Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation
Tóm tắt
Từ khóa
Tài liệu tham khảo
Al-Balool, 2011, Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant, Genome Res., 21, 1788, 10.1101/gr.116442.110
Ashburner, 2000, Gene ontology: tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556
Ashwal-Fluss, 2014, circRNA Biogenesis Competes with Pre-mRNA Splicing, Mol. Cell, 56, 55, 10.1016/j.molcel.2014.08.019
Berezikov, 2011, Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence, Genome Res., 21, 203, 10.1101/gr.116657.110
Brown, 2014, Diversity and dynamics of the Drosophila transcriptome, Nature, 512, 393, 10.1038/nature12962
Calarco, 2009, Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein, Cell, 138, 898, 10.1016/j.cell.2009.06.012
Capel, 1993, Circular transcripts of the testis-determining gene Sry in adult mouse testis, Cell, 73, 1019, 10.1016/0092-8674(93)90279-Y
Chintapalli, 2007, Using FlyAtlas to identify better Drosophila melanogaster models of human disease, Nat. Genet., 39, 715, 10.1038/ng2049
Cocquerelle, 1993, Mis-splicing yields circular RNA molecules, FASEB journal, 7, 155, 10.1096/fasebj.7.1.7678559
Danan, 2012, Transcriptome-wide discovery of circular RNAs in Archaea, Nucleic Acids Res., 40, 3131, 10.1093/nar/gkr1009
Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635
Grabowski, 1981, The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena, Cell, 23, 467, 10.1016/0092-8674(81)90142-2
Graveley, 2011, The developmental transcriptome of Drosophila melanogaster, Nature, 471, 473, 10.1038/nature09715
Grimson, 2007, MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, 27, 91, 10.1016/j.molcel.2007.06.017
Gu, 2009, Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs, Nat. Struct. Mol. Biol., 16, 144, 10.1038/nsmb.1552
Guo, 2014, Expanded identification and characterization of mammalian circular RNAs, Genome Biol., 15, 409, 10.1186/s13059-014-0409-z
Hansen, 2013, Natural RNA circles function as efficient microRNA sponges, Nature, 495, 384, 10.1038/nature11993
Hilgers, 2011, Neural-specific elongation of 3′ UTRs during Drosophila development, Proc. Natl. Acad. Sci. USA, 108, 15864, 10.1073/pnas.1112672108
Houseley, 2006, Noncanonical RNAs from transcripts of the Drosophila muscleblind gene, J. Hered., 97, 253, 10.1093/jhered/esj037
Jeck, 2013, Circular RNAs are abundant, conserved, and associated with ALU repeats, RNA, 19, 141, 10.1261/rna.035667.112
Lim, 2001, A computational analysis of sequence features involved in recognition of short introns, Proc. Natl. Acad. Sci. USA, 98, 11193, 10.1073/pnas.201407298
McManus, 2010, Global analysis of trans-splicing in Drosophila, Proc. Natl. Acad. Sci. USA, 107, 12975, 10.1073/pnas.1007586107
Memczak, 2013, Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, 495, 333, 10.1038/nature11928
Miura, 2013, Widespread and extensive lengthening of 3′ UTRs in the mammalian brain, Genome Res., 23, 812, 10.1101/gr.146886.112
Okamura, 2008, The regulatory activity of microRNA∗ species has substantial influence on microRNA and 3′ UTR evolution, Nat. Struct. Mol. Biol., 15, 354, 10.1038/nsmb.1409
Roy, 2010, Identification of functional elements and regulatory circuits by Drosophila modENCODE, Science, 330, 1787, 10.1126/science.1198374
Ruby, 2007, Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs, Genome Res., 17, 1850, 10.1101/gr.6597907
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
Sanger, 1976, Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures, Proc. Natl. Acad. Sci. USA, 73, 3852, 10.1073/pnas.73.11.3852
Schnall-Levin, 2010, Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3’UTRs, Proc. Natl. Acad. Sci. USA, 107, 15751, 10.1073/pnas.1006172107
Smibert, 2012, Global patterns of tissue-specific alternative polyadenylation in Drosophila, Cell Reports, 1, 277, 10.1016/j.celrep.2012.01.001
Wen, 2014, Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines, Genome Res., 24, 1236, 10.1101/gr.161554.113