Structural Insights Into the RNA Methyltransferase Domain Of
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'Next- Generation' Sequencing Data Analysis
Novel Algorithm Development for ‘Next- Generation’ Sequencing Data Analysis Agne Antanaviciute Submitted in accordance with the requirements for the degree of Doctor of Philosophy University of Leeds School of Medicine Leeds Institute of Biomedical and Clinical Sciences 12/2017 ii The candidate confirms that the work submitted is her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly given within the thesis where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement ©2017 The University of Leeds and Agne Antanaviciute The right of Agne Antanaviciute to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. Acknowledgements I would like to thank all the people who have contributed to this work. First and foremost, my supervisors Dr Ian Carr, Professor David Bonthron and Dr Christopher Watson, who have provided guidance, support and motivation. I could not have asked for a better supervisory team. I would also like to thank my collaborators Dr Belinda Baquero and Professor Adrian Whitehouse for opening new, interesting research avenues. A special thanks to Dr Belinda Baquero for all the hard wet lab work without which at least half of this thesis would not exist. Thanks to everyone at the NGS Facility – Carolina Lascelles, Catherine Daley, Sally Harrison, Ummey Hany and Laura Crinnion – for the generation of NGS data used in this work and creating a supportive and stimulating work environment. -
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. -
Large-Scale Functional Prediction of Individual M6a RNA Methylation Sites from an RNA Co-Methylation Network
Wu et al. BMC Bioinformatics (2019) 20:223 https://doi.org/10.1186/s12859-019-2840-3 RESEARCHARTICLE Open Access m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co- methylation network Xiangyu Wu1,2, Zhen Wei1,2, Kunqi Chen1,2, Qing Zhang1,4, Jionglong Su5, Hui Liu6, Lin Zhang6* and Jia Meng1,3* Abstract Background: Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. Results: To date, the study of epitranscriptome layer gene regulation is mostly focused on the function of mediator proteins of RNA methylation, i.e., the readers, writers and erasers. There is limited investigation of the functional relevance of individual m6A RNA methylation site. To address this, we annotated human m6A sites in large-scale based on the guilt-by-association principle from an RNA co-methylation network. It is constructed based on public human MeRIP-Seq datasets profiling the m6A epitranscriptome under 32 independent experimental conditions. By systematically examining the network characteristics obtained from the RNA methylation profiles, a total of 339,158 putative gene ontology functions associated with 1446 human m6A sites were identified. These are biological functions that may be regulated at epitranscriptome layer via reversible m6A RNA methylation. The results were further validated on a soft benchmark by comparing to a random predictor. Conclusions: An online web server m6Acomet was constructed to support direct query for the predicted biological functions of m6A sites as well as the sites exhibiting co-methylated patterns at the epitranscriptome layer. -
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. -
B01P) Gene Alias: IME4, M6A, MGC4336, MT-A70, Spo8
METTL3 purified MaxPab mouse Gene Symbol: METTL3 polyclonal antibody (B01P) Gene Alias: IME4, M6A, MGC4336, MT-A70, Spo8 Catalog Number: H00056339-B01P Gene Summary: This gene encodes the 70 kDa subunit of MT-A which is part of Regulatory Status: For research use only (RUO) N6-adenosine-methyltransferase. This enzyme is involved in the posttranscriptional methylation of internal Product Description: Mouse polyclonal antibody raised adenosine residues in eukaryotic mRNAs, forming against a full-length human METTL3 protein. N6-methyladenosine. [provided by RefSeq] Immunogen: METTL3 (NP_062826.2, 1 a.a. ~ 580 a.a) References: full-length human protein. 1. Synaptic N6-methyladenosine (m6A) epitranscriptome Sequence: reveals functional partitioning of localized transcripts. MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLR Merkurjev D, Hong WT, Iida K, Oomoto I, Goldie BJ, NPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELAT Yamaguti H, Ohara T, Kawaguchi SY, Hirano T, Martin DPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQ KC, Pellegrini M, Wang DO. Nat Neurosci. 2018 DGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHS Jul;21(7):1004-1014. doi: 10.1038/s41593-018-0173-6. KLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTV Epub 2018 Jun 27. AAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEI 2. The RNA Methyltransferase Complex of WTAP, ESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKF METTL3, and METTL14 Regulates Mitotic Clonal RSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFR Expansion in Adipogenesis. Kobayashi M, Ohsugi M, RIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMD Sasako T, Awazawa M, Umehara T, Iwane A, Kobayashi SEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWIC -
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. -
N6-Methyladenosine RNA Modification Regulates Embryonic Neural Stem Cell Self-Renewal Through Histone Modifications
