Overlapping genes in vertebrate genomes

Adelman, 1987, Two mammalian genes transcribed from opposite strands of the same DNA locus, Science, 235, 1514, 10.1126/science.3547652 Aparicio, 2002, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes, Science, 297, 1301, 10.1126/science.1072104 Aravin, 2001, Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline, Curr. Biol., 11, 1017, 10.1016/S0960-9822(01)00299-8 Armes, 1996, Surfeit locus gene homologs are widely distributed in invertebrate genomes, Mol. Cell. Biol., 16, 5591, 10.1128/MCB.16.10.5591 Arriza, 1987, Cloning of human mineralocorticoid receptor complementary DNA: structural and functional kinship with the glucocorticoid receptor, Science, 237, 268, 10.1126/science.3037703 Bachman, 1999, The 5′ region of the COX4 gene contains a novel overlapping gene NOC4, Mamm. Genome, 10, 506, 10.1007/s003359901031 Barrell, 1976, Overlapping genes in bacteriophage phiX174, Nature, 264, 34, 10.1038/264034a0 Batshake, 1996, The mouse genes for the EP1 prostanoid receptor and the PKN protein kinase overlap, Biochem. Biophys. Res. Commun., 227, 70, 10.1006/bbrc.1996.1469 Boi, 2004, Shedding Light on the dark side of the genome: overlapping genes in higher eukaryotes, Curr. Genomics, 5, 509, 10.2174/1389202043349020 Bristow, 1993, Tenascin-X: a novel extracellular matrix protein encoded by the human XB gene overlapping P450c21B, J. Cell Biol., 122, 265, 10.1083/jcb.122.1.265 Burke, 1998, Alternative gene form discovery and candidate gene selection from gene indexing projects, Genome Res., 8, 276, 10.1101/gr.8.3.276 Chen, 2003, Alterations in PMS2, MSH2 and MLH1 expression in human prostate cancer, Int. J. Oncol., 22, 1033 Chu, 2002, Natural antisense (rTSalpha) RNA induces site-specific cleavage of thymidylate synthase mRNA, Biochim. Biophys. Acta, 1587, 183, 10.1016/S0925-4439(02)00081-9 Cooper, 1998, Divergently transcribed overlapping genes expressed in liver and kidney and located in the 11p15.5 imprinted domain, Genomics, 49, 38, 10.1006/geno.1998.5221 Cullen, 2002, RNA interference: antiviral defense and genetic tool, Nat. Immunol., 3, 597, 10.1038/ni0702-597 Dan, 2002, Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution, Nucl. Acids Res., 30, 2906, 10.1093/nar/gkf407 Duhig, 1998, The human Surfeit locus, Genomics, 52, 72, 10.1006/geno.1998.5372 Edgar, 2003, The gene structure and expression of human ABHD1: overlapping polyadenylation signal sequence with Sec12, BMC Genomics, 4, 18, 10.1186/1471-2164-4-18 Farrell, 1995, Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene, J. Biol. Chem., 270, 3400, 10.1074/jbc.270.7.3400 Gangopadhyay, 1997, Unusual genome organisation in Entamoeba histolytica leads to two overlapping transcripts, Mol. Biochem. Parasitol., 89, 73, 10.1016/S0166-6851(97)00110-2 Gibbs, 2004, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, 428, 493, 10.1038/nature02426 Gilley, 1997, Fugu genome is not a good mammalian model, Nature, 385, 305, 10.1038/385305a0 Glover, 1998, Cloning and characterization of MS5 from Arabidopsis: a gene critical in male meiosis, Plant J., 15, 345, 10.1046/j.1365-313X.1998.00216.x Gould, 1992, Exaptation—a missing term in the science of form, Paleobiology, 8, 4, 10.1017/S0094837300004310 Hannon, 2002, RNA interference, Nature, 418, 244, 10.1038/418244a Hastings, 1997, Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels, Nucl. Acids Res., 25, 4296, 10.1093/nar/25.21.4296 Heikkila, 1993, Directional regulatory activity of cis-acting elements in the bidirectional alpha 1(IV) and alpha 