Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Weikard, Rosemarie ^a   Goldammer, Tom ^a   Eberlein, Annett ^a   Kuehn, Christa ^a  

^a LEIBNIZ INSTITUTE FOR FARM ANIMAL BIOLOGY FBN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA; KV CHANNEL INTERACTING PROTEIN;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME 6; CONTROLLED STUDY; COW; EXON; EXON TRAPPING SEQUENCE; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; GENETIC TRANSCRIPTION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; QUANTITATIVE TRAIT LOCUS; SEQUENCE HOMOLOGY; ANIMAL; CATTLE; CHROMOSOME; CHROMOSOME 4; CHROMOSOME MAP; GENE EXPRESSION PROFILING; GENETICS; GENOME; GENOMICS; HUMAN; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SYNTENY;

BACTERIA (MICROORGANISMS); BOVINAE;

ANIMALS; CATTLE; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 4; CHROMOSOMES, MAMMALIAN; CLONING, MOLECULAR; DNA; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HUMANS; KV CHANNEL-INTERACTING PROTEINS; QUANTITATIVE TRAIT LOCI; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SYNTENY;

EID: 65649146487     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-186     Document Type: Article

References (66)

1. Reprogen QTL Map of Dairy Cattle Traits http://www.vetsci.usyd.edu.au/ reprogen/QTL_Map/
2. Bovine QTL Viewer at Texas A&M University http://genomes.sapac.edu.au/bovineqtl/
3. Cattle QTL database http://www.animalgenome.org/QTLdb/cattle.html
4. Itoh T Watanabe T Ihara N Mariani P Beattie CW Sugimoto Y Takasuga A A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci Genomics 2005, 85:413-424. 10.1016/j.ygeno.2004.12.007 15780744
5. Jann OC Aerts J Jones M Hastings N Law A McKay S Marques E Prasad A Yu J Moore SS Floriot S Mahe MF Eggen A Silveri L Negrini R Milanesi E jmone-Marsan P Valentini A Marchitelli C Savarese MC Janitz M Herwig R Hennig S Gorni C Connor EE Sonstegard TS Smith T Drogemuller C Williams JL A second generation radiation hybrid map to aid the assembly of the bovine genome sequence BMC Genomics 2006, 7:283. 1636650 17087818 10.1186/1471-2164-7-283
6. McKay SD Schnabel RD Murdoch BM Aerts J Gill CA Gao C Li C Matukumalli LK Stothard P Wang Z Van Tassell CP Williams JL Taylor JF Moore SS Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping Anim Genet 2007, 38:120-125. 2063635 17302794 10.1111/j.1365-2052.2006.01564.x
7. Weikard R Kühn C Goldammer T Laurent P Womack JE Schwerin M Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping Genomics 2002, 79:768-776. 10.1006/ geno.2002.6778 12036290
8. Weikard R Goldammer T Laurent P Womack JE Kuehn C A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits BMC Genomics 2006, 7:53. 1475854 16542434 10.1186/1471-2164-7-53
9. Weikard R Goldammer T Womack JE Kuehn C Forward to a detailed sequence map of bovine chromosome 6 Cytogenet Genome Res 2007, 116:72-79. 10.1159/ 000097420 17268181
10. Everts-van der Wind A Larkin DM Green CA Elliott JS Olmstead CA Chiu R Schein JE Marra MA Womack JE Lewin HA A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution Proc Natl Acad Sci USA 2005, 102:18526-18531. 1317968 16339895 10.1073/pnas.0509285102
11. Zhang Z Pang AWC Gerstein M Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human BMC Evol Biol 2007, 7(suppl 1):S14. 1796608 17288572 10.1186/ 1471-2148-7-S1-S14
12. Kumar CG Larson JH Band MR Lewin HA Discovery and characterization of 91 novel transcripts expressed in cattle placenta BMC Genomics 2007, 8:113. 1884150 17488528 10.1186/1471-2164-8-113
13. Larson JH Kumar CG Everts RE Green CA Everts-van der Wind A Band MR Lewin HA Discovery of eight novel divergent homologs expressed in cattle placenta Physiol Genomics 2006, 25:405-413. 10.1152/ physiolgenomics.00307.2005 16554549
14. Degrelle SA Campion E Cabau C Piumi F Reinaud P Richard C Renard JP Hue I Molecular evidence for a critical period in mural trophoblast development in bovine blastocysts Dev Biol 2005, 288:448-460. 10.1016/ j.ydbio.2005.09.043 16289134
15. Ghanem N Holker M Rings F Jennen D Tholen E Sirard MA Torner H Kanitz W Schellander K Tesfaye D Alterations in transcript abundance of bovine oocytes recovered at growth and dominance phases of the first follicular wave BMC Dev Biol 2007, 7:90. 1976425 17662127 10.1186/1471-213X-7-90
