The Antisense Transcriptome and the Human Brain (original) (raw)

References

• Abou-Sleiman PM, Muqit MM, Wood NW (2006) Expanding insights of mitochondrial dysfunction in Parkinson’s disease. Nat Rev Neurosci 7:207–219
  Article CAS PubMed Google Scholar
• Aid T, Kazantseva A, Piirsoo M, Palm K, Timmusk T (2007) Mouse and rat BDNF gene structure and expression revisited. J Neurosci Res 85:525–535
  Article PubMed Central CAS PubMed Google Scholar
• Ali IU, Schriml LM, Dean M (1999) Mutational spectra of PTEN/MMAC1 gene: a tumor suppressor with lipid phosphatase activity. J Natl Cancer Inst 91:1922–1932
  Article CAS PubMed Google Scholar
• Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106
  Article PubMed Central CAS PubMed Google Scholar
• Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169
  Article PubMed Central PubMed Google Scholar
• Andrew SE, Goldberg YP, Kremer B, Telenius H, Theilmann J, Adam S, Starr E, Squitieri F, Lin B, Kalchman MA et al (1993) The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington’s disease. Nat Genet 4:398–403
  Article CAS PubMed Google Scholar
• Barton AJ, Pearson RC, Najlerahim A, Harrison PJ (1993) Pre- and postmortem influences on brain RNA. J Neurochem 61:1–11
  Article CAS PubMed Google Scholar
• Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, Bonilla F, de Herreros AG (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22:756–769
  Article PubMed Central CAS PubMed Google Scholar
• Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 22:615–626
  Article PubMed Central CAS PubMed Google Scholar
• Binder DK, Scharfman HE (2004) Brain-derived neurotrophic factor. Growth Factors 22:123–131
  Article PubMed Central CAS PubMed Google Scholar
• Blencowe BJ (2006) Alternative splicing: new insights from global analyses. Cell 126:37–47
  Article CAS PubMed Google Scholar
• Borodina T, Adjaye J, Sultan M (2011) A strand-specific library preparation protocol for RNA sequencing. Methods Enzymol 500:79–98
  Article CAS PubMed Google Scholar
• Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622
  Article CAS PubMed Google Scholar
• Butterfield DA (2002) Amyloid beta-peptide (1-42)-induced oxidative stress and neurotoxicity: implications for neurodegeneration in Alzheimer’s disease brain. A review. Free Radic Res 36:1307–1313
  Article CAS PubMed Google Scholar
• Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23:1534–1545
  Article PubMed Central CAS PubMed Google Scholar
• Chen J, Sun M, Kent WJ, Huang X, Xie H, Wang W, Zhou G, Shi RZ, Rowley JD (2004) Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32:4812–4820
  Article PubMed Central CAS PubMed Google Scholar
• Chen WL, Lin JW, Huang HJ, Wang SM, Su MT, Lee-Chen GJ, Chen CM, Hsieh-Li HM (2008) SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology. Brain Res 1233:176–184
  Article CAS PubMed Google Scholar
• Chung DW, Rudnicki DD, Yu L, Margolis RL (2011) A natural antisense transcript at the Huntington’s disease repeat locus regulates HTT expression. Hum Mol Genet 20:3467–3477
  Article PubMed Central CAS PubMed Google Scholar
• Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ (2015) The RNA binding protein quaking regulates formation of circRNAs. Cell 160:1125–1134
  Article CAS PubMed Google Scholar
• Cookson MR (2005) The biochemistry of Parkinson’s disease. Annu Rev Biochem 74:29–52
  Article CAS PubMed Google Scholar
• Courtney E, Kornfeld S, Janitz K, Janitz M (2010) Transcriptome profiling in neurodegenerative disease. J Neurosci Methods 193:189–202
  Article CAS PubMed Google Scholar
• Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, He M, Assefa S, Bahler J, Kingsley RA, Parkhill J, Bentley SD, Dougan G, Thomson NR (2009) A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res 37:e148
  Article PubMed Central PubMed CAS Google Scholar
• Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR (2015) A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci U S A 112:7285–7290
  Article PubMed Central CAS PubMed Google Scholar
• Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR (2012) Landscape of transcription in human cells. Nature 489:101–108
  Article PubMed Central CAS PubMed Google Scholar
• Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR (2008) Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet 40:977–986
  Article PubMed Central CAS PubMed Google Scholar
• Eng C (2003) PTEN: one gene, many syndromes. Hum Mutat 22:183–198
  Article CAS PubMed Google Scholar
• Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L (2006) Complex loci in human and mouse genomes. PLoS Genet 2:e47
  Article PubMed Central PubMed CAS Google Scholar
• Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14:723–730
  Article PubMed Central CAS PubMed Google Scholar
• Faghihi MA, Zhang M, Huang J, Modarresi F, Van der Brug MP, Nalls MA, Cookson MR, St-Laurent G 3rd, Wahlestedt C (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11:R56
  Article PubMed Central PubMed CAS Google Scholar
• Fukumoto H, Cheung BS, Hyman BT, Irizarry MC (2002) Beta-secretase protein and activity are increased in the neocortex in Alzheimer disease. Arch Neurol 59:1381–1389
  Article PubMed Google Scholar
• Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86
  Article PubMed Central PubMed Google Scholar
• Goffin A, Hoefsloot LH, Bosgoed E, Swillen A, Fryns JP (2001) PTEN mutation in a family with Cowden syndrome and autism. Am J Med Genet 105:521–524
  Article CAS PubMed Google Scholar
• Griffin RJ, Moloney A, Kelliher M, Johnston JA, Ravid R, Dockery P, O’Connor R, O’Neill C (2005) Activation of Akt/PKB, increased phosphorylation of Akt substrates and loss and altered distribution of Akt and PTEN are features of Alzheimer’s disease pathology. J Neurochem 93:105–117
  Article CAS PubMed Google Scholar
• Grimm JW, Lu L, Hayashi T, Hope BT, Su TP, Shaham Y (2003) Time-dependent increases in brain-derived neurotrophic factor protein levels within the mesolimbic dopamine system after withdrawal from cocaine: implications for incubation of cocaine craving. J Neurosci 23:742–747
  CAS PubMed Google Scholar
• Gubler U (1987a) Second-strand cDNA synthesis: classical method. Methods Enzymol 152:325–329
  Article CAS PubMed Google Scholar
• Gubler U (1987b) Second-strand cDNA synthesis: mRNA fragments as primers. Methods Enzymol 152:330–335
  Article CAS PubMed Google Scholar
• Guo JU, Agarwal V, Guo H, Bartel DP (2014) Expanded identification and characterization of mammalian circular RNAs. Genome Biol 15:409
  Article PubMed Central PubMed CAS Google Scholar
• Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076
  Article PubMed Central CAS PubMed Google Scholar
• Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P (2006) The complexity of the mammalian transcriptome. J Physiol 575:321–332
  Article PubMed Central CAS PubMed Google Scholar
• Hagerman RJ, Leehey M, Heinrichs W, Tassone F, Wilson R, Hills J, Grigsby J, Gage B, Hagerman PJ (2001) Intention tremor, parkinsonism, and generalized brain atrophy in male carriers of fragile X. Neurology 57:127–130
  Article CAS PubMed Google Scholar
• Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384–388
  Article CAS PubMed Google Scholar
• He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The antisense transcriptomes of human cells. Science 322:1855–1857
  Article PubMed Central CAS PubMed Google Scholar
• Ho EC, Donaldson ME, Saville BJ (2010) Detection of antisense RNA transcripts by strand-specific RT-PCR. Methods Mol Biol 630:125–138
  Article CAS PubMed Google Scholar
• Holsinger RM, Schnarr J, Henry P, Castelo VT, Fahnestock M (2000) Quantitation of BDNF mRNA in human parietal cortex by competitive reverse transcription-polymerase chain reaction: decreased levels in Alzheimer’s disease. Brain Res Mol Brain Res 76:347–354
