Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Grigoriadis, Anita ^a,e   Oliver, Gavin R ^b   Tanney, Austin ^b   Kendrick, Howard ^c   Smalley, Matt J ^f   Jat, Parmjit ^d   Neville, A Munro ^a  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (Australia)

^b Almac Sciences   (United Kingdom)

^c INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e KING'S COLLEGE LONDON   (United Kingdom)

^f NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; MESSENGER RNA; OLIGONUCLEOTIDE; SENSE OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; BREAST CANCER; BREAST EPITHELIUM; CANCER CELL; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE TECHNOLOGY; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIMARY TUMOR; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; GENE EXPRESSION PROFILING; GENETICS; HUMAN GENOME; MAMMARY GLAND; METABOLISM; METHODOLOGY; NUCLEIC ACID PROBE; TUMOR CELL LINE;

ANTISENSE ELEMENTS (GENETICS); CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; MAMMARY GLANDS, HUMAN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 68849101462     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-324     Document Type: Article

References (43)

1. Wagner EG Simons RW Antisense RNA control in bacteria, phages, and plasmids Annu Rev Microbiol 1994, 48:713-742. 10.1146/ annurev.mi.48.100194.003433 7826024
2. Yelin R Dahary D Sorek R Levanon EY Goldstein O Shoshan A Diber A Biton S Tamir Y Khosravi R Nemzer S Pinner E Walach S Bernstein J Savitsky K Rotman G Widespread occurrence of antisense transcription in the human genome Nat Biotechnol 2003, 21:379-386. 10.1038/nbt808 12640466
3. Katayama S Tomaru Y Kasukawa T Waki K Nakanishi M Nakamura M Nishida H Yap CC Suzuki M Kawai J Suzuki H Carninci P Hayashizaki Y Wells C Frith M Ravasi T Pang KC Hallinan J Mattick J Hume DA Lipovich L Batalov S Engstrom PG Mizuno Y Faghihi MA Sandelin A Chalk AM Mottagui-Tabar S Liang Z Lenhard B Wahlestedt C Antisense transcription in the mammalian transcriptome Science 2005, 309:1564-1566. 10.1126/science.1112009 16141073
4. Chen J Sun M Kent WJ Huang X Xie H Wang W Zhou G Shi RZ Rowley JD Over 20% of human transcripts might form sense-antisense pairs Nucleic Acids Res 2004, 32:4812-4820. 519112 15356298 10.1093/nar/gkh818
5. Birney E Stamatoyannopoulos JA Dutta A Guigo R Gingeras TR Margulies EH Weng Z Snyder M Dermitzakis ET Thurman RE Kuehn MS Taylor CM Neph S Koch CM Asthana S Malhotra A Adzhubei I Greenbaum JA Andrews RM Flicek P Boyle PJ Cao H Carter NP Clelland GK Davis S Day N Dhami P Dillon SC Dorschner MO Fiegler H Giresi PG Goldy J Hawrylycz M Haydock A Humbert R James KD Johnson BE Johnson EM Frum TT Rosenzweig ER Karnani N Lee K Lefebvre GC Navas PA Neri F Parker SC Sabo PJ Sandstrom R Shafer A Vetrie D Weaver M Wilcox S Yu M Collins FS Dekker J Lieb JD Tullius TD Crawford GE Sunyaev S Noble WS Dunham I Denoeud F Reymond A Kapranov P Rozowsky J Zheng D Castelo R Frankish A Harrow J Ghosh S Sandelin A Hofacker IL Baertsch R Keefe D Dike S Cheng J Hirsch HA Sekinger EA Lagarde J Abril JF Shahab A Flamm C Fried C Hackermuller J Hertel J Lindemeyer M Missal K Tanzer A Washietl S Korbel J Emanuelsson O Pedersen JS Holroyd N Taylor R Swarbreck D Matthews N Dickson MC Thomas DJ Weirauch MT Gilbert J et al Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007 447 799 816 2212820 17571346 10.1038/nature05874
6. Galante PA Vidal DO de Souza JE Camargo AA de Souza SJ Sense-antisense pairs in mammals: Functional and evolutionary considerations Genome Biol 2007, 8:R40. 1868933 17371592 10.1186/gb-2007-8-3-r40
