript 1 (MALAT1) have been found to be up-regulated in some human cancers. The main objective of this study was to investigate the expression level and biological function of MALAT1 in gastric cancer (GC). Methods: Quantificational real-time polymerase chain reaction (qRT-PCR) was performed to detect the mRNA levels of MALAT1 in 78 paired gastric carcinoma tissues and adjacent normal tissues, and the associations of MALAT1 expres- sion with the clinicopathological features were analyzed, and the prognosis of gastric carcinoma patients was evalu- ated. The HMGB2 mRNA and protein expressions were detected by qRT-PCR and western-blot analysis. Luciferase reporter assay was used to determine miR-1297 was a target of MALAT1. Results: In this study, we demonstrated MALAT1 was up-regulation in GC tissues compared with adjacent normal tissues and higher MALAT1 expression was correlated with local invasion, lymph node metastasis and TNM stage. Patients with higher MALAT1 expression predicted a shorter survival and poor prognosis. Functionally, we revealed that MALAT1 promoted cells proliferation and invasion in GC. Mechanistically, our results demonstrated that MALAT1 was negatively correlation with miR-1297 and functioned as a molecular sponging miR-1297, antagonizing its ability to suppress HMGB2 expression. -
NF-Κb-HOTAIR Axis Links DNA Damage Response, Chemoresistance and Cellular Senescence in Ovarian Cancer
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Oncogene Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 October 14. Published in final edited form as: Oncogene. 2016 October 13; 35(41): 5350–5361. doi:10.1038/onc.2016.75. NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer Ali R. Özeş1, David F. Miller2, Osman N. Özeş3, Fang Fang2, Yunlong Liu4,5,6, Daniela Matei6,7,8, Tim Huang9, and Kenneth P. Nephew1,2,6,8,10,* 1Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA 2Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA 3Department of Medical Biology and Genetics, Akdeniz University, Antalya, Turkey 4Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA 5Center for Computational Biology and Bioinformatics, Indianapolis, Indiana 46202, USA 6Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana 46202, USA 7Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA 8Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA 9Department of Molecular Medicine/Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900 10Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA Abstract The transcription factor nuclear factor kappa B (NF-κB) and the long non-coding RNA (lncRNA) HOTAIR (HOX transcript antisense RNA) play diverse functional roles in cancer. In this study, we show that upregulation of HOTAIR induced platinum resistance in ovarian cancer, and increased HOTAIR levels were observed in recurrent platinum-resistant ovarian tumors vs. -
KDM1A Microenvironment, Its Oncogenic Potential, And
Ismail et al. Epigenetics & Chromatin (2018) 11:33 https://doi.org/10.1186/s13072-018-0203-3 Epigenetics & Chromatin REVIEW Open Access KDM1A microenvironment, its oncogenic potential, and therapeutic signifcance Tayaba Ismail1, Hyun‑Kyung Lee1, Chowon Kim1, Taejoon Kwon2, Tae Joo Park2* and Hyun‑Shik Lee1* Abstract The lysine-specifc histone demethylase 1A (KDM1A) was the frst demethylase to challenge the concept of the irreversible nature of methylation marks. KDM1A, containing a favin adenine dinucleotide (FAD)-dependent amine oxidase domain, demethylates histone 3 lysine 4 and histone 3 lysine 9 (H3K4me1/2 and H3K9me1/2). It has emerged as an epigenetic developmental regulator and was shown to be involved in carcinogenesis. The functional diversity of KDM1A originates from its complex structure and interactions with transcription factors, promoters, enhancers, onco‑ proteins, and tumor-associated genes (tumor suppressors and activators). In this review, we discuss the microenviron‑ ment of KDM1A in cancer progression that enables this protein to activate or repress target gene expression, thus making it an important epigenetic modifer that regulates the growth and diferentiation potential of cells. A detailed analysis of the mechanisms underlying the interactions between KDM1A and the associated complexes will help to improve our understanding of epigenetic regulation, which may enable the discovery of more efective anticancer drugs. Keywords: Histone demethylation, Carcinogenesis, Acute myeloid leukemia, KDM1A, TLL Background X-chromosome, that are involved in the regulation of Epigenetic modifcations are crucial for physiological development. Additionally, these alterations may repre- development and steady-state gene expression in eukary- sent aberrant markers indicating the development of dif- otes [1] and are required for various biological processes ferent types of cancer and other diseases [5–7]. -