  Article CAS PubMed Google Scholar
• Holsinger RM, McLean CA, Collins SJ, Masters CL, Evin G (2004) Increased beta-Secretase activity in cerebrospinal fluid of Alzheimer’s disease subjects. Ann Neurol 55:898–899
  Article PubMed Google Scholar
• Howells DW, Porritt MJ, Wong JY, Batchelor PE, Kalnins R, Hughes AJ, Donnan GA (2000) Reduced BDNF mRNA expression in the Parkinson’s disease substantia nigra. Exp Neurol 166:127–135
  Article CAS PubMed Google Scholar
• Hu X, Hicks CW, He W, Wong P, Macklin WB, Trapp BD, Yan R (2006a) Bace1 modulates myelination in the central and peripheral nervous system. Nat Neurosci 9:1520–1525
  Article CAS PubMed Google Scholar
• Hu Z, Zhang A, Storz G, Gottesman S, Leppla SH (2006b) An antibody-based microarray assay for small RNA detection. Nucleic Acids Res 34, e52
  Article PubMed Central PubMed CAS Google Scholar
• Huber M, Wei TF, Muller UR, Lefebvre PA, Marla SS, Bao YP (2004) Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA. Nucleic Acids Res 32:e137
  Article PubMed Central PubMed CAS Google Scholar
• illumina, Inc. (2011, 14 April 2011). “Getting Started with RNA-Seq Data Analysis.” Retrieved 14 May, 2015, from http://www.illumina.com/documents/products/datasheets/datasheet_rnaseq_analysis.pdf
• Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32:453–461
  Article PubMed Central CAS PubMed Google Scholar
• Johnson JM, Edwards S, Shoemaker D, Schadt EE (2005) Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 21:93–102
  Article CAS PubMed Google Scholar
• Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Grander D, Morris KV (2013) A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 20:440–446
  Article PubMed Central CAS PubMed Google Scholar
• Kawakami E, Watanabe T, Fujii K, Goto H, Watanabe S, Noda T, Kawaoka Y (2011) Strand-specific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA. J Virol Methods 173:1–6
  Article PubMed Central CAS PubMed Google Scholar
• Kishino T, Lalande M, Wagstaff J (1997) UBE3A/E6-AP mutations cause Angelman syndrome. Nat Genet 15:70–73
  Article CAS PubMed Google Scholar
• Klein D (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8:257–260
  Article CAS PubMed Google Scholar
• Kokaia Z, Metsis M, Kokaia M, Bengzon J, Elmer E, Smith ML, Timmusk T, Siesjo BK, Persson H, Lindvall O (1994) Brain insults in rats induce increased expression of the BDNF gene through differential use of multiple promoters. Eur J Neurosci 6:587–596
  Article CAS PubMed Google Scholar
• Koob MD, Moseley ML, Schut LJ, Benzow KA, Bird TD, Day JW, Ranum LP (1999) An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat Genet 21:379–384
  Article CAS PubMed Google Scholar
• Kumari D, Biacsi RE, Usdin K (2011) Repeat expansion affects both transcription initiation and elongation in Friedreich ataxia cells. J Biol Chem 286:4209–4215
  Article PubMed Central CAS PubMed Google Scholar
• Laird FM, Cai H, Savonenko AV, Farah MH, He K, Melnikova T, Wen H, Chiang HC, Xu G, Koliatsos VE, Borchelt DR, Price DL, Lee HK, Wong PC (2005) BACE1, a major determinant of selective vulnerability of the brain to amyloid-beta amyloidogenesis, is essential for cognitive, emotional, and synaptic functions. J Neurosci 25:11693–11709
  Article PubMed Central CAS PubMed Google Scholar
• Landers M, Bancescu DL, Le Meur E, Rougeulle C, Glatt-Deeley H, Brannan C, Muscatelli F, Lalande M (2004) Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res 32:3480–3492
  Article PubMed Central CAS PubMed Google Scholar
• Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21:400–404
  Article CAS PubMed Google Scholar
• Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7:709–715
  Article PubMed Central CAS PubMed Google Scholar
