Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22

Genome Research

Volumn 16, Issue 1, 2006, Pages 45-54

  Lipovich, Leonard ^a,b   King, Mary Claire ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CHROMOSOME 22; DNA SPLICING; GENE CLUSTER; GENE STRUCTURE; GENETIC DIFFERENCE; HUMAN; HUMAN CHROMOSOME; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RODENT; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION;

ANIMALS; CHROMOSOMES, HUMAN, PAIR 22; EUCHROMATIN; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MICE; OPEN READING FRAMES; TRANSCRIPTION, GENETIC;

PRIMATES; RODENTIA;

EID: 30044440332     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.3883606     Document Type: Article

References (58)

1. Adachi, N. and Lieber, M.R. 2002. Bidirectional gene organization: A common architectural feature of the human genome. Cell 109: 807-809.
2. Andres, A.M., Soldevila, M., Saitou, N., Volpini, V., Calafell, F., and Bertranpetit, J. 2003. Understanding the dynamics of Spinocerebellar ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes. Neurosci. Lett. 336: 143-146.
3. Angiolillo, A., Russo, G., Porcellini, A., Smaldone, S., D'Alessandro, F., and Pietropaolo, C. 2002. The human homologue of the mouse Surf5 gene encodes multiple alternatively spliced transcripts. Gene 284: 169-178.
4. Burset, M., Seledtsov, I.A., and Solovyev, V.V. 2000. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 28: 4364-4375.
5. Caffrey, J.J., Safrany, S.T., Yang, X., and Shears, S.B. 2000. Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases: An expanding Nudt family. J. Biol. Chem. 275: 12730-12736.
6. Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata, K., Itoh, M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki, D., et al. 2003. Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res. 13: 1273-1289.
7. Chong, A., Zhang, G., and Bajic, V.B. 2004. Information for the Coordinates of Exons (ICE): A human splice sites database. Genomics 84: 762-766.
8. Collins, J.E., Goward, M.E., Cole, C.G., Smink, L.J., Huckle, E.J., Knowles, S., Bye, J.M., Beare, D.M., and Dunham, I. 2003. Reevaluating human gene annotation: A second-generation analysis of chromosome 22. Genome Res. 13: 27-36.
9. Courseaux, A. and Nahon, J.L. 2001. Birth of two chimeric genes in the Hominidae lineage. Science 291: 1293-1297.
10. Delihas, N. and Forst, S. 2001. MicF: An antisense RNA gene involved in response of Escherichia coli to global stress factors. J. Mol. Biol. 313: 1-12.
11. Edgar, A.J. 2003. The gene structure and expression of human ABHD1: Overlapping polyadenylation signal sequence with Sec12. BMC Genomics 4: 18.
12. Ejima, Y. and Yang, L. 2003. Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Hum. Mol. Genet. 12: 1321-1328.
13. Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
14. Feng, J., Funk, W.D., Wang, S.S., Weinrich, S.L., Avilion, A.A., Chiu, C.P., Adams, R.R., Chang, E., Allsopp, R.C., and Yu, J. 1995. The RNA component of human telomerase. Science 269: 1236-1241.
15. Gardiner, K., Fortna, A., Bechtel, L., and Davisson, M.T. 2003. Mouse models of Down syndrome: How useful can they be? Comparison of the gene content of human chromosome 21 with orthologous mouse genomic regions. Gene 318: 137-147.
16. Harrington, J.J., Sherf, B., Rundlett, S., Jackson, P.D., Perry, R., Cain, S., Leventhal, C., Thornton, M., Ramachandran, R., Whittington, J., et al. 2001. Creation of genome-wide protein expression libraries using random activation of gene expression. Nat. Biotechnol. 19: 440-445.
17. Hildebrandt, M. and Nellen, W. 1992. Differential antisense transcription from the Dictyostelium EB4 gene locus: Implications on antisense-mediated regulation of mRNA stability. Cell 69: 197-204.
18. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., et al. 2002. The Ensembl genome database project. Nucleic Acids Res. 30: 38-41.
19. International Human Genome Sequencing Consortium (IHGSC). 2004. Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
20. Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P., and Gingeras, T.R. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
21. Kawashima, I., Mita-Honjo, K., and Takiguchi, Y. 1992. Characterization of the primate-specific repetitive DNA element MER1. DNA Seq. 2: 313-318.
22. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006.
23. Kiyosawa, H., Yamanaka, I., Osato, N., Kondo, S., and Hayashizaki, Y. 2003. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13: 1324-1334.
24. Kramer, C., Loros, J.J., Dunlap, J.C., and Crosthwaite, S.K. 2003. Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421: 948-952.
25. Kumar, A., Harrison, P.M., Cheung, K.H., Lan, N., Echols, N., Bertone, P., Miller, P., Gerstein, M.B., and Snyder, M. 2002. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20: 58-63.
26. Kutach, A.K. and Kadonaga, J.T. 2000. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20: 4754-4764.
27. Larsson, T.P., Murray, C.G., Hill, T., Fredriksson, R., and Schioth, H.B. 2005. Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery. FEBS Lett. 579: 690-698.
