Boi S, Solda' G, Tenchini ML: Shedding light on the dark side of the genome: overlapping genes in higher eukaryotes. Current Genomics. 2004, 5: 509-524. 10.2174/1389202043349020.
Article
CAS
Google Scholar
Makalowska I, Lin CF, Makalowski W: Overlapping genes in vertebrate genomes. Comput Biol Chem. 2005, 29 (1): 1-12. 10.1016/j.compbiolchem.2004.12.006.
Article
PubMed
CAS
Google Scholar
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038/nature05874.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C: The transcriptional landscape of the mammalian genome. Science. 2005, 309 (5740): 1559-1563. 10.1126/science.1112014.
Article
PubMed
CAS
Google Scholar
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005, 308 (5725): 1149-1154. 10.1126/science.1108625.
Article
PubMed
CAS
Google Scholar
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L: Complex Loci in human and mouse genomes. PLoS Genet. 2006, 2 (4): e47-10.1371/journal.pgen.0020047.
Article
PubMed
PubMed Central
Google Scholar
Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR: Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005, 15 (7): 987-997. 10.1101/gr.3455305.
Article
PubMed
CAS
PubMed Central
Google Scholar
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J: Antisense transcription in the mammalian transcriptome. Science. 2005, 309 (5740): 1564-1566. 10.1126/science.1112009.
Article
PubMed
Google Scholar
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 (16): 4812-4820. 10.1093/nar/gkh818.
Article
PubMed
CAS
PubMed Central
Google Scholar
Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ: Sense-antisense pairs in mammals: functional/evolutionary considerations. Genome Biol. 2007, 8 (3): R40-10.1186/gb-2007-8-3-r40.
Article
PubMed
PubMed Central
Google Scholar
Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G: In search of antisense. Trends Biochem Sci. 2004, 29 (2): 88-94. 10.1016/j.tibs.2003.12.002.
Article
PubMed
CAS
Google Scholar
Sun M, Hurst LD, Carmichael GG, Chen J: Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res. 2006, 16 (7): 922-933. 10.1101/gr.5210006.
Article
PubMed
CAS
PubMed Central
Google Scholar
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I: Mammalian overlapping genes: the comparative perspective. Genome Res. 2004, 14 (2): 280-286. 10.1101/gr.1590904.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 2006, 34 (12): 3465-3475. 10.1093/nar/gkl473.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lapidot M, Pilpel Y: Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep. 2006, 7 (12): 1216-1222. 10.1038/sj.embor.7400857.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li AW, Murphy PR: Expression of alternatively spliced FGF-2 antisense RNA transcripts in the central nervous system: regulation of FGF-2 mRNA translation. Mol Cell Endocrinol. 2000, 170 (1-2): 233-242. 10.1016/S0303-7207(00)00440-8.
Article
PubMed
CAS
Google Scholar
Munroe SH, Lazar MA: Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem. 1991, 266 (33): 22083-22086.
PubMed
CAS
Google Scholar
Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM, Vaughn JC: RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. Rna. 2003, 9 (6): 698-710. 10.1261/rna.2120703.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sleutels F, Zwart R, Barlow DP: The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature. 2002, 415 (6873): 810-813.
Article
PubMed
CAS
Google Scholar
Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet. 2003, 34 (2): 157-165. 10.1038/ng1157.
Article
PubMed
CAS
Google Scholar
Bejanin S, Cervini R, Mallet J, Berrard S: A unique gene organization for two cholinergic markers, choline acetyltransferase and a putative vesicular transporter of acetylcholine. J Biol Chem. 1994, 269 (35): 21944-21947.
PubMed
CAS
Google Scholar
Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A: Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007, 445 (7128): 666-670. 10.1038/nature05519.
Article
PubMed
CAS
Google Scholar
Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD: Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. PLoS Genet. 2005, 1 (2): e18-10.1371/journal.pgen.0010018.
Article
PubMed
PubMed Central
Google Scholar
Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ, Spector DL: Regulating gene expression through RNA nuclear retention. Cell. 2005, 123 (2): 249-263. 10.1016/j.cell.2005.08.033.
Article
PubMed
CAS
Google Scholar
Dahary D, Elroy-Stein O, Sorek R: Naturally occurring antisense: transcriptional leakage or real overlap?. Genome Res. 2005, 15 (3): 364-368. 10.1101/gr.3308405.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kiyosawa H, Yamanaka I, Osato N, Kondo S, Hayashizaki Y: Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 2003, 13 (6B): 1324-1334. 10.1101/gr.982903.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R: Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol. 2003, 21 (4): 379-386. 10.1038/nbt808.
Article
PubMed
CAS
Google Scholar
Pang KC, Frith MC, Mattick JS: Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 2006, 22 (1): 1-5. 10.1016/j.tig.2005.10.003.