• Li R, Lindholm K, Yang LB, Yue X, Citron M, Yan R, Beach T, Sue L, Sabbagh M, Cai H, Wong P, Price D, Shen Y (2004) Amyloid beta peptide load is correlated with increased beta-secretase activity in sporadic Alzheimer’s disease patients. Proc Natl Acad Sci U S A 101:3632–3637
  Article PubMed Central CAS PubMed Google Scholar
• Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930
  Article CAS PubMed Google Scholar
• Lipovich L, Tarca AL, Cai J, Jia H, Chugani HT, Sterner KN, Grossman LI, Uddin M, Hof PR, Sherwood CC, Kuzawa CW, Goodman M, Wildman DE (2014) Developmental changes in the transcriptome of human cerebral cortex tissue: long noncoding RNA transcripts. Cereb Cortex 24:1451–1459
  Article PubMed Google Scholar
• Liu QR, Walther D, Drgon T, Polesskaya O, Lesnick TG, Strain KJ, de Andrade M, Bower JH, Maraganore DM, Uhl GR (2005) Human brain derived neurotrophic factor (BDNF) genes, splicing patterns, and assessments of associations with substance abuse and Parkinson’s disease. Am J Med Genet B Neuropsychiatr Genet 134B:93–103
  Article PubMed Google Scholar
• Liu QR, Lu L, Zhu XG, Gong JP, Shaham Y, Uhl GR (2006) Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. Brain Res 1067:1–12
  Article CAS PubMed Google Scholar
• Loring JF, Wen X, Lee JM, Seilhamer J, Somogyi R (2001) A gene expression profile of Alzheimer’s disease. DNA Cell Biol 20:683–695
  Article CAS PubMed Google Scholar
• Lu B (2003) BDNF and activity-dependent synaptic modulation. Learn Mem 10:86–98
  Article PubMed Google Scholar
• Lukiw WJ (2013) Circular RNA (circRNA) in Alzheimer’s disease (AD). Front Genet 4:307
  PubMed Central PubMed Google Scholar
• Ma H, Lesne S, Kotilinek L, Steidl-Nichols JV, Sherman M, Younkin L, Younkin S, Forster C, Sergeant N, Delacourte A, Vassar R, Citron M, Kofuji P, Boland LM, Ashe KH (2007) Involvement of beta-site APP cleaving enzyme 1 (BACE1) in amyloid precursor protein-mediated enhancement of memory and activity-dependent synaptic plasticity. Proc Natl Acad Sci U S A 104:8167–8172
  Article PubMed Central CAS PubMed Google Scholar
• Majounie E, Renton AE, Mok K, Dopper EG, Waite A, Rollinson S, Chio A, Restagno G, Nicolaou N, Simon-Sanchez J, van Swieten JC, Abramzon Y, Johnson JO, Sendtner M, Pamphlett R, Orrell RW, Mead S, Sidle KC, Houlden H, Rohrer JD, Morrison KE, Pall H, Talbot K, Ansorge O, Chromosome ALSFTDC, FFA F r n o, Consortium I, Hernandez DG, Arepalli S, Sabatelli M, Mora G, Corbo M, Giannini F, Calvo A, Englund E, Borghero G, Floris GL, Remes AM, Laaksovirta H, McCluskey L, Trojanowski JQ, Van Deerlin VM, Schellenberg GD, Nalls MA, Drory VE, Lu CS, Yeh TH, Ishiura H, Takahashi Y, Tsuji S, Le Ber I, Brice A, Drepper C, Williams N, Kirby J, Shaw P, Hardy J, Tienari PJ, Heutink P, Morris HR, Pickering-Brown S, Traynor BJ (2012) Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study. Lancet Neurol 11:323–330
  Article PubMed Central CAS PubMed Google Scholar
• Malzac P, Webber H, Moncla A, Graham JM, Kukolich M, Williams C, Pagon RA, Ramsdell LA, Kishino T, Wagstaff J (1998) Mutation analysis of UBE3A in Angelman syndrome patients. Am J Hum Genet 62:1353–1360
  Article PubMed Central CAS PubMed Google Scholar
• Mamanova L, Turner DJ (2011) Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq). Nat Protoc 6:1736–1747
  Article CAS PubMed Google Scholar
• Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, Ost TW, Collins JE, Turner DJ (2010) FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods 7:130–132
  Article PubMed Central CAS PubMed Google Scholar
• Matsuura T, Sutcliffe JS, Fang P, Galjaard RJ, Jiang YH, Benton CS, Rommens JM, Beaudet AL (1997) De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome. Nat Genet 15:74–77
  Article CAS PubMed Google Scholar
• Mattick JS (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2:986–991
  Article PubMed Central CAS PubMed Google Scholar
