The development of a sensitive fluorescent protein-based transcript reporter for high throughput screening of negative modulators of lncRNAs

Genes and Diseases - Tập 5 Số 1 - Trang 62-74 - 2018
Zongyue Zeng1,2, Bo Huang3,1,2, Shifeng Huang4,2, Ruyi Zhang1,2, Shujuan Yan1,2, Xinyi Yu4,2, Yi Shu2,5, Chen Zhao4,2, Jiayan Lei4,2, Wenwen Zhang6,2, Chao Yang2,5, Ke Wu1,2, Ying Wu7,2, Liping An8,2, Xiaojuan Ji2,5, Gong Cheng9,2, Chengfu Yuan10,2, Linghuan Zhang2,5, Wei Liu4,2, Yixiao Feng4,2, Bo Zhang2,5, Zhengyu Dai, Yi Shen4,2, Xi Wang4,2, Wenping Luo, Rex C. Haydon, Hue H. Luu, Lijun Zhou, Russell R. Reid, Tong‐Chuan He10,2, Xingye Wu7,2
1Ministry of Education Key Laboratory of Diagnostic Medicine and School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
2Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
3Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
4Departments of Clinical Laboratory Medicine, General Surgery, Orthopedic Surgery, Nephrology, and Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
5The Children’s Hospital, Chongqing Medical University, Chongqing 400014, China
6Department of Laboratory Medicine and Clinical Diagnostics, The Affiliated Yantai Hospital, Binzhou Medical University, Yantai 264100, China
7Department of Immunology and Microbiology, Beijing University of Chinese Medicine, Beijing 100029, China
8Key Laboratory of Orthopaedic Surgery of Gansu Province and the Department of Orthopaedic Surgery, The Second Hospital of Lanzhou University, Lanzhou, 730030, China
9Department of Surgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan 430071, China
10Department of Biochemistry and Molecular Biology, China Three Gorges University School of Medicine, Yichang 443002, China

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Mattick, 2006, Non-coding RNA, Hum Mol Genet, 15, R17, 10.1093/hmg/ddl046

Guttman, 2009, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, 458, 223, 10.1038/nature07672

Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014

Brosnan, 2009, The long and the short of noncoding RNAs, Curr Opin Cell Biol, 21, 416, 10.1016/j.ceb.2009.04.001

Jacquier, 2009, The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs, Nat Rev Genet, 10, 833, 10.1038/nrg2683

Kapranov, 2007, Genome-wide transcription and the implications for genomic organization, Nat Rev Genet, 8, 413, 10.1038/nrg2083

Berretta, 2009, Pervasive transcription constitutes a new level of eukaryotic genome regulation, EMBO Rep, 10, 973, 10.1038/embor.2009.181

Djebali, 2012, Landscape of transcription in human cells, Nature, 489, 101, 10.1038/nature11233

Quinn, 2015, Unique features of long non-coding RNA biogenesis and function, Nat Rev Genet, 17, 47, 10.1038/nrg.2015.10

Quinodoz, 2014, Long noncoding RNAs: an emerging link between gene regulation and nuclear organization, Trends Cell Biol, 24, 651, 10.1016/j.tcb.2014.08.009

Johnsson, 2014, Evolutionary conservation of long non-coding RNAs; sequence, structure, function, Biochim Biophys Acta, 1840, 1063, 10.1016/j.bbagen.2013.10.035

Hung, 2010, Long noncoding RNA in genome regulation: prospects and mechanisms, RNA Biol, 7, 582, 10.4161/rna.7.5.13216

St Laurent, 2015, The Landscape of long noncoding RNA classification, Trends Genet, 31, 239, 10.1016/j.tig.2015.03.007

Iyer, 2015, The landscape of long noncoding RNAs in the human transcriptome, Nat Genet, 47, 199, 10.1038/ng.3192

Mellor, 2016, The interleaved genome, Trends Genet, 32, 57, 10.1016/j.tig.2015.10.006

Geisler, 2013, RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts, Nat Rev Mol Cell Biol, 14, 699, 10.1038/nrm3679

Cech, 2014, The noncoding RNA revolution-trashing old rules to forge new ones, Cell, 157, 77, 10.1016/j.cell.2014.03.008

Grote, 2015, Long noncoding RNAs in organogenesis: making the difference, Trends Genet, 31, 329, 10.1016/j.tig.2015.02.002