28. Lee, R.C. and Ambros, V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
29. Lewin, B. 2000. Genes VII. Oxford University Press, New York.
30. Long, M., Deutsch, M., Wang, W., Betran, E., Brunet, F.G., and Zhang, J. 2003. Origin of new genes: Evidence from experimental and computational analyses. Genetica 118: 171-182.
31. Margolin, J. 2001. From comparative and functional genomics to practical decisions in the clinic: A view from the trenches. Genome Res. 11: 923-925.
32. Mattick, J.S. 2003. Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25: 930-939.
33. Millar, R., Conklin, D., Lofton-Day, C., Hutchinson, E., Troskie, B., Illing, N., Sealfon, S.C., Hapgood, J. 1999. A novel human GnRH receptor homolog gene: Abundant and wide tissue distribution of the antisense transcript. J. Endocrinol. 162: 117-126.
34. Misra, S., Crosby, M.A., Mungall, C.J., Matthews, B.B., Campbell, K.S., Hradecky, P., Huang, Y., Kaminker, J.S., Millburn, G.H., Prochnik, S.E., et al. 2002. Annotation of the Drosophila melanogaster euchromatic genome: A systematic review. Genome Biol. 3: research0083.
35. Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L.G., Hume, D.A., Hayashizaki, Y., and Tomita, M. 2003. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 13: 1301-1306.
36. Ohlsson, R., Paldi, A., and Graves, J.A. 2001. Did genomic imprinting and X chromosome inactivation arise from stochastic expression? Trends Genet. 17: 136-141.
37. Okazaki, Y. and Hume, D.A. 2003. A guide to the mammalian genome. Genome Res. 13: 1267-1272.
38. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
39. Qvist, H., Sjostrom, H., and Noren, O. 1998. The TATA-less, GC-rich porcine dipeptidylpeptidase IV (DPPIV) promoter shows bidirectional activity. Biol. Chem. 379: 75-81.
40. Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Nelson, F.K., Miller, P., Gerstein, M., et al. 2003. The transcriptional activity of human chromosome 22. Genes & Dev. 17: 529-540.
41. Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L., and Bradley, A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14: 1902-1910.
42. Seki, Y., Ikeda, S., Kiyohara, H., Ayabe, H., Seki, T., and Matsui, H. 2002. Sequencing analysis of a putative human O-sialoglycoprotein endopeptidase gene (OSGEP) and analysis of a bidirectional promoter between the OSGEP and APEX genes. Gene 285: 101-108.
43. Shendure, J. and Church, G.M. 2002. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 3: research0044.
44. Shklar, M., Strichman-Almashanu, L., Shmueli, O., Shmoish, M., Safran, M., and Lancet, D. 2005. GeneTide - Terra Incognita Discovery Endeavor: A new transcriptome focused member of the GeneCards/GeneNote suite of databases. Nucleic Acids Res. 33: D556-D561.
45. Shoemaker, D.D., Schadt, E.E., Armour, C.D., He, Y.D., Garrett-Engele, P., McDonagh, P.D., Loerch, P.M., Leonardson, A., Lum, P.Y., Cavet, G., et al. 2001. Experimental annotation of the human genome using microarray technology. Nature 409: 922-927.
46. Sleutels, F., Zwart, R., and Barlow, D.P. 2002. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415: 810-813.
47. Smith, M.L., Mitchell, P.J., and Crouse, G.F. 1990. Analysis of the mouse Dhfr/Rep-3 major promoter region by using linker-scanning and internal deletion mutations and DNase I footprinting. Mol. Cell. Biol. 10: 6003-6012.
48. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12: 1611-1618.
49. Strausberg, R.L., Feingold, E.A., Grouse, L.H., Derge, J.G., Klausner, R.D., Collins, F.S., Wagner, L., Shenmen, C.M., Schuler, G.D., Altschul, S.F., et al. 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl. Acad. Sci. 99: 16899-16903.
50. Suzuki, Y., Tsunoda, T., Sese, J., Taira, H., Mizushima-Sugano, J., Hata, H., Ota, T., Isogai, T., Tanaka, T., Nakamura, Y., et al. 2001. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11: 677-684.
51. Topper, J.N. and Clayton, D.A. 1990. Characterization of human MRP/Th RNA and its nuclear gene: Full length MRP/Th RNA is an active endoribonuclease when assembled as an RNP. Nucleic Acids Res. 18: 793-799.
52. Trinklein, N.D., Aldred, S.F., Hartman, S.J., Schroeder, D.I., Otillar, R.P., and Myers, R.M. 2004. An abundance of bidirectional promoters in the human genome. Genome Res. 14: 62-66.
53. Tufarelli, C., Stanley, J.A., Garrick, D., Sharpe, J.A., Ayyub, H., Wood, W.G., and Higgs, D.R. 2003. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet. 34: 157-165.
54. Veeramachaneni, V., Makalowski, W., Galdzicki, M., Sood, R., and Makalowska, I. 2004. Mammalian overlapping genes: The comparative perspective. Genome Res. 14: 280-286.
55. Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001. Spidey: A tool for mRNA-to-genomic alignments. Genome Res. 11: 1952-1957.
56. Yelin, R., Dahary, D., Sorek, R., Levanon, E.Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., et al. 2003. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21: 379-386.
57. http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker; RepeatMasker.
58. http://cgap.nci.nih.gov/Tissues/LibraryFinder; cDNA Library Finder.