• Mattick JS, Makunin IV (2005) Small regulatory RNAs in mammals. Hum Mol Genet 14 Spec No 1:R121–R132
  Article PubMed CAS Google Scholar
• Mehler MF, Mattick JS (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 87:799–823
  Article CAS PubMed Google Scholar
• Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338
  Article CAS PubMed Google Scholar
• Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155–159
  Article CAS PubMed Google Scholar
• Metsis M, Timmusk T, Arenas E, Persson H (1993) Differential usage of multiple brain-derived neurotrophic factor promoters in the rat brain following neuronal activation. Proc Natl Acad Sci U S A 90:8802–8806
  Article PubMed Central CAS PubMed Google Scholar
• Mills JD, Kavanagh T, Kim WS, Chen BJ, Kawahara Y, Halliday GM, Janitz M (2013a) Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe. PLoS One 8:e78480
  Article PubMed Central CAS PubMed Google Scholar
• Mills JD, Kawahara Y, Janitz M (2013b) Strand-specific RNA-Seq provides greater resolution of transcriptome profiling. Curr Genomics 14:173–181
  Article PubMed Central CAS PubMed Google Scholar
• Mills JD, Nalpathamkalam T, Jacobs HI, Janitz C, Merico D, Hu P, Janitz M (2013c) RNA-Seq analysis of the parietal cortex in Alzheimer’s disease reveals alternatively spliced isoforms related to lipid metabolism. Neurosci Lett 536:90–95
• Mills JD, Kim WS, Halliday GM, Janitz M (2014) Transcriptome analysis of grey and white matter cortical tissue in multiple system atrophy. Neurogenetics 16(2):107–122
  Article PubMed CAS Google Scholar
• Mills JD, Chen J, Kim WS, Waters PD, Prabowo AS, Aronica E, Halliday GM, Janitz M (2015a) Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter. Neurogenetics 6(3):201–213
  Article CAS Google Scholar
• Mills JD, Kavanagh T, Kim WS, Chen B, Waters PD, Halliday GM, Janitz M (2015b) High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation. Mol Brain 8:2
  Article PubMed Central PubMed CAS Google Scholar
• Mirnics K, Middleton FA, Lewis DA, Levitt P (2001) Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse. Trends Neurosci 24:479–486
  Article CAS PubMed Google Scholar
• Moazed D (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457:413–420
  Article PubMed Central CAS PubMed Google Scholar
• Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, van der Brug MP, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30:453–459
  Article PubMed Central CAS PubMed Google Scholar
• Montgomery MK, Xu S, Fire A (1998) RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci U S A 95:15502–15507
  Article PubMed Central CAS PubMed Google Scholar
• Napoli E, Ross-Inta C, Wong S, Hung C, Fujisawa Y, Sakaguchi D, Angelastro J, Omanska-Klusek A, Schoenfeld R, Giulivi C (2012) Mitochondrial dysfunction in Pten haplo-insufficient mice with social deficits and repetitive behavior: interplay between Pten and p53. PLoS One 7:e42504
  Article PubMed Central CAS PubMed Google Scholar
• Nelson DL, Orr HT, Warren ST (2013) The unstable repeats—three evolving faces of neurological disease. Neuron 77:825–843
  Article PubMed Central CAS PubMed Google Scholar
• Nemes JP, Benzow KA, Moseley ML, Ranum LP, Koob MD (2000) The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum Mol Genet 9:1543–1551
  Article CAS PubMed Google Scholar
• Numan S, Lane-Ladd SB, Zhang L, Lundgren KH, Russell DS, Seroogy KB, Nestler EJ (1998) Differential regulation of neurotrophin and trk receptor mRNAs in catecholaminergic nuclei during chronic opiate treatment and withdrawal. J Neurosci 18:10700–10708
  CAS PubMed Google Scholar
• Olsavsky KM, Page JL, Johnson MC, Zarbl H, Strom SC, Omiecinski CJ (2007) Gene expression profiling and differentiation assessment in primary human hepatocyte cultures, established hepatoma cell lines, and human liver tissues. Toxicol Appl Pharmacol 222:42–56