Bohmdorfer, 2015, Control of chromatin structure by long noncoding RNA, Trends Cell Biol, 25, 623, 10.1016/j.tcb.2015.07.002

Han, 2015, Long non-coding RNA and chromatin remodeling, RNA Biol, 12, 1094, 10.1080/15476286.2015.1063770

Sabin, 2013, Dogma derailed: the many influences of RNA on the genome, Mol Cell, 49, 783, 10.1016/j.molcel.2013.02.010

Vance, 2014, Transcriptional regulatory functions of nuclear long noncoding RNAs, Trends Genet, 30, 348, 10.1016/j.tig.2014.06.001

Roberts, 2014, Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs, Epigenetics, 9, 13, 10.4161/epi.26700

Ma, 2013, On the classification of long non-coding RNAs, RNA Biol, 10, 925, 10.4161/rna.24604

Ulitsky, 2013, lincRNAs: genomics, evolution, and mechanisms, Cell, 154, 26, 10.1016/j.cell.2013.06.020

Kim, 2014, Traffic into silence: endomembranes and post-transcriptional RNA silencing, Embo J, 33, 968, 10.1002/embj.201387262

Jonas, 2015, Towards a molecular understanding of microRNA-mediated gene silencing, Nat Rev Genet, 16, 421, 10.1038/nrg3965

Batista, 2013, Long noncoding RNAs: cellular address codes in development and disease, Cell, 152, 1298, 10.1016/j.cell.2013.02.012

Migliore, 2013, Resistance to targeted therapies: a role for microRNAs?, Trends Mol Med, 19, 633, 10.1016/j.molmed.2013.08.002

Xia, 2014, Mechanism of cancer drug resistance and the involvement of noncoding RNAs, Curr Med Chem, 21, 3029, 10.2174/0929867321666140414101939

Malek, 2014, Correlation of long non-coding RNA expression with metastasis, drug resistance and clinical outcome in cancer, Oncotarget, 5, 8027, 10.18632/oncotarget.2469

Turner, 2012, Genetic heterogeneity and cancer drug resistance, Lancet Oncol, 13, e178, 10.1016/S1470-2045(11)70335-7

Esteller, 2011, Non-coding RNAs in human disease, Nat Rev Genet, 12, 861, 10.1038/nrg3074

Taft, 2010, Non-coding RNAs: Regulators of disease, J Pathol, 220, 126, 10.1002/path.2638

Wahlestedt, 2013, Targeting long non-coding RNA to therapeutically upregulate gene expression, Nat Rev Drug Discov, 12, 433, 10.1038/nrd4018

Kapusta, 2014, Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications, Trends Genet, 30, 439, 10.1016/j.tig.2014.08.004

Alam, 1990, Reporter genes: application to the study of mammalian gene transcription, Anal Biochem, 188, 245, 10.1016/0003-2697(90)90601-5

Kain, 2001, Overview of genetic reporter systems, Curr Protoc Mol Biol

Li, 1998, Generation of destabilized green fluorescent protein as a transcription reporter, J Biol Chem, 273, 34970, 10.1074/jbc.273.52.34970

Wu, 2014, Overexpression of Ad5 precursor terminal protein accelerates recombinant adenovirus packaging and amplification in HEK-293 packaging cells, Gene Ther, 21, 629, 10.1038/gt.2014.40

Wei, 2017, Engineering the rapid adenovirus production and amplification (RAPA) cell line to expedite the generation of recombinant adenoviruses, Cell Physiol Biochem, 41, 2383, 10.1159/000475909

He, 2011, Tetrandrine inhibits Wnt/beta-catenin signaling and suppresses tumor growth of human colorectal cancer, Mol Pharmacol, 79, 211, 10.1124/mol.110.068668

Huang, 2012, Conditionally immortalized mouse embryonic fibroblasts retain proliferative activity without compromising multipotent differentiation potential, PLoS One, 7, 10.1371/journal.pone.0032428

Huang, 2012, Growth hormone synergizes with BMP9 in osteogenic differentiation by activating the JAK/STAT/IGF1 pathway in murine multilineage cells, J Bone Miner Res, 27, 1566, 10.1002/jbmr.1622

