Conserved alternative and antisense transcripts at the programmed cell death 2 locus

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Mihola, Ondrej ^a   Forejt, Jiri ^a   Trachtulec, Zdenek ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; GENE PRODUCT; MESSENGER RNA; PROGRAMMED CELL DEATH 2 PROTEIN; PROTEIN PDCD2; TATA BINDING PROTEIN; UNCLASSIFIED DRUG; APOPTOSIS REGULATORY PROTEIN; PDCD2 PROTEIN, MOUSE;

ALLELE; ALTERNATIVE RNA SPLICING; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; APOPTOSIS; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL NUCLEUS; CONTROLLED STUDY; EXON; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DETERMINATION; PROTEIN DOMAIN; RNA ANALYSIS; SYNTENY; ANIMAL; CHICKEN; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; GENETICS; GENOME IMPRINTING; HUMAN; MALE; MOLECULAR GENETICS; POLYMERASE CHAIN REACTION; RAT;

ALLELES; ALTERNATIVE SPLICING; ANIMALS; APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; CHICKENS; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENOMIC IMPRINTING; HUMANS; MALE; MICE; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RATS; RNA, MESSENGER;

EID: 33847252918     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-20     Document Type: Article

References (51)

1. Trachtulec Z Forejt J Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast Mamm Genome 2001 12 227-231 10.1007/s003350010259 11252172
2. Trachtulec Z Mihola O Vlcek C Himmelbauer H Paces V Forejt J Positional cloning of the Hybrid sterility 1 gene: Fine genetic mapping and evaluation of two candidate genes Biol J Linn Soc 2005 84 637-641 10.1111/j.1095-8312.2005.00460.x
3. Trachtulec Z Vlcek C Mihola O Forejt J Comparative analysis of the PDCD2-TBP-PSMB1 region in vertebrates Gene 2004 335 151-157 10.1016/ j.gene.2004.03.021 15194198
4. Trachtulec Z Hamvas RM Forejt J Lehrach HR Vincek V Klein J Linkage of TATA-binding protein and proteasome subunit C5 genes in mice and humans reveals synteny conserved between mammals and invertebrates Genomics 1997 44 1-7 10.1006/geno.1997.4839 9286694
5. Owens GP Hahn WE Cohen JJ Identification of mRNAs associated with programmed cell death in immature thymocytes Mol Cell Biol 1991 11 4177-4188 361239 2072913
6. Woloschak GE Chang-Liu CM Panozzo J Libertin CR Low doses of neutrons induce changes in gene expression Radiat Res 1994 138 S56-59 10.2307/ 3578762 8146328
7. Shakib K Norman JT Fine LG Brown LR Godovac-Zimmermann J Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus Proteomics 2005 5 2819-2838 10.1002/pmic.200401108 15942958
8. Kaushik N Fear D Richards SC McDermott CR Nuwaysir EF Kellam P Harrison TJ Wilkinson RJ Tyrrell DA Holgate ST Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome J Clin Pathol 2005 58 826-832 10.1136/jcp.2005.025718 16049284
9. Vaux DL Hacker G Cloning of mouse RP-8 cDNA and its expression during apoptosis of lymphoid and myeloid cells DNA Cell Biol 1995 14 189-193 7880439
10. D'Mello SR Galli C SGP2, ubiquitin, 14 K lectin and RP8 mRNAs are not induced in neuronal apoptosis Neuroreport 1993 4 355-358 10.1097/ 00001756-199304000-00003 8388743
11. Chen Q Qian K Yan C Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells Mol Cell Biochem 2005 280 185-191 10.1007/s11010-005-8910-z 16311922
12. Baron BW Anastasi J Thirman MJ Furukawa Y Fears S Kim DC Simone F Birkenbach M Montag A Sadhu A The human programmed cell death-2 (PDCD2) gene is a target of BCL6 repression: Implications for a role of BCL6 in the down-regulation of apoptosis Proc Natl Acad Sci USA 2002 99 2860-2865 122438 11854457 10.1073/pnas.042702599
13. Kusam S Vasanwala FH Dent AL Transcriptional repressor BCL-6 immortalizes germinal center-like B cells in the absence of p53 function Oncogene 2004 23 839-844 10.1038/sj.onc.1207065 14737119
14. Scarr RB Sharp PA PDCD2 is a negative regulator of HCF-1 (C1) Oncogene 2002 21 5245-5254 10.1038/sj.onc.1205647 12149646
15. Steinemann D Gesk S Zhang Y Harder L Pilarsky C Hinzmann B Martin-Subero JI Calasanz MJ Mungall A Rosenthal A Identification of candidate tumor-suppressor genes in 6q27 by combined deletion mapping and electronic expression profiling in lymphoid neoplasms Genes Chromosomes Cancer 2003 37 421-426 10.1002/gcc.10231 12800155
16. Chistiakov DA Seryogin YA Turakulov RI Savost'anov KV Titovich EV Zilberman LI Kuraeva TL Dedov II Nosikov VV Evaluation of IDDM8 susceptibility locus in a Russian simplex family data set J Autoimmun 2005 24 243-250 10.1016/j.jaut.2005.01.017 15848047
17. Owerbach D Pina L Gabbay KH Association of a CAG/CAA repeat sequence in the TBP gene with type I diabetes Biochem Biophys Res Commun 2004 323 865-869 10.1016/j.bbrc.2004.08.159 15381080
18. Browning VL Bergstrom RA Daigle S Schimenti JC A haplolethal locus uncovered by deletions in the mouse T complex Genetics 2002 160 675-682 1461990 11861570
19. Bergstrom DE Bergstrom RA Munroe RJ Lee BK Browning VL You Y Eicher EM Schimenti JC Overlapping deletions spanning the proximal two-thirds of the mouse t complex Mamm Genome 2003 14 817-829 10.1007/ s00335-003-2298-4 14724736