7. Yin Y Zhao Y Wang J Liu C Chen S Chen R Zhao H antiCODE: A natural sense-antisense transcripts database BMC Bioinformatics 2007, 8:319. 1997216 17760969 10.1186/1471-2105-8-319
8. Oeder S Mages J Flicek P Lang R Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets BMC Genomics 2007, 8:200. 1929078 17598913 10.1186/1471-2164-8-200
9. Rosok O Sioud M Systematic identification of sense-antisense transcripts in mammalian cells Nat Biotechnol 2004, 22:104-108. 10.1038/nbt925 14704709
10. Kiyosawa H Mise N Iwase S Hayashizaki Y Abe K Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized Genome Res 2005, 15:463-74. 1074361 15781571 10.1101/gr.3155905
11. Lapidot M Pilpel Y Genome-wide natural antisense transcription: Coupling its regulation to its different regulatory mechanisms EMBO Rep 2006, 7:1216-1222. 1794690 17139297 10.1038/sj.embor.7400857
12. Yu W Gius D Onyango P Muldoon-Jacobs K Karp J Feinberg AP Cui H Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA Nature 2008, 451:202-206. 10.1038/nature06468 18185590
13. Beltran M Puig I Pena C Garcia JM Alvarez AB Pena R Bonilla F de Herreros AG A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition Genes Dev 2008, 22:756-769. 2275429 18347095 10.1101/gad.455708
14. Wahl MB Heinzmann U Imai K LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome Bioinformatics 2008, 21:1389-1392. 10.1093/bioinformatics/bti205
15. Quere R Manchon L Lejeune M Clement O Pierrat F Bonafoux B Commes T Piquemal D Marti J Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression Nucleic Acids Res 2004, 32:e163. 534641 15561998 10.1093/nar/gnh161
16. Ge X Wu Q Jung YC Chen J Wang SM A large quantity of novel human antisense transcripts detected by LongSAGE Bioinformatics 2006, 22:2475-2479. 10.1093/bioinformatics/btl429 16895931
17. Ge X Rubinstein WS Jung YC Wu Q Genome-wide analysis of antisense transcription with Affymetrix exon array BMC Genomics 2008, 9:27. 2257944 18211689 10.1186/1471-2164-9-27
18. Almac Diagnostics website http://www.almacgroup.com/diagnostics/
19. Tanney A Oliver GR Farztdinov V Kennedy R Mulligan J Fulton C Farragher S Field J Johnston P Harkin DP Proutski V Mulligan K Generation of a non-small cell lung cancer transcriptome microarray BMC Med Genomics 2008, 1:20. 2426710 18513400 10.1186/1755-8794-1-20
20. Grigoriadis A Mackay A Reis-Filho JS Steele D Iseli C Stevenson BJ Jongeneel CV Valgeirsson H Fenwick K Iravani M Leao M Simpson AJ Strausberg RL Jat PS Ashworth A Neville AM O'Hare MJ Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data Breast Cancer Res 2006, 8:R56. 1779497 17014703 10.1186/bcr1604
21. Johnson JM Edwards S Shoemaked D Schadt EE Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments Trends Genet 2005, 21:93. 10.1016/j.tig.2004.12.009 15661355
22. Iseli C Stevenson BJ de Souza SJ Samaia HB Camargo AA Buetow KH Strausberg RL Simpson AJ Bucher P Jongeneel CV Long-range heterogeneity at the 3′ ends of human mRNAs Genome Res 2002, 12:1068-1074. 186619 12097343
23. Jongeneel CV Delorenzi M Iseli C Zhou D Haudenschild CD Khrebtukova I Kuznetsov D Stevenson BJ Strausberg RL Simpson AJ An atlas of human gene expression from massively parallel signature sequencing (MPSS) Genome Res 2005, 15:1007-1014. 1172045 15998913 10.1101/gr.4041005
24. Werner A Schmutzler G Carlile M Miles CG Peters H Expression profiling of antisense transcripts on DNA arrays Physiol Genomics 2007, 28:294-300. 17105753
25. Perocchi F Xu Z Clauder-Munster S Steinmetz LM Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D NAR 2007, 35(19):e128. 2095812 17897965 10.1093/nar/gkm683
