LncRNA Structural Characteristics in Epigenetic Regulation

The rapid development of new generation sequencing technology has deepened the understanding of genomes and functional products. RNA-sequencing studies in mammals show that approximately 85% of the DNA sequences have RNA products, for which the length greater than 200 nucleotides (nt) is called long non-coding RNAs (lncRNA). LncRNAs now have been shown to play important epigenetic regulatory roles in key molecular processes, such as gene expression, genetic imprinting, histone modification, chromatin dynamics, and other activities by forming specific structures and interacting with all kinds of molecules. This paper mainly discusses the correlation between the structure and function of lncRNAs with the recent progress in epigenetic regulation, which is important to the understanding of the mechanism of lncRNAs in physiological and pathological processes.

[1]  S. Oliviero,et al.  RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data , 2016, Bioinform..

[2]  E. Westhof,et al.  The interaction networks of structured RNAs. , 2006, Nucleic acids research.

[3]  Christian N. S. Pedersen,et al.  RNA Pseudoknot Prediction in Energy-Based Models , 2000, J. Comput. Biol..

[4]  Xudong Zhang,et al.  Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder , 2016, Science.

[5]  Yunli Zhou,et al.  Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. , 2010, Endocrinology.

[6]  Howard Y. Chang,et al.  Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.

[7]  Howard Y. Chang,et al.  Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.

[8]  Yi Xiao,et al.  Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation , 2017, Current protocols in bioinformatics.

[9]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[10]  Lei Wang,et al.  ALDB: A Domestic-Animal Long Noncoding RNA Database , 2015, PloS one.

[11]  H. Taylor,et al.  H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase , 2015, Nature Communications.

[12]  Joe C. Liang,et al.  Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.

[13]  Jernej Ule,et al.  hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1 , 2015, Nature.

[14]  Tian-Tian Sun,et al.  LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern. , 2016, Cancer discovery.

[15]  Howard Y. Chang,et al.  Understanding the transcriptome through RNA structure , 2011, Nature Reviews Genetics.

[16]  W. Winkler,et al.  RNA allostery glimpsed , 2006, Nature Structural &Molecular Biology.

[17]  Y. Mo,et al.  Negative regulation of lncRNA GAS5 by miR-21 , 2013, Cell Death and Differentiation.

[18]  Jenny C. Chang,et al.  The lncRNA BORG Drives Breast Cancer Metastasis and Disease Recurrence , 2017, Scientific Reports.

[19]  A. Gabory,et al.  The H19 locus: Role of an imprinted non‐coding RNA in growth and development , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[20]  Jennifer A. Mitchell,et al.  The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin , 2008, Science.

[21]  Tianxiang Chen,et al.  LncRNAs: emerging biomarkers in gastric cancer. , 2015, Future oncology.

[22]  Catherine A. Wakeman,et al.  Structure and Mechanism of a Metal-Sensing Regulatory RNA , 2007, Cell.

[23]  John L Rinn,et al.  RNA traffic control of chromatin complexes. , 2010, Current opinion in genetics & development.

[24]  T. Ishiwata,et al.  Expression and role of long non-coding RNA H19 in carcinogenesis. , 2018, Frontiers in bioscience.

[25]  Zhao Su,et al.  Genome-Wide Analysis of RNA Secondary Structure. , 2016, Annual review of genetics.

[26]  K. Morris,et al.  The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene , 2017, Proceedings of the National Academy of Sciences.

[27]  RNA: Detailed probing of RNA structure in vivo , 2015, Nature Reviews Genetics.

[28]  N. Brockdorff,et al.  The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. , 2010, Developmental cell.

[29]  Ming Sun,et al.  LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1. , 2016, Cancer research.

[30]  Vladimir B. Bajic,et al.  FARNA: knowledgebase of inferred functions of non-coding RNA transcripts , 2016, Nucleic acids research.

[31]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.

[32]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[33]  J. Rinn,et al.  A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.

[34]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[35]  Z. Tao,et al.  lncRNA-MIAT regulates microvascular dysfunction by functioning as a competing endogenous RNA. , 2015, Circulation research.

[36]  Li Yang,et al.  The long noncoding RNA regulation at the MYC locus. , 2015, Current opinion in genetics & development.

[37]  Qinghua Shi,et al.  mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing , 2013, RNA biology.

[38]  J. Woolford,et al.  Mod-seq: high-throughput sequencing for chemical probing of RNA structure , 2014, RNA.

[39]  Alessio Colantoni,et al.  Revealing protein–lncRNA interaction , 2015, Briefings Bioinform..

[40]  Jason G. Underwood,et al.  High-Throughput Nuclease Probing of RNA Structures Using FragSeq. , 2016, Methods in molecular biology.

[41]  Karissa Y. Sanbonmatsu,et al.  Structural architecture of the human long non-coding RNA, steroid receptor RNA activator , 2012, Nucleic acids research.

[42]  Bjarne Knudsen,et al.  Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .

[43]  International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome , 2004 .

