Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Costa, Valerio ^a   Angelini, Claudia ^b   D'Apice, Luciana ^c   Mutarelli, Margherita ^d   Casamassimi, Amelia ^e   Sommese, Linda ^e   Gallo, Maria Assunta ^f   Aprile, Marianna ^a   Esposito, Roberta ^a   Leone, Luigi ^a   Donizetti, Aldo ^a   Crispi, Stefania ^a   Rienzo, Monica ^e   Sarubbi, Berardo ^e   Calabrò, Raffaele ^e   Picardi, Marco ^g   Salvatore, Paola ^h   Infante, Teresa ⁱ   de Berardinis, Piergiuseppe ^c   Napoli, Claudio ^e,i   Ciccodicola, Alfredo ^a   more..

^a INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

^b CNR   (Italy)

^c INSTITUTE OF PROTEIN BIOCHEMISTRY   (Italy)

^d TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^e SECOND UNIVERSITY OF NAPLES   (Italy)

^f Centro Diagnostico San Ciro (CDS)   (Italy)

^g UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^h CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

ⁱ IRCCS SDN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RIBOSOME RNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSCRIPTOME; UNTRANSLATED RNA; RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CLINICAL FEATURE; CONTROLLED STUDY; DOWN SYNDROME; ENDOTHELIUM CELL; FEASIBILITY STUDY; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC LINKAGE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PATHOGENESIS; RNA ANALYSIS; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STEM CELL; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; TRISOMY 21; CHEMISTRY; CONFORMATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; INTRON;

ALTERNATIVE SPLICING; DOWN SYNDROME; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; INTRONS; NUCLEIC ACID CONFORMATION; RNA;

EID: 79955399112     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018493     Document Type: Article

References (81)

