Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

Molecular Cell - Tập 58 - Trang 870-885 - 2015
Agnieszka Rybak-Wolf1, Christin Stottmeister1, Petar Glažar1, Marvin Jens1, Natalia Pino2, Sebastian Giusti2, Mor Hanan3, Mikaela Behm4, Osnat Bartok3, Reut Ashwal-Fluss3, Margareta Herzog1, Luisa Schreyer1, Panagiotis Papavasileiou1, Andranik Ivanov1, Marie Öhman4, Damian Refojo2,5, Sebastian Kadener3, Nikolaus Rajewsky1
1Systems Biology of Gene Regulatory Elements, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
2Molecular Neurobiology, Max Planck Institute of Psychiatry, 80804 Munich, Germany
3The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
4Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
5Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET – Partner Institute of the Max Planck Society, C1425FQD Buenos Aires, Argentina

Tài liệu tham khảo

Ashwal-Fluss, 2014, circRNA biogenesis competes with pre-mRNA splicing, Mol. Cell, 56, 55, 10.1016/j.molcel.2014.08.019 Bernstein, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Bramham, 2007, Dendritic mRNA: transport, translation and function, Nat. Rev. Neurosci., 8, 776, 10.1038/nrn2150 Burnette, 2005, Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements, Genetics, 170, 661, 10.1534/genetics.104.039701 Capel, 1993, Circular transcripts of the testis-determining gene Sry in adult mouse testis, Cell, 73, 1019, 10.1016/0092-8674(93)90279-Y Conn, 2015, The RNA binding protein Quaking regulates formation of circRNAs, Cell, 160, 1125, 10.1016/j.cell.2015.02.014 Cunningham, 2015, Ensembl 2015, Nucleic Acids Res., 43, D662, 10.1093/nar/gku1010 Daniel, 2014, Alu elements shape the primate transcriptome by cis-regulation of RNA editing, Genome Biol., 15, R28, 10.1186/gb-2014-15-2-r28 Dubin, 1995, Inverted repeats are necessary for circularization of the mouse testis Sry transcript, Gene, 167, 245, 10.1016/0378-1119(95)00639-7 Glažar, 2014, circBase: a database for circular RNAs, RNA, 20, 1666, 10.1261/rna.043687.113 Gray, 1960, The isolation of synaptic vesicles from the central nervous system, J. Physiol., 153, 35 Hansen, 2011, miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA, EMBO J., 30, 4414, 10.1038/emboj.2011.359 Hansen, 2013, Natural RNA circles function as efficient microRNA sponges, Nature, 495, 384, 10.1038/nature11993 Herculano-Houzel, 2009, The human brain in numbers: a linearly scaled-up primate brain, Front. Hum. Neurosci., 3, 31, 10.3389/neuro.09.031.2009 Hinrichs, 2006, The UCSC Genome Browser Database: update 2006, Nucleic Acids Res., 34, D590, 10.1093/nar/gkj144 Huttner, 1983, Synapsin I (protein I), a nerve terminal-specific phosphoprotein. III. Its association with synaptic vesicles studied in a highly purified synaptic vesicle preparation, J. Cell Biol., 96, 1374, 10.1083/jcb.96.5.1374 Ivanov, 2015, Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals, Cell Rep., 10, 170, 10.1016/j.celrep.2014.12.019 Jeck, 2014, Detecting and characterizing circular RNAs, Nat. Biotechnol., 32, 453, 10.1038/nbt.2890 Jeck, 2013, Circular RNAs are abundant, conserved, and associated with ALU repeats, RNA, 19, 141, 10.1261/rna.035667.112 Krek, 2005, Combinatorial microRNA target predictions, Nat. Genet., 37, 495, 10.1038/ng1536 Lasda, 2014, Circular RNAs: diversity of form and function, RNA, 20, 1829, 10.1261/rna.047126.114 Liang, 2014, Short intronic repeat sequences facilitate circular RNA production, Genes Dev., 28, 2233, 10.1101/gad.251926.114 Lukiw, 2013, Circular RNA (circRNA) in Alzheimer’s disease (AD), Front. Genet., 4, 307, 10.3389/fgene.2013.00307 McBurney, 1993, P19 embryonal carcinoma cells, Int. J. Dev. Biol., 37, 135 Memczak, 2013, Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, 495, 333, 10.1038/nature11928 Monzo, 2012, A method for generating high-yield enriched neuronal cultures from P19 embryonal carcinoma cells, J. Neurosci. Methods, 204, 87, 10.1016/j.jneumeth.2011.11.008 Ng, 2013, The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis, Mol. Cell, 51, 349, 10.1016/j.molcel.2013.07.017 Osenberg, 2010, Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing, PLoS ONE, 5, e11173, 10.1371/journal.pone.0011173 Pollard, 2010, Detection of nonneutral substitution rates on mammalian phylogenies, Genome Res., 20, 110, 10.1101/gr.097857.109 Rieder, 2015, Dynamic response of RNA editing to temperature in Drosophila, BMC Biol., 13, 1, 10.1186/s12915-014-0111-3 Ross, 1983, Coordinate morphological and biochemical interconversion of human neuroblastoma cells, J. Natl. Cancer Inst., 71, 741 Salzman, 2012, Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types, PLoS ONE, 7, e30733, 10.1371/journal.pone.0030733 Salzman, 2013, Cell-type specific features of circular RNA expression, PLoS Genet., 9, e1003777, 10.1371/journal.pgen.1003777 Savva, 2012, Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in Drosophila, Nat. Commun., 3, 790, 10.1038/ncomms1789 Shtrichman, 2012, Altered A-to-I RNA editing in human embryogenesis, PLoS ONE, 7, e41576, 10.1371/journal.pone.0041576 Starke, 2015, Exon circularization requires canonical splice signals, Cell Rep., 10, 103, 10.1016/j.celrep.2014.12.002 Wahlstedt, 2009, Large-scale mRNA sequencing determines global regulation of RNA editing during brain development, Genome Res., 19, 978, 10.1101/gr.089409.108 Westholm, 2014, Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation, Cell Rep., 9, 1966, 10.1016/j.celrep.2014.10.062 Zhang, 2014, Complementary sequence-mediated exon circularization, Cell, 159, 134, 10.1016/j.cell.2014.09.001