PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

Bruno, 2011, Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay, Mol. Cell, 42, 500, 10.1016/j.molcel.2011.04.018 Chi, 2009, Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps, Nature, 460, 479, 10.1038/nature08170 Darnell, 2013, RNA protein interaction in neurons, Annu. Rev. Neurosci., 36, 243, 10.1146/annurev-neuro-062912-114322 Derti, 2012, A quantitative atlas of polyadenylation in five mammals, Genome Res., 22, 1173, 10.1101/gr.132563.111 Di Giammartino, 2011, Mechanisms and consequences of alternative polyadenylation, Mol. Cell, 43, 853, 10.1016/j.molcel.2011.08.017 Elkon, 2013, Alternative cleavage and polyadenylation: extent, regulation and function, Nat. Rev. Genet., 14, 496, 10.1038/nrg3482 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Grimson, 2007, MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, 27, 91, 10.1016/j.molcel.2007.06.017 Hilgers, 2011, Neural-specific elongation of 3′ UTRs during Drosophila development, Proc. Natl. Acad. Sci. USA, 108, 15864, 10.1073/pnas.1112672108 Hoque, 2013, Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing, Nat. Methods, 10, 133, 10.1038/nmeth.2288 Jaffe, 2015, Developmental regulation of human cortex transcription and its clinical relevance at single base resolution, Nat. Neurosci., 18, 154, 10.1038/nn.3898 Jenal, 2012, The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites, Cell, 149, 538, 10.1016/j.cell.2012.03.022 Ji, 2009, Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development, Proc. Natl. Acad. Sci. USA, 106, 7028, 10.1073/pnas.0900028106 Kahvejian, 2001, The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation, Cold Spring Harb. Symp. Quant. Biol., 66, 293, 10.1101/sqb.2001.66.293 Lianoglou, 2013, Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression, Genes Dev., 27, 2380, 10.1101/gad.229328.113 Licatalosi, 2010, RNA processing and its regulation: global insights into biological networks, Nat. Rev. Genet., 11, 75, 10.1038/nrg2673 Licatalosi, 2008, HITS-CLIP yields genome-wide insights into brain alternative RNA processing, Nature, 456, 464, 10.1038/nature07488 Martin, 2012, Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor I in the regulation of 3′ UTR length, Cell Rep., 1, 753, 10.1016/j.celrep.2012.05.003 Masamha, 2014, CFIm25 links alternative polyadenylation to glioblastoma tumour suppression, Nature, 510, 412, 10.1038/nature13261 Meza-Sosa, 2014, microRNAs: key triggers of neuronal cell fate, Front. Cell. Neurosci., 8, 175, 10.3389/fncel.2014.00175 Miura, 2013, Widespread and extensive lengthening of 3′ UTRs in the mammalian brain, Genome Res., 23, 812, 10.1101/gr.146886.112 Miura, 2014, Alternative polyadenylation in the nervous system: to what lengths will 3′ UTR extensions take us?, BioEssays, 36, 766, 10.1002/bies.201300174 Moore, 2014, Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis, Nat. Protoc., 9, 263, 10.1038/nprot.2014.012 Nam, 2002, Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription, Proc. Natl. Acad. Sci. USA, 99, 6152, 10.1073/pnas.092140899 Nam, 2014, Global analyses of the effect of different cellular contexts on microRNA targeting, Mol. Cell, 53, 1031, 10.1016/j.molcel.2014.02.013 Nunes, 2010, A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence, EMBO J., 29, 1523, 10.1038/emboj.2010.42 Okaty, 2011, A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain, PLoS ONE, 6, e16493, 10.1371/journal.pone.0016493 Ozsolak, 2010, Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation, Cell, 143, 1018, 10.1016/j.cell.2010.11.020 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Schultz, 2005, Modification of human hearing loss by plasma-membrane calcium pump PMCA2, N. Engl. J. Med., 352, 1557, 10.1056/NEJMoa043899 Shepard, 2011, Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq, RNA, 17, 761, 10.1261/rna.2581711 Shi, 2012, Alternative polyadenylation: new insights from global analyses, RNA, 18, 2105, 10.1261/rna.035899.112 Shi, 2009, Molecular architecture of the human pre-mRNA 3′ processing complex, Mol. Cell, 33, 365, 10.1016/j.molcel.2008.12.028 Smibert, 2012, Global patterns of tissue-specific alternative polyadenylation in Drosophila, Cell Rep., 1, 277, 10.1016/j.celrep.2012.01.001 Smrt, 2010, MicroRNA miR-137 regulates neuronal maturation by targeting ubiquitin ligase mind bomb-1, Stem Cells, 28, 1060, 10.1002/stem.431 Strehler, 2001, Role of alternative splicing in generating isoform diversity among plasma membrane calcium pumps, Physiol. Rev., 81, 21, 10.1152/physrev.2001.81.1.21 Takagaki, 1997, RNA recognition by the human polyadenylation factor CstF, Mol. Cell. Biol., 17, 3907, 10.1128/MCB.17.7.3907 Tan, 2013, MicroRNA-128 governs neuronal excitability and motor behavior in mice, Science, 342, 1254, 10.1126/science.1244193 Tian, 2013, Alternative cleavage and polyadenylation: the long and short of it, Trends Biochem. Sci., 38, 312, 10.1016/j.tibs.2013.03.005 Ulitsky, 2012, Extensive alternative polyadenylation during zebrafish development, Genome Res., 22, 2054, 10.1101/gr.139733.112 Utomo, 1999, Temporal, spatial, and cell type-specific control of Cre-mediated DNA recombination in transgenic mice, Nat. Biotechnol., 17, 1091, 10.1038/15073 Venkataraman, 2005, Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition, Genes Dev., 19, 1315, 10.1101/gad.1298605 Wang, 2013, Genome-wide maps of polyadenylation reveal dynamic mRNA 3′-end formation in mammalian cell lineages, RNA, 19, 413, 10.1261/rna.035360.112 Weyn-Vanhentenryck, 2014, HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism, Cell Rep., 6, 1139, 10.1016/j.celrep.2014.02.005 Yao, 2012, Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation, Proc. Natl. Acad. Sci. USA, 109, 18773, 10.1073/pnas.1211101109 Yao, 2013, Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3′ processing, RNA, 19, 1781, 10.1261/rna.042317.113 Zhang, 2014, An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex, J. Neurosci., 34, 11929, 10.1523/JNEUROSCI.1860-14.2014