Best practice standards for circular RNA research

[1]  J. Kjems,et al.  The emerging roles of circRNAs in cancer and oncology , 2021, Nature Reviews Clinical Oncology.

[2]  Andrew L. Lemire,et al.  EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization , 2021, Cell.

[3]  I. Bozzoni,et al.  Circ-Hdgfrp3 shuttles along neurites and is trapped in aggregates formed by ALS-associated mutant FUS , 2021, iScience.

[4]  J. Kjems,et al.  Nanopore long-read sequencing of circRNAs. , 2021, Methods.

[5]  J. Kjems,et al.  Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons , 2021, Nature Communications.

[6]  A. Panda,et al.  Emerging Role of Circular RNA–Protein Interactions , 2021, Non-coding RNA.

[7]  Howard Y. Chang,et al.  Structured elements drive extensive circular RNA translation. , 2021, Molecular cell.

[8]  Morten T. Jarlstad Olesen,et al.  Circular RNAs as microRNA sponges: evidence and controversies. , 2021, Essays in biochemistry.

[9]  F. Zhao,et al.  Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long , 2021, Nature Biotechnology.

[10]  J. Wilusz,et al.  Best practices to ensure robust investigation of circular RNAs: pitfalls and tips , 2021, EMBO reports.

[11]  T. B. Hansen.  Signal and noise in circRNA translation. , 2021, Methods.

[12]  Lasse Sommer Kristensen,et al.  Profiling of circRNAs using an enzyme-free digital counting method. , 2021, Methods.

[13]  J. Clohessy,et al.  Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs , 2021, Genome biology.

[14]  M. Gorospe,et al.  AUF1 ligand circPCNX reduces cell proliferation by competing with p21 mRNA to increase p21 production. , 2021, Nucleic acids research.

[15]  Lan Lin,et al.  isoCirc catalogs full-length circular RNA isoforms in human transcriptomes , 2021, Nature Communications.

[16]  Gene W. Yeo,et al.  Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression , 2020, Genome medicine.

[17]  Aniruddha Das,et al.  Seeing Is Believing: Visualizing Circular RNAs , 2020, Non-coding RNA.

[18]  M. Gorospe,et al.  Practical guide for circular RNA analysis: Steps, tips, and resources , 2020, Wiley interdisciplinary reviews. RNA.

[19]  Debbie L C van den Berg,et al.  Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts , 2020, Nucleic acids research.

[20]  J. Kjems,et al.  Spatial expression analyses of the putative oncogene ciRS-7 in cancer reshape the microRNA sponge theory , 2020, Nature Communications.

[21]  S. Kadener,et al.  An in vivo strategy for knockdown of circular RNAs , 2020, Cell Discovery.

[22]  Xiang Li,et al.  Screening for functional circular RNAs using the CRISPR–Cas13 system , 2020, Nature Methods.

[23]  Ruth L. Seal,et al.  A guide to naming human non‐coding RNA genes , 2020, The EMBO journal.

[24]  N. Rajewsky,et al.  A Highly Conserved Circular RNA Is Required to Keep Neural Cells in a Progenitor State in the Mammalian Brain. , 2020, Cell reports.

[25]  Simon W. Jones,et al.  circSamd4 represses myogenic transcriptional activity of PUR proteins. , 2020, Nucleic acids research.

[26]  Howard Y. Chang,et al.  N6-Methyladenosine Modification Controls Circular RNA Immunity. , 2019, Molecular cell.

[27]  Sebastian Kadener,et al.  Past, present, and future of circRNAs , 2019, The EMBO journal.

[28]  Jørgen Kjems,et al.  The biogenesis, biology and characterization of circular RNAs , 2019, Nature Reviews Genetics.

[29]  Mei-Sheng Xiao,et al.  An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3′ ends , 2019, Nucleic acids research.

[30]  Zhong Zhou,et al.  CircACC1 Regulates Assembly and Activation of AMPK Complex under Metabolic Stress. , 2019, Cell metabolism.

[31]  Catherine L. Worth,et al.  The Translational Landscape of the Human Heart , 2019, Cell.

[32]  Akinobu Matsumoto,et al.  Intragenic antagonistic roles of protein and circRNA in tumorigenesis , 2019, Cell Research.

[33]  S. Conn,et al.  SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias , 2019, RNA.

[34]  Zhaocai Zhou,et al.  Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity , 2019, Cell.