ARTICLES https://doi.org/10.1038/s41593-017-0057-1 Corrected: Publisher Correction N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications Yang Wang1, Yue Li 2, Minghui Yue3,4, Jun Wang1, Sandeep Kumar5, Robert J. Wechsler-Reya1, Zhaolei Zhang6, Yuya Ogawa3,4, Manolis Kellis2, Gregg Duester 5 and Jing Crystal Zhao 1* Internal N6-methyladenosine (m6A) modification is widespread in messenger RNAs (mRNAs) and is catalyzed by heterodimers of methyltransferase-like protein 3 (Mettl3) and Mettl14. To understand the role of m6A in development, we deleted Mettl14 in embryonic neural stem cells (NSCs) in a mouse model. Phenotypically, NSCs lacking Mettl14 displayed markedly decreased proliferation and premature differentiation, suggesting that m6A modification enhances NSC self-renewal. Decreases in the NSC pool led to a decreased number of late-born neurons during cortical neurogenesis. Mechanistically, we discovered a genome-wide increase in specific histone modifications in Mettl14 knockout versus control NSCs. These changes correlated with altered gene expression and observed cellular phenotypes, suggesting functional significance of altered histone modi- fications in knockout cells. Finally, we found that m6A regulates histone modification in part by destabilizing transcripts that encode histone-modifying enzymes. Our results suggest an essential role for m6A in development and reveal m6A-regulated histone modifications as a previously unknown mechanism of gene regulation in mammalian cells. ost-transcriptional modification of mRNA has emerged as an (VZ) showed a decrease in number relative to those seen in control important mechanism for gene regulation. Among internal mice, and this reduction was accompanied by fewer late-born corti- mRNA modifications, m6A is by far the most abundant, tagging cal neurons. -
Related Genes in TP53-Mutant Non-Small-Cell Lung Cancer
Expression and Prognostic Signicance of m6A- Related Genes in TP53-Mutant Non-Small-Cell Lung Cancer Zhuochen Zhao First Aliated Hospital of Zhengzhou University Junhu Wan First Aliated Hospital of Zhengzhou University Manman Guo First Aliated Hospital of Zhengzhou University Yangxia Wang First Aliated Hospital of Zhengzhou University Zhengwu Yang First Aliated Hospital of Zhengzhou University Zhuofang Li First Aliated Hospital of Zhengzhou University Liang Ming ( [email protected] ) First Aliated Hospital of Zhengzhou University Research Article Keywords: TP53 mutant, N-6-methylation, NSCLC, prognostic, bioinformatics Posted Date: December 29th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-127631/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Background: TP53 is an important tumor suppressor gene on human chromosome 17. TP53 mutations have been conrmed in more than 60% of tumor patients' somatic cells. N6-methyladenosine is an enzyme that plays an important role in mRNA splicing, translation, and stabilization. It is a common internal modication of nucleotides, that is regulated by methyltransferases ("writer"), binding proteins ("reader"), and demethylases ("eraser"). However, its role in TP53 mutant non-small-cell lung cancer remains unknown. In this study, we investigated 17 common N-6-Methyladenosine regulators' contributions and prognostic values. Results: Wilcox test showed that 9 of 17 m6A regulators were expressed differently between TP53 mutant and wild type NSCLC (p<0.05). A new way of tumor typing is attempted by consensus clustering. Using univariate cox regression analysis, ALKBH5, HNRNPA2B1 were associated with the prognostic of TP53 mutant patients. -
RNA M6 a Modification Enzymes Shape Innate Responses to DNA by Regulating Interferon Β
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press RNA m6A modification enzymes shape innate responses to DNA by regulating interferon β Rosa M. Rubio,1 Daniel P. Depledge,1 Christopher Bianco,1 Letitia Thompson,1 and Ian Mohr1,2 1Department of Microbiology, 2Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA Modification of mRNA by N6-adenosine methylation (m6A) on internal bases influences gene expression in eukaryotes. How the dynamic genome-wide landscape of m6A-modified mRNAs impacts virus infection and host immune responses remains poorly understood. Here, we show that type I interferon (IFN) production triggered by dsDNA or human cytomegalovirus (HCMV) is controlled by the cellular m6A methyltrasferase subunit METTL14 and ALKBH5 demethylase. While METTL14 depletion reduced virus reproduction and stimulated dsDNA- or HCMV-induced IFNB1 mRNA accumulation, ALKBH5 depletion had the opposite effect. Depleting METTL14 increased both nascent IFNB1 mRNA production and stability in response to dsDNA. In contrast, ALKBH5 deple- tion reduced nascent IFNB1 mRNA production without detectably influencing IFN1B mRNA decay. Genome-wide transcriptome profiling following ALKBH5 depletion identified differentially expressed genes regulating antiviral immune responses, while METTL14 depletion altered pathways impacting metabolic reprogramming, stress responses, and aging. Finally, we determined that IFNB1 mRNA was m6A-modified within both the coding sequence and the 3′ untranslated region (UTR). This establishes that the host m6A modification machinery controls IFNβ production triggered by HCMV or dsDNA. Moreover, it demonstrates that responses to nonmicrobial dsDNA in uninfected cells, which shape host immunity and contribute to autoimmune disease, are regulated by enzymes controlling m6A epitranscriptomic changes. -
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. -
51104 METTL14 (D8K8W) Rabbit Mab
Revision 1 C 0 2 - t METTL14 (D8K8W) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 4 0 1 Web: [email protected] 1 www.cellsignal.com 5 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB H M R Mk Endogenous 65 Rabbit IgG Q9HCE5 57721 Product Usage Information 5. Ping, X.L. et al. (2014) Cell Res 24, 177-89. 6. Lin, S. et al. (2016) Mol Cell 62, 335-45. Application Dilution 7. Jin, D.I. et al. (2012) Cancer Sci 103, 2102-9. 8. Jo, H.J. et al. (2013) J Gastroenterol 48, 1271-82. Western Blotting 1:1000 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity METTL14 (D8K8W) Rabbit mAb recognizes endogenous levels of total METL14 protein. Species Reactivity: Human, Mouse, Rat, Monkey Species predicted to react based on 100% sequence homology: Chicken, Xenopus Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Pro130 of human METTL14 protein. Background Methyltransferase-like protein 3 (METTL3) and methytransferase-like protein 14 (METTL14) are the two catalytic subunits of an N6-methyltransferase complex that methylates adenosine residues in RNA (1). Methylation of adenosine residues regulates mRNA splicing, processing, translation efficiency, editing and stability, in addition to regulating primary miRNA processing, and is critical for proper regulation of the circadian clock, embryonic stem cell self-renewal, immune tolerance, response to various stimuli, meiosis and mouse fertility (2,3).