1. Okoniewski MJ, Miller CJ, (2006) Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7: 276.
2. Napoli C, Lerman LO, Sica V, Lerman A, Tajana G, et al. (2003) Microarray analysis: a novel research tool for cardiovascular scientists and physicians. Heart 89: 597-604.
3. Harbers M, Carninci P, (2005) Tag-based approaches for transcriptome research and genome annotation. Nat Methods 2: 495-502.
4. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW, (1995) Serial analysis of gene expression. Science 270: 484-487.
5. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634.
6. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776-15781.
7. Salvatore P, Casamassimi A, Sommese L, Fiorito C, Ciccodicola A, et al. (2008) Detrimental effects of Bartonella henselae are counteracted by L-arginine and nitric oxide in human endothelial progenitor cells. Proc Natl Acad Sci U S A 105: 9427-9432.
8. Napoli C, de Nigris F, Welch JS, Calara FB, Stuart RO, et al. (2002) Maternal hypercholesterolemia during pregnancy promotes early atherogenesis in LDL receptor-deficient mice and alters aortic gene expression determined by microarray. Circulation 105: 1360-1367.
9. El-Meanawy MA, Schelling JR, Pozuelo F, Churpek MM, Ficker EK, et al. (2000) Use of serial analysis of gene expression to generate kidney expression libraries. Am J Physiol Renal Physiol 279: F383-392.
10. Yamashita T, Hashimoto S, Kaneko S, Nagai S, Toyoda N, et al. (2000) Comprehensive gene expression profile of a normal human liver. Biochem Biophys Res Commun 269: 110-116.
11. Pauws E, Moreno JC, Tijssen M, Baas F, de Vijlder JJ, et al. (2000) Serial analysis of gene expression as a tool to assess the human thyroid expression profile and to identify novel thyroidal genes. J Clin Endocrinol Metab 85: 1923-1927.
12. Costa V, Sommese L, Casamassimi A, Colicchio R, Angelini C, et al. (2010) Impairment of circulating endothelial progenitors in Down syndrome. BMC Med Genomics 3: 40.
13. Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, et al. (2009) The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A 106: 12031-12036.
14. Sommer CA, Pavarino-Bertelli EC, Goloni-Bertollo EM, Henrique-Silva F, (2008) Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome 51: 19-29.
15. Malagó W Jr, Sommer CA, Del Cistia Andrade C, Soares-Costa A, Abrao Possik P, et al. (2005) Gene expression profile of human Down syndrome leukocytes. Croat Med J 46: 647-656.
16. Brochier C, Gaillard MC, Diguet E, Caudy N, Dossat C, et al. (2008) Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models. Physiol Genomics 33: 170-179.
17. Grünblatt E, Zander N, Bartl J, Jie L, Monoranu CM, et al. (2007) Comparison analysis of gene expression patterns between sporadic Alzheimer's and Parkinson's disease. J Alzheimers Dis 12: 291-311.
18. Xu PT, Li YJ, Qin XJ, Kroner C, Green-Odlum A, et al. (2007) A SAGE study of apolipoprotein E3/3 E3/4 and E4/4 allele-speciWc gene expression in hippocampus in Alzheimer disease. Mol Cell Neurosci 36: 313-331.
19. Yang Z, Gagarin D, St Laurent G 3rd, Hammell N, Toma I, et al. (2009) Cardiovascular inflammation and lesion cell apoptosis: a novel connection via the interferon-inducible immunoproteasome. Arterioscler Thromb Vasc Biol 29: 1213-1219.
20. Gnatenko DV, Dunn JJ, McCorkle SR, Weissmann D, Perrotta PL, et al. (2003) Transcript profiling of human platelets using microarray and serial analysis of gene expression. Blood 101: 2285-2293.
21. Esposito G, Imitola J, Lu J, De Filippis D, Scuderi C, et al. (2008) Genomic and functional profiling of human Down syndrome neural progenitors implicates S100B and aquaporin 4 in cell injury. Hum Mol Genet 17: 440-457.
22. Li CM, Guo M, Salas M, Schupf N, Silverman W, et al. (2006) Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21. BMC Med Genet 7: 24.
23. Mao R, Zielke CL, Zielke HR, Pevsner J, (2003) Global up-regulation of chromosome 21 gene expression in the developing Down syndrome brain. Genomics 81: 457-467.
24. FitzPatrick DR, Ramsay J, McGill NI, Shade M, Carothers AD, et al. (2002) Transcriptome analysis of human autosomal trisomy. Hum Mol Genet 11: 3249-3256.
25. ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
26. Costa V, Angelini C, De Feis I, Ciccodicola A, (2010) Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010: 853916.
27. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009) mRNA-Seq wholetranscriptome analysis of a single cell. Nat Methods 6: 377-382.
28. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, et al. (2009) High-resolution analysis of the 5-end transcriptome using a next generation DNA sequencer. PLoS ONE 4: e4108.
29. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
30. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
31. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-Seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
32. Lindberg J, Lundeberg J, (2010) The plasticity of the mammalian transcriptome. Genomics 95: 1-6.
33. Jacquier A, (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genetics 10: 833-844.
34. Kuhn DE, Nuovo GJ, Martin MM, Malana GE, Pleister AP, et al. (2008) Human chromosome 21-derived miRNAs are overexpressed in down syndrome brains and hearts. Biochem Biophys Res Commun 370: 473-477.
35. Takumi T, (2010) A humanoid mouse model of autism. Brain Dev 32: 753-758.
36. Duker AL, Ballif BC, Bawle EV, Person RE, Mahadevan S, et al. (2010) Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome. Eur J Hum Genet Jun 30.
37. Lin AE, Basson CT, Goldmuntz E, Magoulas PL, McDermott DA, et al. (2008) Adults with genetic syndromes and cardiovascular abnormalities: clinical history and management. Genet Med 10: 469-494.
38. Abildgaard L, Ellebaek E, Gustafsson G, Abrahamsson J, Hovi L, et al. (2006) Optimal treatment intensity in children with Down syndrome and myeloid leukaemia: data from 56 children treated on NOPHO-AML protocols and a review of the literature. Ann Hematol 85: 275-280.