  Article PubMed Central CAS PubMed Google Scholar
• Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM (2010) Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143:1018–1029
  Article PubMed Central CAS PubMed Google Scholar
• Pan C, Kumar C, Bohl S, Klingmueller U, Mann M (2009) Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Mol Cell Proteomics 8:443–450
  Article PubMed Central CAS PubMed Google Scholar
• Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123
  Article PubMed Central PubMed CAS Google Scholar
• Pastori C, Peschansky VJ, Barbouth D, Mehta A, Silva JP, Wahlestedt C (2014) Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long noncoding RNAs differentially expressed in fragile X syndrome and fragile X-associated tremor/ataxia syndrome. Hum Genet 133:59–67
  Article PubMed Central CAS PubMed Google Scholar
• Pelechano V, Steinmetz LM (2013) Gene regulation by antisense transcription. Nat Rev Genet 14:880–893
  Article CAS PubMed Google Scholar
• Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, Zhu Y, Zhang W, Liang Y, Hu X, Tan X, Guo J, Dong Z, Liang Y, Bao L, Wang J (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253–260
  Article CAS PubMed Google Scholar
• Perocchi F, Xu Z, Clauder-Munster S, Steinmetz LM (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35:e128
  Article PubMed Central PubMed CAS Google Scholar
• Petit A, Kawarai T, Paitel E, Sanjo N, Maj M, Scheid M, Chen F, Gu Y, Hasegawa H, Salehi-Rad S, Wang L, Rogaeva E, Fraser P, Robinson B, St George-Hyslop P, Tandon A (2005) Wild-type PINK1 prevents basal and induced neuronal apoptosis, a protective effect abrogated by Parkinson disease-related mutations. J Biol Chem 280:34025–34032
  Article CAS PubMed Google Scholar
• Philippe N, Salson M, Commes T, Rivals E (2013) CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biol 14:R30
  Article PubMed Central PubMed CAS Google Scholar
• Plaskon NE, Adelman ZN, Myles KM (2009) Accurate strand-specific quantification of viral RNA. PLoS One 4:e7468
  Article PubMed Central PubMed CAS Google Scholar
• Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033–1038
  Article PubMed Central CAS PubMed Google Scholar
• Pontier DB, Gribnau J (2011) Xist regulation and function explored. Hum Genet 130:223–236
  Article PubMed Central PubMed Google Scholar
• Pruunsild P, Kazantseva A, Aid T, Palm K, Timmusk T (2007) Dissecting the human BDNF locus: bidirectional transcription, complex splicing, and multiple promoters. Genomics 90:397–406
  Article PubMed Central CAS PubMed Google Scholar
• Qureshi IA, Mehler MF (2012) Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 13:528–541
  Article PubMed Central CAS PubMed Google Scholar
• Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323
  Article PubMed Central CAS PubMed Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140
  Article PubMed Central CAS PubMed Google Scholar
• Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative Genomics Viewer. Nat Biotechnol 29:24–26
  Article PubMed Central CAS PubMed Google Scholar
• Rougeulle C, Lalande M (1998) Angelman syndrome: how many genes to remain silent? Neurogenetics 1:229–237
  Article CAS PubMed Google Scholar
• Rougeulle C, Cardoso C, Fontes M, Colleaux L, Lalande M (1998) An imprinted antisense RNA overlaps UBE3A and a second maternally expressed transcript. Nat Genet 19:15–16
  Article CAS PubMed Google Scholar
• Ruprecht RM, Goodman NC, Spiegelman S (1973) Conditions for the selective synthesis of DNA complementary to template RNA. Biochim Biophys Acta 294:192–203
  Article CAS Google Scholar
• Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7:e30733
  Article PubMed Central CAS PubMed Google Scholar
• Schaefer M, Pollex T, Hanna K, Lyko F (2009) RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res 37:e12
  Article PubMed Central PubMed CAS Google Scholar