2(IV) collagen gene promoter, J. Biol. Chem., 268, 24677, 10.1016/S0021-9258(19)74519-0 Hirotsune, 2003, An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene, Nature, 423, 91, 10.1038/nature01535 Huckaby, 1987, Structure of the chromosomal chicken progesterone receptor gene, Proc. Natl. Acad. Sci. U.S.A., 84, 8380, 10.1073/pnas.84.23.8380 Inouye, 1988, Small RNAs in the prokaryotes: a growing list of diverse roles, Cell, 53, 5, 10.1016/0092-8674(88)90480-1 Ito, 2000, A core-promoter region functions bi-directionally for human opioid-receptor-like gene ORL1 and its 5′-adjacent gene GAIP, J. Mol. Biol., 304, 259, 10.1006/jmbi.2000.4212 Ito, 1997, A serine/threonine protein kinase gene isolated by an in vivo binding procedure using the Arabidopsis floral homeotic gene product, AGAMOUS, Plant Cell Physiol., 38, 248, 10.1093/oxfordjournals.pcp.a029160 Jankowski, 1986, In vitro expression of two proteins from overlapping reading frames in a eukaryotic DNA sequence, J. Mol. Evol., 24, 61, 10.1007/BF02099952 Joseph, 1998, The rat androgen-binding protein (ABP/SHBG) gene contains triplet repeats similar to unstable triplets: evidence that the ABP/SHBG and the fragile X-related 2 genes overlap, Steroids, 63, 2, 10.1016/S0039-128X(97)00087-1 Karlin, 2002, Associations between human disease genes and overlapping gene groups and multiple amino acid runs, Proc. Natl. Acad. Sci. U.S.A., 99, 17008, 10.1073/pnas.262658799 Kasper, 2002, Different structural organization of the encephalopsin gene in man and mouse, Gene, 295, 27, 10.1016/S0378-1119(02)00799-0 Keese, 1992, Origins of genes: “big bang” or continuous creation?, Proc. Natl. Acad. Sci. U.S.A., 89, 9489, 10.1073/pnas.89.20.9489 Kennerson, 1997, The Charcot-Marie-Tooth binary repeat contains a gene transcribed from the opposite strand of a partially duplicated region of the COX10 gene, Genomics, 46, 61, 10.1006/geno.1997.5012 Khochbin, 1989, An antisense RNA involved in p53 mRNA maturation in murine erythroleukemia cells induced to differentiate, EMBO J., 8, 4107, 10.1002/j.1460-2075.1989.tb08595.x Kimelman, 1989, An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes, Cell, 59, 687, 10.1016/0092-8674(89)90015-9 Kiyosawa, 2002, Speculations on the role of natural antisense transcripts in mammalian X chromosome evolution, Cytogenet. Genome Res., 99, 151, 10.1159/000071587 Kiyosawa, 2003, Antisense transcripts with FANTOM2 clone set and their implications for gene regulation, Genome Res., 13, 1324, 10.1101/gr.982903 Knee, 1994, Basic fibroblast growth factor sense (FGF) and antisense (gfg) RNA transcripts are expressed in unfertilized human oocytes and in differentiated adult tissues, Biochem. Biophys. Res. Commun., 205, 577, 10.1006/bbrc.1994.2704 Krystal, 1990, N-myc mRNA forms an RNA–RNA duplex with endogenous antisense transcripts, Mol. Cell. Biol., 10, 4180, 10.1128/MCB.10.8.4180 Kumar, 1998, Antisense RNA: function and fate of duplex RNA in cells of higher eukaryotes, Microbiol. Mol. Biol. Rev., 62, 1415, 10.1128/MMBR.62.4.1415-1434.1998 Laabi, 1994, The BCMA gene, preferentially expressed during B lymphoid maturation, is bidirectionally transcribed, Nucl. Acids Res., 22, 1147, 10.1093/nar/22.7.1147 Lavorgna, 2004, In search of antisense, Trends Biochem. Sci., 29, 88, 10.1016/j.tibs.2003.12.002 Lavorgna, 2004, AntiHunter: searching BLAST output for EST antisense transcripts, Bioinformatics, 20, 583, 10.1093/bioinformatics/btg460 Lazar, 1990, Gene expression from the c-erbA alpha/Rev-ErbA alpha genomic locus. Potential regulation of alternative splicing