[35]  Daniel G. Anderson,et al.  RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo. , 2019, Molecular cell.

[36]  T. B. Hansen,et al.  Noncoding AUG circRNAs constitute an abundant and conserved subclass of circles , 2018, Life Science Alliance.

[37]  Qian Wang,et al.  Circbank: a comprehensive database for circRNA with standard nomenclature , 2019, RNA biology.

[38]  S. Jaffrey,et al.  Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts , 2019, Nature Biotechnology.

[39]  P. Khavari,et al.  Methods to study RNA–protein interactions , 2019, Nature Methods.

[40]  F. Zhao,et al.  Reconstruction of full-length circular RNAs enables isoform-level quantification , 2019, Genome Medicine.

[41]  A. Hoffman,et al.  A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1 , 2018, Genome Biology.

[42]  Wenguang Chang,et al.  A circular transcript of ncx1 gene mediates ischemic myocardial injury by targeting miR-133a-3p , 2018, Theranostics.

[43]  K. Livak,et al.  SMARTer single cell total RNA sequencing , 2018, bioRxiv.

[44]  Yuan Gao,et al.  Circular RNA identification based on multiple seed matching , 2018, Briefings Bioinform..

[45]  A. Asokan,et al.  Tissue-Dependent Expression and Translation of Circular RNAs with Recombinant AAV Vectors In Vivo , 2018, Molecular therapy. Nucleic acids.

[46]  J. Kjems,et al.  Enzyme-free digital counting of endogenous circular RNA molecules in B-cell malignancies , 2018, Laboratory Investigation.

[47]  F. Nicassio,et al.  Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation , 2018, Nature Communications.

[48]  Xiang Li,et al.  The Biogenesis, Functions, and Challenges of Circular RNAs. , 2018, Molecular cell.

[49]  Li Yang,et al.  CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison , 2018, Genom. Proteom. Bioinform..

[50]  S. Konermann,et al.  Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors , 2018, Cell.

[51]  Thomas B. Hansen,et al.  Improved circRNA Identification by Combining Prediction Algorithms , 2018, Front. Cell Dev. Biol..

[52]  Wei Yan,et al.  Template switching causes artificial junction formation and false identification of circular RNAs , 2018, bioRxiv.

[53]  Jernej Ule,et al.  Advances in CLIP Technologies for Studies of Protein-RNA Interactions. , 2018, Molecular cell.

[54]  Trees-Juen Chuang,et al.  Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells , 2018, Nucleic acids research.

[55]  M. Hardt,et al.  Selective release of circRNAs in platelet-derived extracellular vesicles , 2018, Journal of extracellular vesicles.

[56]  J. Kjems,et al.  Circular RNAs are abundantly expressed and upregulated during human epidermal stem cell differentiation , 2017, RNA biology.

[57]  Aviv Regev,et al.  RNA targeting with CRISPR–Cas13 , 2017, Nature.

[58]  B. Blencowe,et al.  An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms , 2017, Genome research.

[59]  Carmen Birchmeier,et al.  Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function , 2017, Science.

[60]  Yi Xing,et al.  Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs. , 2017, Cell reports.

[61]  Kevin R. Parker,et al.  ciRS-7 exonic sequence is embedded in a long non-coding RNA locus , 2017, bioRxiv.

[62]  Howard Y. Chang,et al.  Sensing Self and Foreign Circular RNAs by Intron Identity. , 2017, Molecular cell.

[63]  F. Muntoni,et al.  Gapmer Antisense Oligonucleotides Suppress the Mutant Allele of COL6A3 and Restore Functional Protein in Ullrich Muscular Dystrophy , 2017, Molecular therapy. Nucleic acids.

[64]  Dawood B. Dudekula,et al.  High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs , 2017, Nucleic acids research.

[65]  N. Rajewsky,et al.  Translation of CircRNAs , 2017, Molecular cell.

[66]  N. Rajewsky,et al.  Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis , 2017, Molecular cell.

[67]  J. Salzman,et al.  Detecting circular RNAs: bioinformatic and experimental challenges , 2016, Nature Reviews Genetics.

[68]  Vikram Agarwal,et al.  Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression , 2016, Molecular cell.

[69]  O. Rossbach,et al.  CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs , 2016, Scientific Reports.