Kumagai, 2013, A bilirubin-inducible fluorescent protein from eel muscle, Cell, 153, 1602, 10.1016/j.cell.2013.05.038

Liao, 2017, lncRNA H19 mediates BMP9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) through Notch signaling, Oncotarget, 8, 53581, 10.18632/oncotarget.18655

He, 1998, A simplified system for generating recombinant adenoviruses, Proc Natl Acad Sci U S A., 95, 2509, 10.1073/pnas.95.5.2509

Luo, 2007, A protocol for rapid generation of recombinant adenoviruses using the AdEasy system, Nat Protoc, 2, 1236, 10.1038/nprot.2007.135

Deng, 2014, A simplified and versatile system for the simultaneous expression of multiple siRNAs in mammalian cells using Gibson DNA Assembly, PLoS One, 9, 10.1371/journal.pone.0113064

Luo, 2007, Selection and validation of optimal siRNA target sites for RNAi-mediated gene silencing, Gene, 395, 160, 10.1016/j.gene.2007.02.030

Zhao, 2014, Adenovirus-mediated gene transfer in mesenchymal stem cells can be significantly enhanced by the cationic polymer polybrene, PLoS One, 9, 10.1371/journal.pone.0092908

Liao, 2017, Characterization of retroviral infectivity and superinfection resistance during retrovirus-mediated transduction of mammalian cells, Gene Ther, 24, 333, 10.1038/gt.2017.24

Kong, 2013, Destabilization of heterologous proteins mediated by the GSK3beta phosphorylation domain of the beta-catenin protein, Cell Physiol Biochem, 32, 1187, 10.1159/000354518

Huang, 2009, Retinoic acid signalling induces the differentiation of mouse fetal liver-derived hepatic progenitor cells, Liver Int, 29, 1569, 10.1111/j.1478-3231.2009.02111.x

Zhu, 2009, Activation of RXR and RAR signaling promotes myogenic differentiation of myoblastic C2C12 cells, Differentiation, 78, 195, 10.1016/j.diff.2009.06.001

Bi, 2009, Wnt antagonist SFRP3 inhibits the differentiation of mouse hepatic progenitor cells, J Cell Biochem, 108, 295, 10.1002/jcb.22254

Untergasser, 2012, Primer3–new capabilities and interfaces, Nucleic Acids Res, 40, e115, 10.1093/nar/gks596

Zhang, 2015, TqPCR: a touchdown qPCR assay with significantly improved detection sensitivity and amplification efficiency of SYBR Green qPCR, PLoS One, 10

Schenborn, 1999, Reporter gene vectors and assays, Mol Biotechnol, 13, 29, 10.1385/MB:13:1:29

Jiang, 2008, Recent developments of biological reporter technology for detecting gene expression, Biotechnol Genet Eng Rev, 25, 41, 10.5661/bger-25-41

Contag, 2002, Advances in in vivo bioluminescence imaging of gene expression, Annu Rev Biomed Eng, 4, 235, 10.1146/annurev.bioeng.4.111901.093336

Ray, 2007, Noninvasive imaging of molecular events with bioluminescent reporter genes in living subjects, Methods Mol Biol., 411, 131, 10.1007/978-1-59745-549-7_10

Welsh, 2012, Cellular bioluminescence imaging, Cold Spring Harb Protoc, 2012, 10.1101/pdb.top070607

Prescher, 2010, Guided by the light: visualizing biomolecular processes in living animals with bioluminescence, Curr Opin Chem Biol, 14, 80, 10.1016/j.cbpa.2009.11.001

Navarro, 2016, A novel destabilizing domain based on a small-molecule dependent fluorophore, ACS Chem Biol, 11, 2101, 10.1021/acschembio.6b00234

Funahashi, 2016, Eel green fluorescent protein is associated with resistance to oxidative stress, Comp Biochem Physiol C Toxicol Pharmacol, 181–182, 35, 10.1016/j.cbpc.2015.12.009

Dixit, 2003, Cell damage and reactive oxygen species production induced by fluorescence microscopy: effect on mitosis and guidelines for non-invasive fluorescence microscopy, Plant J, 36, 280, 10.1046/j.1365-313X.2003.01868.x

Shitashima, 2017, Two distinct fluorescence states of the ligand-induced Green fluorescent protein UnaG, Biophys J, 113, 2805, 10.1016/j.bpj.2017.10.022