Nested genes in the human genome

Genomics

Volumn 86, Issue 4, 2005, Pages 414-422

  Yu, Peng ^a,b   Ma, Dalong ^a,b   Xu, Mingxu ^a,b  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

Comparative analysis; Evolution; Gene within a gene; Inverse expression; Nested gene; Overlapping gene

Indexed keywords

ARTICLE; CHICKEN; DNA MICROARRAY; FISH; GENE; GENE EXPRESSION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CODE; GENETIC CONSERVATION; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; MICROARRAY ANALYSIS; NESTED GENE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOGENE; SIGNAL TRANSDUCTION; TISSUE SPECIFICITY;

ANIMALS; CHICKENS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENOME, HUMAN; HUMANS; INTRONS; MICE; MICROARRAY ANALYSIS; NESTED GENES; ORGAN SPECIFICITY; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY; TAKIFUGU;

EID: 33644549987     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2005.06.008     Document Type: Article

References (44)

1. S. Henikoff, M.A. Keene, K. Fechtel, and J.W. Fristrom Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands Cell 44 1986 33 42
2. B. Levinson, S. Kenwrick, D. Lakich, G. Hammonds Jr., and J. Gitschier A transcribed gene in an intron of the human factor VIII gene Genomics 7 1990 1 11
3. S. Misra Annotation of the Drosophila melanogaster euchromatic genome: a systematic review Genome Biol. 3 2002 0083.1-22
4. Dunham The DNA sequence of human chromosome 22 Nature 402 1999 489 495
5. S. Karlin, C. Chen, A.J. Gentles, and M. Cleary Associations between human disease genes and overlapping gene groups and multiple amino acid runs Proc. Natl. Acad. Sci. USA 99 2002 17008 17013
6. L.W. Hillier The DNA sequence of human chromosome 7 Nature 424 2003 157 164
7. J.P. Bachellerie, J. Cavaille, and A. Huttenhofer The expanding snoRNA world Biochimie 84 2002 775 790
8. T. Miyata, and T. Yasunaga Evolution of overlapping genes Nature 272 1978 532 535
9. V. Veeramachaneni, W. Makalowski, M. Galdzicki, R. Sood, and I. Makalowska Mammalian overlapping genes: the comparative perspective Genome Res. 14 2004 280 286
10. A.A. Habib, J.R. Gulcher, T. Hognason, L. Zheng, and K. Stefansson The OMgp gene, a second growth suppressor within the NF1 gene Oncogene 16 1998 1525 1531
11. T.A. Silverman, M. Noguchi, and B. Safer Role of sequences within the first intron in the regulation of expression of eukaryotic initiation factor 2 alpha J. Biol. Chem. 267 1992 9738 9742
12. Wutz Imprinted expression of the Igf2r gene depends on an intronic CpG island Nature 389 1997 745 749
13. C.M. Farrell, and L.N. Lukens 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 1995 3400 3408
14. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
15. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
16. K.D. Pruitt, T. Tatusova, and D.R. Maglott NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 33 2005 D501 D504
17. L. Benjamin Genes VII 2000 Oxford Univ. Press New York
18. M. Ashburner Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 25 2000 25 29
19. E. Camon The Gene Ontology Annotation (GOA) database: sharing knowledge in Uniprot with Gene Ontology Nucleic Acids Res. 32 2004 D262 D266
20. M. Clamp Ensembl 2002: accommodating comparative genomics Nucleic Acids Res. 31 2003 38 42
21. W.H. Li Molecular Evolution 1997 Sinauer Sunderland, MA
22. A.L. Hughes Adaptive Evolution of Genes and Genomes 1999 Oxford Univ. Press New York
23. F.A. Kondrashov, I.B. Rogozin, Y.I. Wolf, and E.V. Koonin Selection in the evolution of gene duplications Genome Biol. 3 2002 008.1-9
24. A.I. Su A gene atlas of the mouse and human protein-encoding transcriptomes Proc. Natl. Acad. Sci. USA 101 2004 6062 6067
25. S. Jenisch Corneodesmosin gene polymorphism demonstrates strong linkage disequilibrium with HLA and association with psoriasis vulgaris Tissue Antigens 54 1999 439 449
26. E. Levy-Nissenbaum Hypotrichosis simplex of the scalp is associated with nonsense mutations in CDSN encoding corneodesmosin Nat. Genet. 34 2003 151 153
27. H. Kiyosawa, I. Yamanaka, N. Osato, S. Kondo, and Y. Hayashizaki Antisense transcripts with FANTOM2 clone set and their implications for gene regulation Genome Res. 13 2003 1324 1334
28. R. Yelin Widespread occurrence of antisense transcription in the human genome Nat. Biotechnol. 21 2003 379 386
29. J. Chen Over 20% of human transcripts might form sense-antisense pairs Nucleic Acids Res. 32 2004 4812 4820
30. N. Terryn, and P. Rouze The sense of naturally transcribed antisense RNAs in plants Trends Plant Sci. 5 2000 394 396
31. S. Boi, G. Soldà, and M.L. Tenchini Shedding light on the dark side of the genome: overlapping genes in higher eukaryotes Curr. Genom. 5 2004 509 524
32. C. Vanhee-Brossollet, and C. Vaquero Do natural antisense transcripts make sense in eukaryotes? Gene 211 1998 1 9
33. Q. Wang, and G.G. Carmichael Effects of length and location on the cellular response to double-stranded RNA Microbiol. Mol. Biol. Rev. 68 2004 432 452
34. C.W. Gibson, N.H. Thomson, W.R. Abrams, and J. Kirkham Nested genes: biological implications and use of AFM for analysis Gene 2005 (E-publication ahead of print)
35. C. Esnault, J. Maestre, and T. Heidmann Human LINE retrotransposons generate processed pseudogenes Nat. Genet. 24 2000 363 367
36. H.H. Kazazian Jr. L1 retrotransposons shape the mammalian genome Science 289 2000 1152 1153
37. A.V. Rynditch, S. Zoubak, L. Tsyba, N. Tryapitsina-Guley, and G. Bernardi The regional integration of retroviral sequences into the mosaic genomes of mammals Gene 222 1998 1 16
38. W.J. Kent BLAT-The BLAST-like alignment tool Genome Res. 12 2002 656 664
39. D. Karolchik The UCSC Genome Browser Database Nucleic Acids Res. 31 2003 51 54
40. S. Schwartz Human-mouse alignments with BLASTZ Genome Res. 13 2003 103 107
41. Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci. 13 1997 555 556
42. G.M. Cooper Characterization of evolutionary rates and constraints in three mammalian genomes Genome Res. 14 2004 539 548
43. E.I. Boyle GOTermFinder-Open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes Bioinformatics 20 2004 3710 3715
44. M. Biswas Applications of InterPro in protein annotation and genome analysis Brief Bioinform. 3 2002 285 295