26. Zhang Y Li J Kong L Gao G Liu Q Wei L NATsDB: Natural Antisense Transcripts DataBase NAR 2007, 35:D156-D161. 1635336 17082204 10.1093/ nar/gkl782
27. Jansen B Wacheck V Heere-Ress E Schlagbauer-Wadl H Hoeller C Lucas T Hoermann M Hollenstein U Wolff K Pehamberger H Chemosensitisation of malignant melanoma by BCL2 antisense therapy Lancet 2000, 356:1728-1733. 10.1016/S0140-6736(00)03207-4 11095261
28. Page MJ Amess B Townsend RR Parekh R Herath A Brusten L Zvelebil MJ Stein RC Waterfield MD Davies SC O'Hare KJ Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties Proc Natl Acad Sci USA 1999, 96:12589-12594. 23001 10535966 10.1073/pnas.96.22.12589
29. Adam PJ Berry J Loader JA Tyson KL Craggs G Smith P De Belin J Steers G Pezzella F Sachsenmeir KF Stamps AC Herath A Sim E O'Hare MJ Harris AL Terrett JA Arylamine N-acetyltransferase-1 is highly expressed in breast cancers and conveys enhanced growth and resistance to etoposide in vitro Mol Cancer Res 2003, 1:826-835. 14517345
30. Jones C Mackay A Grigoriadis A Cossu A Reis-Filho JS Fulford L Dexter T Davies S Bulmer K Ford E Parry S Budroni M Palmieri G Neville AM O'Hare MJ Lakhani SR Expression profiling of purified normal human luminal and myoepithelial breast cells: Identification of novel prognostic markers for breast cancer Cancer Res 2004, 64:3037-3045. 10.1158/ 0008-5472.CAN-03-2028 15126339
31. Brenner S Johnson M Bridgham J Golda G Lloyd DH Johnson D Luo S McCurdy S Foy M Ewan M Roth R George D Eletr S Albrecht G Vermaas E Williams SR Moon K Burcham T Pallas M DuBridge RB Kirchner J Fearon K Mao J Corcoran K Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays Nat Biotechnol 2000, 18:630-634. 10.1038/ 76469 10835600
32. Brenner S Williams SR Vermaas EH Storck T Moon K McCollum C Mao JI Luo S Kirchner JJ Eletr S DuBridge RB Burcham T Albrecht G In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs Proc Natl Acad Sci USA 2000, 97:1665-1670. 26493 10677516 10.1073/pnas.97.4.1665
33. ArrayExpress website http://www.ebi.ac.uk/arrayexpress
34. The R Project for Statistical Computing http://www.r-project.org/
35. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249 12925520
36. Liu WM Mei R Di X Ryder TB Hubbell E Dee S Webster TA Harrington CA Ho MH Baid J Smeekens SP Analysis of high density expression microarrays with signed-rank call algorithms Bioinformatics 2002, 18:1593-1599. 10.1093/bioinformatics/18.12.1593 12490443
37. Iseli C Stevenson BJ de Souza SJ Samaia HB Camargo AA Buetow KH Strausberg RL Simpson AJ Bucher P Jongeneel CV Long-range heterogeneity at the 3′ ends of human mRNAs Genome Res 2002, 12:1068-1074. 186619 12097343
38. Jongeneel CV Iseli C Stevenson BJ Riggins GJ Lal A Mackay A Harris RA O'Hare MJ Neville AM Simpson AJ Strausberg RL Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing Proc Natl Acad Sci USA 2003, 100:4702-4705. 153619 12671075 10.1073/pnas.0831040100
39. Naef F Huelsken J Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks Nucleic Acids Res 2005, 33:e111. 1178007 16030348 10.1093/nar/gni104
40. Striking Development website http://www.paracel.com
41. Slater G St C Birney E Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 2005, 6:31. 553969 15713233 10.1186/1471-2105-6-31
42. Galante SAS portal http://www.compbio.ludwig.org.br/sense-antisense
43. Sleeman KE Kendrick H Ashworth A Isacke CM Smalley MJ CD24 staining of mouse mammary gland cells defines luminal epithelial, myoepithelial/ basal and non-epithelial cells Breast Cancer Res 2006, 8:R7. 1413978 16417656 10.1186/bcr1371