by opposite strand transcription, J. Biol. Chem., 265, 12859, 10.1016/S0021-9258(19)38238-9 Lazar, 1989, A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbAlpha transcriptional unit, Mol. Cell. Biol., 9, 1128, 10.1128/MCB.9.3.1128 Lehner, 2002, Antisense transcripts in the human genome, Trends Genet., 18, 63, 10.1016/S0168-9525(02)02598-2 Li, 1996, Expression of the rat BFGF antisense RNA transcript is tissue-specific and developmentally regulated, Mol. Cell. Endocrinol., 118, 113, 10.1016/0303-7207(96)03772-0 Li, 1996, The basic fibroblast growth factor (FGF-2) antisense RNA (GFG) is translated into a MutT-related protein in vivo, Biochem. Biophys. Res. Commun., 223, 19, 10.1006/bbrc.1996.0839 Lipman, 1997, Making (anti)sense of non-coding sequence conservation, Nucl. Acids Res., 25, 3580, 10.1093/nar/25.18.3580 Liu, 1999, FAST-2 is a mammalian winged-helix protein which mediates transforming growth factor beta signals, Mol. Cell. Biol., 19, 424, 10.1128/MCB.19.1.424 Makalowski, 2000, Genomic scrap yard: how genomes utilize all that junk, Gene, 259, 61, 10.1016/S0378-1119(00)00436-4 Malavasic, 1990, Complementary transcripts from two genes necessary for normal meiosis in the yeast Saccharomyces cerevisiae, Mol. Cell. Biol., 10, 2809, 10.1128/MCB.10.6.2809 Mao, 2002, Tenascin-X deficiency mimics Ehlers-Danlos syndrome in mice through alteration of collagen deposition, Nat. Genet., 30, 421, 10.1038/ng850 Marcelino, 1999, CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Nat. Genet., 23, 319, 10.1038/15496 Mihalich, 2003, Different basic fibroblast growth factor and fibroblast growth factor-antisense expression in eutopic endometrial stromal cells derived from women with and without endometriosis, J. Clin. Endocrinol. Metab., 88, 2853, 10.1210/jc.2002-021434 Misener, 2000, Extraordinarily high density of unrelated genes showing overlapping and intraintronic transcription units, Biochim. Biophys. Acta, 1492, 269, 10.1016/S0167-4781(00)00096-8 Misra, 2002, Annotation of the Drosophila melanogaster euchromatic genome: a systematic review, Genome Biol., 3 Miyajima, 1989, Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus, Cell, 57, 31, 10.1016/0092-8674(89)90169-4 Morel, 1989, Transcript encoded on the opposite strand of the human steroid 21-hydroxylase/complement component C4 gene locus, Proc. Natl. Acad. Sci. U.S.A., 86, 6582, 10.1073/pnas.86.17.6582 Munroe, 2004, Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns, J. Cell. Biochem., 93, 664, 10.1002/jcb.20252 Murphy, 1994, Identification and characterization of an antisense RNA transcript (gfg) from the human basic fibroblast growth factor gene, Mol. Endocrinol., 8, 852, 10.1210/me.8.7.852 Nakagawa, 2004, Mismatch repair gene PMS2: disease-causing germline mutations are frequent in patients whose tumors stain negative for PMS2 protein, but paralogous genes obscure mutation detection and interpretation, Cancer Res., 64, 4721, 10.1158/0008-5472.CAN-03-2879 Nicolaides, 1995, Analysis of the 5′ region of PMS2 reveals heterogeneous transcripts and a novel overlapping gene, Genomics, 29, 329, 10.1006/geno.1995.9997 Noguchi, 1994, Characterization of an antisense Inr element in the eIF-2 alpha gene, J. Biol. Chem., 269, 29161, 10.1016/S0021-9258(19)62025-9 O’Hanlon, 1995, A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS, Biochem. Biophys. Res. Commun., 210, 556, 10.1006/bbrc.1995.1696 Ohinata, 2002, Male-enhanced antigen-1 gene flanked by two overlapping genes is expressed in late spermatogenesis, Biol. Reprod., 67, 1824, 