[44]  Anne Condon,et al.  RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database , 2008, BMC Bioinformatics.

[45]  Boqin Hu,et al.  CLIPdb: a CLIP-seq database for protein-RNA interactions , 2015, BMC Genomics.

[46]  Anna Marie Pyle,et al.  HOTAIR forms an intricate and modular secondary structure. , 2015, Molecular cell.

[47]  Xiaoyan Lu,et al.  Insight into HOTAIR structural features and functions as landing pads for transcription regulation proteins. , 2017, Biochemical and biophysical research communications.

[48]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[49]  Jan H Bergmann,et al.  Long non-coding RNAs: modulators of nuclear structure and function. , 2014, Current opinion in cell biology.

[50]  Wei Chen,et al.  Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines , 2017, Scientific Reports.

[51]  Philip Hugenholtz,et al.  NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes , 2006, Nucleic Acids Res..

[52]  Yongshuai Jiang,et al.  Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways , 2017, Multiple sclerosis.

[53]  Charles S Bond,et al.  The ins and outs of lncRNA structure: How, why and what comes next? , 2016, Biochimica et biophysica acta.

[54]  Faisal A. Aldaye,et al.  Organization of Intracellular Reactions with Rationally Designed RNA Assemblies , 2011, Science.

[55]  Jeannie T. Lee.  Epigenetic Regulation by Long Noncoding RNAs , 2012, Science.

[56]  Shenmin Zhang,et al.  Circular Noncoding RNA HIPK3 Mediates Retinal Vascular Dysfunction in Diabetes Mellitus , 2017, Circulation.

[57]  Howard Y. Chang,et al.  Structural imprints in vivo decode RNA regulatory mechanisms , 2015, Nature.

[58]  Wei Lin,et al.  A comprehensive overview and evaluation of circular RNA detection tools , 2017, PLoS Comput. Biol..

[59]  Liuqing Yang,et al.  lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals , 2014, Cell.

[60]  Rudolf Jaenisch,et al.  Chromosomal silencing and localization are mediated by different domains of Xist RNA , 2002, Nature Genetics.

[61]  V. Rybin,et al.  The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. , 2011, RNA.

[62]  P. Kapranov,et al.  The Landscape of long noncoding RNA classification. , 2015, Trends in genetics : TIG.

[63]  K. Neugebauer,et al.  RNA-protein interactions in vivo: global gets specific. , 2012, Trends in biochemical sciences.

[64]  D. Gallie.  Faculty Opinions recommendation of The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. , 2015 .

[65]  David H. Mathews,et al.  RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.

[66]  P. Sætrom,et al.  Regulation of Inflammatory Phenotype in Macrophages by a Diabetes-Induced Long Noncoding RNA , 2014, Diabetes.

[67]  S. Raguz,et al.  Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. , 2010, Molecular cell.

[68]  Q. Lu,et al.  Characters, functions and clinical perspectives of long non-coding RNAs , 2016, Molecular Genetics and Genomics.

[69]  George A Calin,et al.  A novel non‐coding RNA lncRNA‐JADE connects DNA damage signalling to histone H4 acetylation , 2013, The EMBO journal.

[70]  G. Tartaglia,et al.  A high-throughput approach to profile RNA structure , 2016, Nucleic acids research.

[71]  Howard Y. Chang,et al.  An inducible long noncoding RNA amplifies DNA damage signaling , 2016, Nature Genetics.

[72]  J. Gu,et al.  Energy stress-induced lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development , 2017, Nature Communications.

[73]  Annette Fenner.  Kidney cancer: AR promotes RCC via lncRNA interaction , 2016, Nature Reviews Urology.

[74]  J. Mattick,et al.  Structural and Functional Annotation of Long Noncoding RNAs. , 2017, Methods in molecular biology.

[75]  N. Friedman,et al.  High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies , 2014, Cell.

[76]  Howard Y. Chang,et al.  Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.

[77]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.

[78]  Li Liu,et al.  Regulation of lncRNA expression , 2014, Cellular & Molecular Biology Letters.

[79]  Yi-Ping Phoebe Chen,et al.  Pairwise RNA secondary structure alignment with conserved stem pattern , 2015, Bioinform..

[80]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[81]  Runsheng Chen,et al.  Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a. , 2017, Cancer research.

[82]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in X Inactivation , 2003, Science.

[83]  Hui Xiao,et al.  NONCODE v3.0: integrative annotation of long noncoding RNAs , 2011, Nucleic Acids Res..

[84]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[85]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[86]  A. Wierzbicki,et al.  Control of Chromatin Structure by Long Noncoding RNA. , 2015, Trends in cell biology.

[87]  Alain Laederach,et al.  Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. , 2014, Human molecular genetics.

[88]  Eric Westhof,et al.  The Dynamic Landscapes of RNA Architecture , 2009, Cell.

[89]  R. Kelley,et al.  Noncoding RNA Genes in Dosage Compensation and Imprinting , 2000, Cell.