39. Hasle H, (2001) Pattern of malignant disorders in individuals with Down's syndrome. Lancet Oncol 2: 429-436.
40. Diller GP, van Eijl S, Okonko DO, Howard LS, Ali O, et al. (2008) Circulating endothelial progenitor cells in patients with Eisenmenger syndrome and idiopathic pulmonary arterial hypertension. Circulation 117: 3020-3030.
41. Holmes DK, Bates N, Murray M, Ladusans EJ, Morabito A, et al. (2006) Hematopoietic progenitor cell deficiency in fetuses and children affected by Down's syndrome. Exp Hematol 34: 1611-1615.
42. Jablonska B, Ford D, Trisler D, Pessac B, (2006) The growth capacity of bone marrow CD34 positive cells in culture is drastically reduced in a murine model of Down syndrome. C R Biol 329: 726-732.
43. Krenning G, van Luyn MJ, Harmsen MC, (2009) Endothelial progenitor cell-based neovascularization: implications for therapy. Trends Mol Med 15: 180-189.
44. Hirschi KK, Ingram DA, Yoder MC, (2008) Assessing identity phenotype and fate of endothelial progenitor cells. Arterioscler Thromb Vasc Biol 28: 1584-1595.
45. Zampetaki A, Kirton JP, Xu Q, (2008) Vascular Repair by Endothelial Progenitor Cells Cardiovasc Res 78: 413-421.
46. Shantsila E, Watson T, Lip GY, (2007) Endothelial progenitor cells in cardiovascular disorders. J Am Coll Cardiol 49: 741-752.
47. Yoder MC, Mead LE, Prater D, Krier TR, Mroueh KN, et al. (2007) Redefining endothelial progenitor cells via clonal analysis and hematopoietic stem/progenitor cell principals. Blood 109: 1801-1809.
48. Sabatier F, Camoin-Jau L, Anfosso F, Sampol J, Dignat-George F, (2009) Circulating endothelial cells microparticles and progenitors: key players towards the definition of vascular competence. J Cell Mol Med 13: 454-471.
49. Napoli C, Balestrieri A, Ignarro LJ, (2007) Therapeutic approaches in vascular repair induced by adult bone marrow cells and circulating progenitor endothelial cells. Curr Pharm Des 13: 3245-3251.
50. Vasa M, Fichtlscherer S, Aicher A, Adler K, Urbich C, et al. (2001) Number and migratory activity of circulating andothelial progenitor cells inversely correlate with risk factors for coronary artery disease. Circ Res 89: E1-7.
51. Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, et al. (2010) The landscape of C. elegans 3′UTRs. Science 329: 432-435.
52. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
53. Core LJ, Waterfall J, Lis JT, (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
54. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, et al. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 45: 81-94.
55. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
56. Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H, (2008) Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics 92: 187-194.
57. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, et al. (2006) Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7: 246.
58. Casamassimi A, Balestrieri ML, Fiorito C, Schiano C, Maione C, et al. (2007) Comparison between total endothelial progenitor cell isolation versus enriched CD133+ culture. J Biochem 141: 503-511.
59. Cloonan N, Xu Q, Faulkner GJ, Taylor DF, Tang DT, et al. (2009) RNA-MATE: a recursive mapping strategy for high-throughput RNAsequencing data. Bioinformatics 25: 2615-2616.
60. Pruitt KD, Tatusova T, Maglott DR, (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes transcripts and proteins. Nucleic Acids Res 35 (Database issue): D61-65.
61. Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, et al. (2008) The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 36 (Database issue): D445-448.
62. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 37 (Database issue): D755-761.
63. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, et al. (2006) The UCSC Known Genes. Bioinformatics 22: 1036-1046.
64. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic Acids Res 37 (Database issue): D690-697.
65. Baek KH, Zaslavsky A, Lynch RC, Britt C, Okada Y, et al. (2009) Down's syndrome suppression of tumour growth and the role of the calcineurin inhibitor DSCR1. Nature 459: 1126-1130.
66. Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, et al. (2010) Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 17: 1030-1034.
67. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, et al. (2009) Small RNAs derived from snoRNAs. RNA 15: 1233-1240.
68. Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
69. Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S, (2010) Identification and classification of small rnas in transcriptome sequence data. Pac Symp Biocomput 2010: 80-87.
70. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, et al. (2010) PANTHER version 7: improved phylogenetic trees orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38 (Database issue): D204-210.
71. Young MD, Wakefield MJ, Smyth GK, Oshlack A, (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11: R14.
72. Ponting CP, Belgard TG, (2010) Transcribed dark matter: meaning or myth? Hum Mol Genet Sep 20.
73. van Bakel H, Nislow C, Blencowe BJ, Hughes TR, (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371.
74. Keren H, Lev-Maor G, Ast G, (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 11: 345-355.
75. 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.
76. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
77. Gremmels H, Fledderus JO, Balkom BW, Verhaar MC, (2011) Transcriptome Analysis in Endothelial Progenitor Cell Biology. Antioxid Redox Signal Feb 14.
78. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
79. Wang L, Feng Z, Wang X, Wang X, Zhang X, (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
80. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Nature Proceedingshttp://precedings.nature.com/documents/4282/version/2.
81. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.