• Scheele C, Petrovic N, Faghihi MA, Lassmann T, Fredriksson K, Rooyackers O, Wahlestedt C, Good L, Timmons JA (2007) The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genomics 8:74
  Article PubMed Central PubMed CAS Google Scholar
• Simons RW (1988) Naturally occurring antisense RNA control—a brief review. Gene 72:35–44
  Article CAS PubMed Google Scholar
• Spiegelman S, Burny A, Das MR, Keydar J, Schlom J, Travnicek M, Watson K (1970) DNA-directed DNA polymerase activity in oncogenic RNA viruses. Nature 227:1029–1031
  Article CAS PubMed Google Scholar
• Su WY, Li JT, Cui Y, Hong J, Du W, Wang YC, Lin YW, Xiong H, Wang JL, Kong X, Gao QY, Wei LP, Fang JY (2012) Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. Cell Res 22:1374–1389
  Article PubMed Central CAS PubMed Google Scholar
• Sultan M, Dokel S, Amstislavskiy V, Wuttig D, Sultmann H, Lehrach H, Yaspo ML (2012) A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods. Biochem Biophys Res Commun 422:643–646
  Article CAS PubMed Google Scholar
• Sun X, He G, Qing H, Zhou W, Dobie F, Cai F, Staufenbiel M, Huang LE, Song W (2006) Hypoxia facilitates Alzheimer’s disease pathogenesis by up-regulating BACE1 gene expression. Proc Natl Acad Sci U S A 103:18727–18732
  Article PubMed Central CAS PubMed Google Scholar
• Taft RJ, Hawkins PG, Mattick JS, Morris KV (2011) The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. Epigenetics Chromatin 4:13
  Article PubMed Central CAS PubMed Google Scholar
• Tapia-Arancibia L, Rage F, Givalois L, Dingeon P, Arancibia S, Beauge F (2001) Effects of alcohol on brain-derived neurotrophic factor mRNA expression in discrete regions of the rat hippocampus and hypothalamus. J Neurosci Res 63:200–208
  Article CAS PubMed Google Scholar
• Terryn N, Rouze P (2000) The sense of naturally transcribed antisense RNAs in plants. Trends Plant Sci 5:394–396
  Article CAS PubMed Google Scholar
• Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192
  Article PubMed Central CAS PubMed Google Scholar
• Tong Y, Zhou W, Fung V, Christensen MA, Qing H, Sun X, Song W (2005) Oxidative stress potentiates BACE1 gene expression and Abeta generation. J Neural Transm 112:455–469
  Article CAS PubMed Google Scholar
• Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
  Article PubMed Central CAS PubMed Google Scholar
• Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
  Article PubMed Central CAS PubMed Google Scholar
• Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet 34:157–165
  Article CAS PubMed Google Scholar
• Twine NA, Janitz K, Wilkins MR, Janitz M (2011) Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease. PLoS One 6:e16266
  Article PubMed Central CAS PubMed Google Scholar
• Valente EM, Abou-Sleiman PM, Caputo V, Muqit MM, Harvey K, Gispert S, Ali Z, Del Turco D, Bentivoglio AR, Healy DG, Albanese A, Nussbaum R, Gonzalez-Maldonado R, Deller T, Salvi S, Cortelli P, Gilks WP, Latchman DS, Harvey RJ, Dallapiccola B, Auburger G, Wood NW (2004) Hereditary early-onset Parkinson’s disease caused by mutations in PINK1. Science 304:1158–1160
  Article CAS PubMed Google Scholar
• Vashist S, Urena L, Goodfellow I (2012) Development of a strand specific real-time RT-qPCR assay for the detection and quantitation of murine norovirus RNA. J Virol Methods 184:69–76
  Article PubMed Central CAS PubMed Google Scholar
• Velmeshev D, Magistri M, Faghihi MA (2013) Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders. Mol Autism 4:32
  Article PubMed Central PubMed CAS Google Scholar
• Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, Horvath S, Mill J, Cantor RM, Blencowe BJ, Geschwind DH (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474:380–384
  Article PubMed Central CAS PubMed Google Scholar
• Vu TH, Hoffman AR (1997) Imprinting of the Angelman syndrome gene, UBE3A, is restricted to brain. Nat Genet 17:12–13
