Evolutionary conservation and function of the human embryonic stem cell specific miR-302/367 cluster

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[1]  K. Hayashibara,et al.  Identification of known and novel germ cell cancer‐specific (embryonic) miRs in serum by high‐throughput profiling , 2015, Andrology.

[2]  A. Siepel,et al.  Diverse modes of evolutionary emergence and flux of conserved microRNA clusters , 2014, RNA.

[3]  D. Haussler,et al.  The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Res..

[4]  Athanasios Fevgas,et al.  DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions , 2014, Nucleic Acids Res..

[5]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[6]  Kimberley M. Smith,et al.  MicroRNAs control the apoptotic threshold in primed pluripotent stem cells through regulation of BIM , 2014, Genes & development.

[7]  H. Park,et al.  MicroRNA-302 induces proliferation and inhibits oxidant-induced cell death in human adipose tissue-derived mesenchymal stem cells , 2014, Cell Death and Disease.

[8]  C. Langford,et al.  5′ isomiR variation is of functional and evolutionary importance , 2014, Nucleic acids research.

[9]  M. Soleimani,et al.  Mir-302 cluster exhibits tumor suppressor properties on human unrestricted somatic stem cells , 2014, Tumor Biology.

[10]  Hsien-Da Huang,et al.  miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions , 2013, Nucleic Acids Res..

[11]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[12]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[13]  Z. Qian,et al.  Dissecting the Roles of miR-302/367 Cluster in Cellular Reprogramming Using TALE-based Repressor and TALEN , 2013, Stem cell reports.

[14]  S. Griffiths-Jones,et al.  Clusters of microRNAs emerge by new hairpins in existing transcripts , 2013, Nucleic acids research.

[15]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[16]  S. Lemon,et al.  Competing and noncompeting activities of miR-122 and the 5′ exonuclease Xrn1 in regulation of hepatitis C virus replication , 2012, Proceedings of the National Academy of Sciences.

[17]  C. Bracken,et al.  IsomiRs--the overlooked repertoire in the dynamic microRNAome. , 2012, Trends in genetics : TIG.

[18]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[19]  R. Malekzadeh,et al.  Down-regulation of miR-302b, an ESC-specific microRNA, in Gastric Adenocarcinoma , 2011, Cell journal.

[20]  C. Sander,et al.  Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. , 2011, Genes & development.

[21]  Mikko Koski,et al.  Chipster: user-friendly analysis software for microarray and other high-throughput data , 2011, BMC Genomics.

[22]  Mitsugu Sekimoto,et al.  Reprogramming of mouse and human cells to pluripotency using mature microRNAs. , 2011, Cell stem cell.

[23]  Maikun Teng,et al.  MicroRNA Cluster 302–367 Enhances Somatic Cell Reprogramming by Accelerating a Mesenchymal-to-Epithelial Transition* , 2011, The Journal of Biological Chemistry.

[24]  W. Filipowicz,et al.  The widespread regulation of microRNA biogenesis, function and decay , 2010, Nature Reviews Genetics.

[25]  Anjali J. Koppal,et al.  Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .

[26]  R. Hart,et al.  miRNA in pluripotent stem cells. , 2010, Regenerative medicine.

[27]  Anton J. Enright,et al.  Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. , 2010, Cancer research.

[28]  Zhaolei Zhang,et al.  Evolution of an X-linked primate-specific micro RNA cluster. , 2010, Molecular biology and evolution.

[29]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[30]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[31]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[32]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[33]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[34]  Ming Yi,et al.  bioDBnet: the biological database network , 2009, Bioinform..

[35]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[36]  Anton J. Enright,et al.  Annotation of mammalian primary microRNAs , 2008, BMC Genomics.

[37]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[38]  L. Laurent.  MicroRNAs in embryonic stem cells and early embryonic development , 2008, Journal of cellular and molecular medicine.

[39]  G. Melen,et al.  Embryonic Stem Cell-Specific miR302-367 Cluster: Human Gene Structure and Functional Characterization of Its Core Promoter , 2008, Molecular and Cellular Biology.

[40]  Megan F. Cole,et al.  Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells , 2008, Cell.

[41]  Robert J. Moore,et al.  A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. , 2008, Genome research.

[42]  N. Warthmann,et al.  Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae. , 2008, Molecular biology and evolution.

[43]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[44]  Anton J. Enright,et al.  Genomic analysis of human microRNA transcripts , 2007, Proceedings of the National Academy of Sciences.

[45]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[46]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.

[47]  Peng Jiang,et al.  MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features , 2007, Nucleic Acids Res..

[48]  Wen-Hsiung Li,et al.  Human polymorphism at microRNAs and microRNA target sites , 2007, Proceedings of the National Academy of Sciences.

[49]  Jin-Wu Nam,et al.  Genomics of microRNA. , 2006, Trends in genetics : TIG.

[50]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[51]  S. Moon,et al.  Human embryonic stem cells express a unique set of microRNAs. , 2004, Developmental biology.

[52]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[53]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[54]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[55]  Anton J. Enright,et al.  MicroRNA targets in Drosophila , 2003, Genome Biology.

[56]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[57]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.

[58]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[59]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[60]  S. Dudoit,et al.  Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. , 2000, Genome research.

[61]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[62]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[63]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[64]  N. Cai,et al.  The microRNA-302-367 cluster suppresses the proliferation of cervical carcinoma cells through the novel target AKT1. , 2013, RNA.

[65]  N. Coleman,et al.  Identification of microRNAs From the miR-371~373 and miR-302 clusters as potential serum biomarkers of malignant germ cell tumors. , 2011, American journal of clinical pathology.

[66]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[67]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..