20. Howell GR Munroe RJ Schimenti JC Transgenic rescue of the mouse t complex haplolethal locus Thl1 Mamm Genome 2005 16 838-846 10.1007/ s00335-005-0045-8 16284799
21. Nikaido I Saito C Mizuno Y Meguro M Bono H Kadomura M Kono T Morris GA Lyons PA Oshimura M Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling Genome Res 2003 13 1402-1409 403673 12819139 10.1101/gr.1055303
22. Kawaji H Kasukawa T Fukuda S Katayama S Kai C Kawai J Carninci P Hayashizaki Y CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis Nucleic Acids Res 2006 34 D632-636 1347397 16381948 10.1093/nar/gkj034
23. Munroe SH Lazar MA Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA J Biol Chem 1991 266 22083-22086 1657988
24. Murphy PR Knee RS Identification and characterization of an antisense RNA transcript (gfg) from the human basic fibroblast growth factor gene Mol Endocrinol 1994 8 852-859 10.1210/me.8.7.852 7984147
25. Wang Q Zhang Z Blackwell K Carmichael GG Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin Curr Biol 2005 15 384-391 10.1016/j.cub.2005.01.046 15723802
26. Carmichael GG Antisense starts making more sense Nat Biotechnol 2003 21 371-372 10.1038/nbt0403-371 12665819
27. Yamauchi J Sugita A Fujiwara M Suzuki K Matsumoto H Yamazaki T Ninomiya Y Ono T Hasegawa T Masushige S Two forms of avian(chicken) TATA-binding protein mRNA generated by alternative polyadenylation Biochem Biophys Res Commun 1997 234 406-411 10.1006/bbrc.1997.6653 9177284
28. Schmidt EE Schibler U High accumulation of components of the RNA polymerase II transcription machinery in rodent spermatids Development 1995 121 2373-2383 7671803
29. Su AI Cooke MP Ching KA Hakak Y Walker JR Wiltshire T Orth AP Vega RG Sapinoso LM Moqrich A Large-scale analysis of the human and mouse transcriptomes Proc Natl Acad Sci USA 2002 99 4465-4470 123671 11904358 10.1073/pnas.012025199
30. Forejt J Hybrid sterility gene located in the T/t- H-2 supergene on chromosome 17 Current trends in histocompatibility New York: Plenum Press Reisfeld S, Ferone RA 1981 103-131
31. Gregorova S Forejt J PWD/Ph and PWK/Ph inbred mouse strains of Mus m. musculus subspecies-a valuable resource of phenotypic variations and genomic polymorphisms Folia Biol (Praha) 2000 46 31-41 10730880
32. Hernandez N TBP, a universal eukaryotic transcription factor? Genes Dev 1993 7 1291-1308 8330735
33. Ruf N Dunzinger U Brinckmann A Haaf T Nurnberg P Zechner U Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes Genomics 2006 87 509-519 10.1016/ j.ygeno.2005.12.007 16455231
34. Pesole G Mignone F Gissi C Grillo G Licciulli F Liuni S Structural and functional features of eukaryotic mRNA untranslated regions Gene 2001 276 73-81 10.1016/S0378-1119(01)00674-6 11591473
35. Lavorgna G Dahary D Lehner B Sorek R Sanderson CM Casari G In search of antisense Trends Biochem Sci 2004 29 88-94 10.1016/j.tibs.2003.12.002 15102435
36. Lazar MA Thyroid hormone receptors: Multiple forms, multiple possibilities Endocr Rev 1993 14 184-193 10.1210/er.14.2.184 8325251
37. Knee R Murphy PR Regulation of gene expression by natural antisense RNA transcripts Neurochem Int 1997 31 379-392 10.1016/S0197-0186(96)00108-8 9246680
38. Namekawa SH Park PJ Zhang LF Shima JE McCarrey JR Griswold MD Lee JT Postmeiotic sex chromatin in the male germline of mice Curr Biol 2006 16 660-667 10.1016/j.cub.2006.01.066 16581510
39. Schmidt EE Schibler U Developmental testis-specific regulation of mRNA levels and mRNA translational efficiencies for TATA-binding protein mRNA isoforms Dev Biol 1997 184 138-149 10.1006/dbio.1997.8514 9142990
40. Nelson P Kiriakidou M Sharma A Maniataki E Mourelatos Z The microRNA world: Small is mighty Trends Biochem Sci 2003 28 534-540 10.1016/ j.tibs.2003.08.005 14559182
41. Good L Translation repression by antisense sequences Cell Mol Life Sci 2003 60 854-861 12827275
42. Werner A Natural antisense transcripts RNA Biol 2005 2 53-62 17132938
43. Werner A Berdal A Natural antisense transcripts: Sound or silence? Physiol Genomics 2005 23 125-131 10.1152/physiolgenomics.00124.2005 16230481
44. 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 21 379-386 10.1038/nbt808 12640466
45. 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
46. 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 1324-1334 403655 12819130 10.1101/gr.982903
47. 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 1564-1566 10.1126/science.1112009 16141073
48. 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 15 463-474 1074361 15781571 10.1101/gr.3155905
49. 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 1559-1563 10.1126/science.1112014 16141072
50. Dahary D Elroy-Stein O Sorek R Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res 2005 15 364-368 551562 15710751 10.1101/gr.3308405
51. Bastos H Lassalle B Chicheportiche A Riou L Testart J Allemand I Fouchet P Flow cytometric characterization of viable meiotic and postmeiotic cells by Hoechst 33342 in mouse spermatogenesis Cytometry A 2005 65 40-49 15779065