Article
PubMed
CAS
Google Scholar
Lehner B, Williams G, Campbell RD, Sanderson CM: Antisense transcripts in the human genome. Trends Genet. 2002, 18 (2): 63-65. 10.1016/S0168-9525(02)02598-2.
Article
PubMed
CAS
Google Scholar
Shendure J, Church GM: Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 2002, 3 (9): RESEARCH0044-10.1186/gb-2002-3-9-research0044.
Article
PubMed
PubMed Central
Google Scholar
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002, 3 (12): RESEARCH0083-10.1186/gb-2002-3-12-research0083.
Article
PubMed
PubMed Central
Google Scholar
Keese PK, Gibbs A: Origins of genes: "big bang" or continuous creation?. Proc Natl Acad Sci USA. 1992, 89 (20): 9489-9493. 10.1073/pnas.89.20.9489.
Article
PubMed
CAS
PubMed Central
Google Scholar
Osato N, Suzuki Y, Ikeo K, Gojobori T: Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics. 2007, 176 (2): 1299-1306. 10.1534/genetics.106.069484.
Article
PubMed
CAS
PubMed Central
Google Scholar
Prescott EM, Proudfoot NJ: Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci USA. 2002, 99 (13): 8796-8801. 10.1073/pnas.132270899.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yu JS, Kokoska RJ, Khemici V, Steege DA: In-frame overlapping genes: the challenges for regulating gene expression. Mol Microbiol. 2007, 63 (4): 1158-1172. 10.1111/j.1365-2958.2006.05572.x.
Article
PubMed
CAS
Google Scholar
Blumenthal T, Gleason KS: Caenorhabditis elegans operons: form and function. Nat Rev Genet. 2003, 4 (2): 112-120. 10.1038/nrg995.
Article
PubMed
CAS
Google Scholar
Cavalcanti AR, Stover NA, Landweber LF: On the paucity of duplicated genes in Caenorhabditis elegans operons. J Mol Evol. 2006, 62 (6): 765-771. 10.1007/s00239-005-0203-3.
Article
PubMed
CAS
Google Scholar
Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M: Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene. 2007, 392 (1–2): 134-141. 10.1016/j.gene.2006.12.005.
Article
PubMed
CAS
Google Scholar
Sun M, Hurst LD, Carmichael GG, Chen J: Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res. 2005, 33 (17): 5533-5543. 10.1093/nar/gki852.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yu WP, Brenner S, Venkatesh B: Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet. 2003, 19 (4): 180-183. 10.1016/S0168-9525(03)00048-9.
Article
PubMed
CAS
Google Scholar
Blencowe BJ: Alternative splicing: new insights from global analyses. Cell. 2006, 126 (1): 37-47. 10.1016/j.cell.2006.06.023.
Article
PubMed
CAS
Google Scholar
Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science. 2003, 302 (5653): 2141-2144. 10.1126/science.1090100.
Article
PubMed
CAS
Google Scholar
Modrek B, Lee CJ: Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet. 2003, 34 (2): 177-180. 10.1038/ng1159.
Article
PubMed
CAS
Google Scholar
Sokal RR, Rohlf FJ: Biometry. 1995, New York, USA: W.H. Freeman & Company, 3
Google Scholar
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J: Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007, 17 (6): 746-759. 10.1101/gr.5660607.
Article
PubMed
CAS
PubMed Central
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z: Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005, 437 (7057): 376-380.
PubMed
CAS
PubMed Central
Google Scholar
Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD: Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet. 2005, 21 (6): 326-329. 10.1016/j.tig.2005.04.006.
Article
PubMed
CAS
Google Scholar
Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, D501-504. 33 Database
The UCSC ftp Web site. [ftp://hgdownload.cse.ucsc.edu/]
The C. elegans Genome Database. [http://www.wormbase.org/]
RIKEN Mouse Genome Project database. [http://fantom.gsc.riken.go.jp/]
The Drosophila melanogaster genome database. [http://flybase.net/]
UCSC Genome Bionformatics Site. [http://genome.ucsc.edu/]
Kent WJ: BLAT–the BLAST-like alignment tool. Genome Res. 2002, 12 (4): 656-664. 10.1101/gr.229202. Article published online before March 2002.
Article
PubMed
CAS
PubMed Central
Google Scholar
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 (20): e163-10.1093/nar/gnh161.
Article
PubMed
PubMed Central
Google Scholar
Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R: Human chromosome 7: DNA sequence and biology. Science. 2003, 300 (5620): 767-772. 10.1126/science.1083423.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yu P, Ma D, Xu M: Nested genes in the human genome. Genomics. 2005, 86 (4): 414-422. 10.1016/j.ygeno.2005.06.008.
Article
PubMed
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410.
Article
PubMed
CAS
Google Scholar
Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA: Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res. 2004, 32 (3): e37-10.1093/nar/gnh031.
Article
PubMed
PubMed Central
Google Scholar