[70]  Yi Zheng,et al.  Comprehensive identification of internal structure and alternative splicing events in circular RNAs , 2016, Nature Communications.

[71]  Li Yang,et al.  The Biogenesis of Nascent Circular RNAs. , 2016, Cell reports.

[72]  Yan Li,et al.  Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs , 2016, Nature Communications.

[73]  M. Dinger,et al.  Endogenous microRNA sponges: evidence and controversy , 2016, Nature Reviews Genetics.

[74]  Jun Cheng,et al.  Specific identification and quantification of circular RNAs from sequencing data , 2016, Bioinform..

[75]  Igor Ulitsky,et al.  Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor , 2015, Nucleic acids research.

[76]  J. Kjems,et al.  Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development , 2015, Genome Biology.

[77]  F. Tang,et al.  Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos , 2015, Genome Biology.

[78]  Qiangfeng Cliff Zhang,et al.  Systematic Discovery of Xist RNA Binding Proteins , 2015, Cell.

[79]  E. Schuman,et al.  Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity , 2015, Nature Neuroscience.

[80]  S. Müller,et al.  RNA circularization strategies in vivo and in vitro , 2015, Nucleic acids research.

[81]  Yang Wang,et al.  Efficient backsplicing produces translatable circular mRNAs , 2015, RNA.

[82]  R. Zeillinger,et al.  Correlation of circular RNA abundance with proliferation – exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues , 2015, Scientific Reports.

[83]  Tim Schneider,et al.  Exon circularization requires canonical splice signals. , 2015, Cell reports.

[84]  Petar Glažar,et al.  circBase: a database for circular RNAs , 2014, RNA.

[85]  Dongming Liang,et al.  Short intronic repeat sequences facilitate circular RNA production , 2014, Genes & development.

[86]  N. Rajewsky,et al.  circRNA biogenesis competes with pre-mRNA splicing. , 2014, Molecular cell.

[87]  D. Bartel,et al.  Expanded identification and characterization of mammalian circular RNAs , 2014, Genome Biology.

[88]  Trees-Juen Chuang,et al.  Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? , 2014, Nucleic acids research.

[89]  Vikram Agarwal,et al.  Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. , 2014, Molecular cell.

[90]  Sebastian D. Mackowiak,et al.  Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.

[91]  J. Kjems,et al.  Natural RNA circles function as efficient microRNA sponges , 2013, Nature.

[92]  Michael K. Slevin,et al.  Circular RNAs are abundant, conserved, and associated with ALU repeats. , 2013, RNA.

[93]  Charles Gawad,et al.  Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types , 2012, PloS one.

[94]  Jørgen Kjems,et al.  miRNA‐dependent gene silencing involving Ago2‐mediated cleavage of a circular antisense RNA , 2011, The EMBO journal.

[95]  D. Weissman,et al.  Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA , 2011, Nucleic acids research.

[96]  R. Palmiter,et al.  Cell-type-specific isolation of ribosome-associated mRNA from complex tissues , 2009, Proceedings of the National Academy of Sciences.

[97]  Scott A. Rifkin,et al.  Imaging individual mRNA molecules using multiple singly labeled probes , 2008, Nature Methods.

[98]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[99]  Michael Q. Zhang,et al.  Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing , 2006, Nucleic acids research.

[100]  Peter Goodfellow,et al.  Circular transcripts of the testis-determining gene Sry in adult mouse testis , 1993, Cell.

[101]  C. Cocquerelle,et al.  Mis‐splicing yields circular RNA molecules , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[102]  M. Puttaraju,et al.  Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons. , 1992, Nucleic acids research.

[103]  Kathleen R. Cho,et al.  Scrambled exons , 1991, Cell.

[104]  Roger A. Garrett,et al.  Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium desulfurococcus mobilis , 1988, Cell.

[105]  T. Cech,et al.  Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage–ligation reaction , 1983, Nature.

[106]  M. Coca-Prados,et al.  Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells , 1979, Nature.

[107]  D. Riesner,et al.  Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[108]  Arturo Díaz Quiroz.  Circular , 1856, The North-Western Medical and Surgical Journal.

[109]  S. Preibisch,et al.  RS-FISH: Precise, interactive and scalable smFISH spot detection using Radial Symmetry , 2021 .

[110]  Lin,et al.  A circular transcript of ncx 1 gene mediates ischemic myocardial injury by targeting miR-133 a-3 p , 2018 .