  Article CAS PubMed Google Scholar
• Wagner EG, Simons RW (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48:713–742
  Article CAS PubMed Google Scholar
• Wang WK, Sung TL, Tsai YC, Kao CL, Chang SM, King CC (2002) Detection of dengue virus replication in peripheral blood mononuclear cells from dengue virus type 2-infected patients by a reverse transcription-real-time PCR assay. J Clin Microbiol 40:4472–4478
  Article PubMed Central CAS PubMed Google Scholar
• Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
  Article PubMed Central CAS PubMed Google Scholar
• Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP (2011) A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PLoS One 6:e26426
  Article PubMed Central CAS PubMed Google Scholar
• Willem M, Garratt AN, Novak B, Citron M, Kaufmann S, Rittger A, DeStrooper B, Saftig P, Birchmeier C, Haass C (2006) Control of peripheral nerve myelination by the beta-secretase BACE1. Science 314:664–666
  Article CAS PubMed Google Scholar
• Williams CA, Lossie A, Driscoll D, Unit RCP (2001) Angelman syndrome: mimicking conditions and phenotypes. Am J Med Genet 101:59–64
  Article CAS PubMed Google Scholar
• Wood EJ, Chin-Inmanu K, Jia H, Lipovich L (2013) Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. Front Genet 4:183
  PubMed Central PubMed Google Scholar
• Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881
  Article PubMed Central CAS PubMed Google Scholar
• Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR (2014) Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 11:41–46
  Article PubMed Central CAS PubMed Google Scholar
• Wutz A, Barlow DP (1998) Imprinting of the mouse Igf2r gene depends on an intronic CpG island. Mol Cell Endocrinol 140:9–14
  Article CAS PubMed Google Scholar
• Xu C, Yang M, Tian J, Wang X, Li Z (2011) MALAT-1: a long non-coding RNA and its important 3’ end functional motif in colorectal cancer metastasis. Int J Oncol 39:169–175
  PubMed Google Scholar
• Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38:662–674
  Article PubMed Central CAS PubMed Google Scholar
• Yoon OK, Brem RB (2010) Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 16:1256–1267
  Article PubMed Central CAS PubMed Google Scholar
• You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C, Wang X, Hou J, Liu H, Sun W, Sambandan S, Chen T, Schuman EM, Chen W (2015) Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci 18:603–610
  Article PubMed Central CAS PubMed Google Scholar
• Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451:202–206
  Article PubMed Central CAS PubMed Google Scholar
• Yu WH, Hovik H, Olsen I, Chen T (2011) Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays. BMC Mol Biol 12:3
  Article PubMed Central CAS PubMed Google Scholar
• Yuki N, Matsumoto S, Tadokoro K, Mochizuki K, Kato M, Yamaguchi T (2006) Significance of liver negative-strand HCV RNA quantitation in chronic hepatitis C. J Hepatol 44:302–309
  Article CAS PubMed Google Scholar
• Zhang Z, Theurkauf WE, Weng Z, Zamore PD (2012) Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3:9
  Article PubMed Central PubMed CAS Google Scholar
• Zhao J, Fu Y, Yasvoina M, Shao P, Hitt B, O’Connor T, Logan S, Maus E, Citron M, Berry R, Binder L, Vassar R (2007) Beta-site amyloid precursor protein cleaving enzyme 1 levels become elevated in neurons around amyloid plaques: implications for Alzheimer’s disease pathogenesis. J Neurosci 27:3639–3649
  Article CAS PubMed Google Scholar
• Zu T, Liu Y, Banez-Coronel M, Reid T, Pletnikova O, Lewis J, Miller TM, Harms MB, Falchook AE, Subramony SH, Ostrow LW, Rothstein JD, Troncoso JC, Ranum LP (2013) RAN proteins and RNA foci from antisense transcripts in C9ORF72 ALS and frontotemporal dementia. Proc Natl Acad Sci U S A 110:E4968–E4977
  Article PubMed Central CAS PubMed Google Scholar

Download references