University of Florida Thesis Or Dissertation Formatting
GENES AND GENOMES OF REPTILES By JENA LIND CHOJNOWSKI A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2010 1 © 2010 Jena Lind Chojnowski 2 To my mother and father and to all those who have overcome their own setbacks, big or small, to succeed in their happiness 3 ACKNOWLEDGMENTS I would like to thank my emotional support system, which includes my mother (my best cheerleader), my friends who had to deal with my venting, and my soccer friends who helped with my frustrations. My undergraduate assistants, especially Vipa Bernhardt, Jenessa Graham, and Rachel Seibert, were crucial in the beginning stages of my work. I would also like to thank my committee members: Mike Miyamoto, Lou Guillette, Jr., Mike Fields, Rebecca Kimball, and my advisor Ed Braun. I would like to thank Mike Miyamoto for always being positive, Lou Guillette for his invaluable technical help and pushing me to the next level, and Mike Fields for showing me there is life outside of the lab. I would like to give special thanks to Rebecca Kimball for helping me every step of the way by not only providing emotional support but also technical and psychological support. Without her expertise I would not be where I am today. Ed Braun, my advisor, is my teacher, my mentor, and my friend, all things necessary for a successful and fruitful pairing, which constitutes our union. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ........................................................................................................... -
MALAT1 Is Associated with Poor Response to Oxaliplatin-Based
Published OnlineFirst January 9, 2017; DOI: 10.1158/1535-7163.MCT-16-0591 Companion Diagnostics and Cancer Biomarkers Molecular Cancer Therapeutics MALAT1 Is Associated with Poor Response to Oxaliplatin-Based Chemotherapy in Colorectal Cancer Patients and Promotes Chemoresistance through EZH2 Peilong Li1, Xin Zhang1, Haiyan Wang2, Lili Wang1, Tong Liu1, Lutao Du1, Yongmei Yang1, and Chuanxin Wang3 Abstract A major reason for oxaliplatin chemoresistance in colorectal E-cadherin expression and inhibits oxaliplatin-induced EMT in cancer is the acquisition of epithelial–mesenchymal transition colorectal cancer cells. EZH2 is highly expressed and associated (EMT) in cancer cells. The long noncoding RNA (lncRNA), with the 30 end region of lncRNA MALAT1 in colorectal cancer, MALAT1, is a highly conserved nuclear ncRNA and a key regulator and this association suppressed the expression of E-cadherin. of metastasis development in several cancers. However, its role in Furthermore, targeted inhibition of MALAT1 or EZH2 reversed oxaliplatin-induced metastasis and chemoresistance is not well EMT and chemoresistance induced by oxaliplatin. Finally, the known. In this study, we aim to investigate the prognostic and interaction between lncRNA MALAT1 and miR-218 was observed, therapeutic role of lncRNA MALAT1 in colorectal cancer patients which further indicated its prognostic value in patients who receiving oxaliplatin-based therapy and further explore the poten- received standard FOLFOX (oxaliplatin combine with 5-fluoro- tial transcriptional regulation through interaction with EZH2 uracil and leucovorin) treatment. In conclusion, this study illu- based on the established HT29 oxaliplatin-resistant cells. Our minates the prognostic role of lncRNA MALAT1 in colorectal results showed that high MALAT1 expression was associated cancer patients receiving oxaliplatin-based treatment and further with reduced patient survival and poor response to oxaliplatin- demonstrates how lncRNA MALAT1 confers a chemoresistant based chemotherapy in advanced colorectal cancer patients. -
Long Non-Coding RNA HOTAIR: a Novel Oncogene (Review)
MOLECULAR MEDICINE REPORTS 12: 5611-5618, 2015 Long non-coding RNA HOTAIR: A novel oncogene (Review) XIN YU1,2* and ZHENG LI1* 1Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Beijing 100730; 2State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, P.R. China Received July 29, 2014; Accepted April 20, 2015 DOI: 10.3892/mmr.2015.4161 Abstract. Long non-coding RNAs (lncRNAs) have been found 1. Introduction to be pervasively transcribed in the genome and are critical regulators of the epigenome. Increasing evidence suggests An oncogene is defined as a mutated gene, whose product that lncRNAs are aberrantly expressed in several types of contributes to the initiation or progression of cancer (1). human cancer and that they are important in the initiation, Activation of oncogenes are critical in the molecular development and metastasis of human cancer. Previous studies pathogenesis of human neoplasms (2). Known oncogene, have revealed that HOX transcript antisense intergenic RNA including Ras, BRAF, β-catenin, and Myc, are predominantly (HOTAIR) was frequently upregulated in various types of protein-coding genes, the functions of which are mediated cancer, including breast cancer, esophageal cancer, lung cancer by their gene products-proteins (3-6). Genome sequencing and gastric cancer. In addition, patients with high expression projects have revealed that the human genome contains levels of HOTAIR have a significantly poorer prognosis, <2% protein coding genes, while>90% of the genome is tran- compared with those with low levels of expression. -