10.1095/biolreprod.101.002550 Okazaki, 2002, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563, 10.1038/nature01266 Osato, 2003, Antisense transcripts with rice full-length cDNAs, Genome Biol., 5, R5, 10.1186/gb-2003-5-1-r5 Pertea, 2003, TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets, Bioinformatics, 19, 651, 10.1093/bioinformatics/btg034 Peterson, 1993, Functional analysis of mRNA 3′ end formation signals in the convergent and overlapping transcription units of the S. cerevisiae genes RHO1 and MRP2, Nucl. Acids Res., 21, 5500, 10.1093/nar/21.23.5500 Petrukhin, 1998, Identification of the gene responsible for Best macular dystrophy, Nat. Genet., 19, 241, 10.1038/915 Prescott, 2002, Transcriptional collision between convergent genes in budding yeast, Proc. Natl. Acad. Sci. U.S.A., 99, 8796, 10.1073/pnas.132270899 Quesada, 1999, OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana, FEBS Lett., 461, 101, 10.1016/S0014-5793(99)01426-X Sadiq, 1994, Developmental regulation of antisense-mediated gene silencing in Dictyostelium, Antisense Res. Dev., 4, 263, 10.1089/ard.1994.4.263 Shendure, 2002, Computational discovery of sense–antisense transcription in the human and mouse genomes, Genome Biol., 3 Shintani, 1999, Origin of gene overlap: the case of TCP1 and ACAT2, Genetics, 152, 743, 10.1093/genetics/152.2.743 Sloan, 1999, The two subunits of human molybdopterin synthase: evidence for a bicistronic messenger RNA with overlapping reading frames, Nucl. Acids Res., 27, 854, 10.1093/nar/27.3.854 Sorek, 2003, A novel algorithm for computational identification of contaminated EST libraries, Nucl. Acids Res., 31, 1067, 10.1093/nar/gkg170 Spencer, 1986, Overlapping transcription units in the dopa decarboxylase region of Drosophila, Nature, 322, 279, 10.1038/322279a0 Stallmeyer, 1999, Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames, Am. J. Hum. Genet., 64, 698, 10.1086/302295 Swalla, 1996, PCNA mRNA has a 3′UTR antisense to yellow crescent RNA and is localized in ascidian eggs and embryos, Dev. Biol., 178, 23, 10.1006/dbio.1996.0195 Tvrdik, 1999, Cig30 and Pitx3 genes are arranged in a partially overlapping tail-to-tail array resulting in complementary transcripts, J. Biol. Chem., 274, 26387, 10.1074/jbc.274.37.26387 Veeramachaneni, 2004, Mammalian overlapping genes: the comparative perspective, Genome Res., 14, 280, 10.1101/gr.1590904 Werner, 2002, Regulation of the NPT gene by a naturally occurring antisense transcript, Cell. Biochem. Biophys., 36, 241, 10.1385/CBB:36:2-3:241 West, 2003, Identification of a novel gene linked to parkin via a bi-directional promoter, J. Mol. Biol., 326, 11, 10.1016/S0022-2836(02)01376-1 Williams, 1986, A mouse locus at which transcription from both DNA strands produces mRNAs complementary at their 3′ ends, Nature, 322, 275, 10.1038/322275a0 Wolfsberg, 1997, A comparison of expressed sequence tags (ESTs) to human genomic sequences, Nucl. Acids Res., 25, 1626, 10.1093/nar/25.8.1626 Yelin, 2003, Widespread occurrence of antisense transcription in the human genome, Nat. Biotechnol., 21, 379, 10.1038/nbt808 Zahraoui, 1987, Nucleotide sequence of the chicken proto-oncogene c-erbA corresponding to domain 1 of v-erbA, Eur. J. Biochem., 166, 63, 10.1111/j.1432-1033.1987.tb13484.x Zhou, 2003, Overlapping gene structure of human VLCAD and DLG4, Gene, 305, 161, 10.1016/S0378-1119(02)01235-0 Zuniga Mejia Borja, 1993, Expression of alternatively spliced bFGF first coding exons and antisense mRNAs during chicken embryogenesis, Dev. Biol., 157, 110, 10.1006/dbio.1993.1116