End Processing and Maturation of MALAT1 Lncrna Xinying Zong1, Shinichi Nakagawa2, Susan M
Nucleic Acids Research Advance Access published January 29, 2016 Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw047 Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA Xinying Zong1, Shinichi Nakagawa2, Susan M. Freier3, Jingyi Fei4, Taekjip Ha4, Supriya G. Prasanth1 and Kannanganattu V. Prasanth1,* 1Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA, 2RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan, 3Ionis Pharmaceuticals, Carlsbad, CA, USA and 4Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA Received July 09, 2015; Revised December 30, 2015; Accepted January 17, 2016 ABSTRACT is critical for the termination of RNA Pol II and also deter- Downloaded from mines the stability, subcellular localization and eventually The RNase P-mediated endonucleolytic cleavage the functionality of the mature RNA (3,4). Recent studies plays a crucial role in the 3 end processing and cellu- have reported the existence of non-canonical 3 end pro- lar accumulation of MALAT1, a nuclear-retained long cessing mechanisms at several lncRNA loci that generate noncoding RNA that promotes malignancy. The regu- non-polyadenylated RNAs (5–7). Among them, metastasis- http://nar.oxfordjournals.org/ lation of this cleavage event is largely undetermined. associated lung adenocarcinoma transcript 1 (MALAT1; Here we characterize a broadly expressed natural an- also known as NEAT2) and multiple endocrine neoplasia- tisense transcript at the MALAT1 locus, designated  (MEN; also known as NEAT1) RNAs are unique as as TALAM1, that positively regulates MALAT1 levels they are highly abundant linear transcripts. -
HOTAIR Is a Negative Prognostic Factor and Exhibits Pro-Oncogenic Activity in Pancreatic Cancer
Oncogene (2013) 32, 1616–1625 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc ORIGINAL ARTICLE HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer K Kim1, I Jutooru2, G Chadalapaka2, G Johnson3, J Frank3, R Burghardt3, S Kim4 and S Safe1,2 HOTAIR is a long intervening non-coding RNA (lincRNA) that associates with the Polycomb Repressive Complex 2 (PRC2) and overexpression is correlated with poor survival for breast, colon and liver cancer patients. In this study, we show that HOTAIR expression is increased in pancreatic tumors compared with non-tumor tissue and is associated with more aggressive tumors. Knockdown of HOTAIR (siHOTAIR) by RNA interference shows that HOTAIR has an important role in pancreatic cancer cell invasion, as reported in other cancer cell lines. In contrast, HOTAIR knockdown in Panc1 and L3.6pL pancreatic cancer cells that overexpress this lincRNA decreased cell proliferation, altered cell cycle progression and induced apoptosis, demonstrating an expanded function of HOTAIR in pancreatic cancer cells compared with other cancer cell lines. Results of gene array studies showed that there was minimal overlap between HOTAIR-regulated genes in pancreatic cells and breast cancer cells, and HOTAIR uniquely suppressed several interferon-related genes and gene sets related to cell cycle progression in pancreatic cancer cells and tumors. Analysis of selected genes suppressed by HOTAIR in Panc1 and L3.6pL cells showed by knockdown of EZH2 and chromatin immunoprecipitation assays that HOTAIR-mediated gene repression was both PRC2-dependent and -independent. HOTAIR knockdown in L3.6pL cells inhibited tumor growth in mouse xenograft model, further demonstrating the pro-oncogenic function of HOTAIR in pancreatic cancer. -
Long Non-Coding RNA Epigenetics
International Journal of Molecular Sciences Review Long Non-Coding RNA Epigenetics Marek Kazimierczyk and Jan Wrzesinski * Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Pozna´n,Poland; [email protected] * Correspondence: [email protected] Abstract: Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes. Keywords: lncRNA epigenetics; RNA modyfiing enzymes; detection modified nucleotides 1. General Remarks Citation: Kazimierczyk, M.; Although almost 80% of the human genome has been transcribed, only 2% of it Wrzesinski, J. Long Non-Coding RNA (mRNA) codes proteins [1,2]. All of the remaining RNAs belong to a vast group of noncod- Epigenetics. Int. J. Mol. Sci. 2021, 22, ing RNAs (ncRNAs). Based on their functions, ncRNAs can be classified as housekeeping 6166.