16. Roberts RM Ealy AD Alexenko AP Han CS Ezashi T Trophoblast interferons Placenta 1999, 20:259-264. 10.1053/plac.1998.0381 10329345
17. Holtenius P Holtenius K New aspects of ketone bodies in energy metabolism of dairy cows: A review J Vet Med A Physiol Pathol Clin Med 1996, 43:579-587.
18. Bell AW Bauman DE Adaptations of glucose metabolism during pregnancy and lactation J Mammary Gland Biol Neoplasia 1997, 2:265-278. 10.1023/ A:1026336505343 10882310
19. Vernon RG Pond CM Adaptations of maternal adipose tissue to lactation J Mammary Gland Biol Neoplasia 1997, 2:231-241. 10.1023/A:1026380220364 10882307
20. Vernon RG Lipid metabolism during lactation: A review of adipose tissue-liver interactions and the development of fatty liver J Dairy Res 2005, 72:460-469. 10.1017/S0022029905001299 16223462
21. Chagas LM Bass JJ Blache D Burke CR Kay JK Lindsay DR Lucy MC Martin GB Meier S Rhodes FM Roche JR Thatcher WW Webb R New perspectives on the roles of nutrition and metabolic priorities in the subfertility of high-producing dairy cows J Dairy Sci 2007, 90:4022-4032. 10.3168/ jds.2006-852 17699018
22. Buckler AJ Chang DD Graw SL Brook JD Haber DA Sharp PA Housman DE Exon Amplification - A Strategy to Isolate Mammalian Genes Based on RNA Splicing Proc Natl Acad Sci USA 1991, 88:4005-4009. 51582 1850845 10.1073/pnas.88.9.4005
23. Church DM Stotler CJ Rutter JL Murrell JR Trofatter JA Buckler AJ Isolation of Genes from Complex Sources of Mammalian Genomic DNA Using Exon Amplification Nature Genet 1994, 6:98-105. 10.1038/ng0194-98 8136842
24. Burn TC Connors TD Klinger KW Landes GM Increased Exon-Trapping Efficiency Through Modifications to the pSPL3 Splicing Vector Gene 1995, 161:183-187. 10.1016/0378-1119(95)00223-S 7665076
25. Korn B Sedlacek Z Kioschis P Konecki D Poustka A Establishment of An Xq27.3-Xqter Specific cDNA Library Using cDNA Selection Cytogenet Cell Genet 1994, 67:356.
26. Sedlacek Z Korn B Konecki DS Siebenhaar R Coy JF Kioschis P Poustka A Construction of A Transcription Map of A 300 Kb Region Around the Human G6PD Locus by Direct cDNA Selection Hum Mol Genet 1993, 2:1865-1869. 10.1093/hmg/2.11.1865 8281148
27. Yaspo ML Gellen L Mott R Korn B Nizetic D Poustka AM Lehrach H Model for A Transcript Map of Human-Chromosome-21 - Isolation of New Coding Sequences from Exon and Enriched cDNA Libraries Hum Mol Genet 1995, 4:1291-1304. 10.1093/hmg/4.8.1291 7581366
28. Lovett M Kere J Hinton LM Direct Selection - A Method for the Isolation of cDNAs Encoded by Large Genomic Regions Proc Natl Acad Sci USA 1991, 88:9628-9632. 52771 1946378 10.1073/pnas.88.21.9628
29. Delmastro RG Wang LP Simmons AD Gallardo TD Clines GA Ashley JA Hilliard CJ Wasmuth JJ Mcpherson JD Lovett M Human Chromosome-Specific cDNA Libraries - New Tools for Gene Identification and Genome Annotation Genome Res 1995, 5:185-194. 10.1101/gr.5.2.185 9132272
30. Parimoo S Patanjali SR Shukla H Chaplin DD Weissman SM cDNA Selection - Efficient PCR Approach for the Selection of cDNAs Encoded in Large Chromosomal DNA Fragments Proc Natl Acad Sci USA 1991, 88:9623-9627. 52770 1946377 10.1073/pnas.88.21.9623
31. NCBI Bos taurus Map Viewer of BTA6 http://www.ncbi.nlm.nih.gov/projects/ mapview/maps.cgi?taxid=9913&chr=6
32. RNAdb 2.0, BLAST Search http://jsm-research.imb.uq.edu.au/rnadb/ seqsearch/default.aspx
33. Tellam RL Capturing benefits from the bovine genome sequence Aust J Exp Agr 2007, 47:1039-1050. 10.1071/EA06032
34. Hillier LW Graves TA Fulton RS Fulton LA Pepin KH Minx P Wagner-McPherson C Layman D Wylie K Sekhon M Becker MC Fewell GA Delehaunty KD Miner TL Nash WE Kremitzki C Oddy L Du H Sun H Bradshaw-Cordum H Ali J Carter J Cordes M Harris A Isak A van Brunt A Nguyen C Du FY Courtney L Kalicki J Ozersky P Abbott S Armstrong J Belter EA Caruso L Cedroni M Cotton M Davidson T Desai A Elliott G Erb T Fronick C Gaige T Haakenson W Haglund K Holmes A Harkins R Kim K Kruchowski SS Strong CM Grewal N Goyea E Hou S Levy A Martinka S Mead K McLellan MD Meyer R Maher JR Tomlinson C Kohlberg SD Kozlowicz-Reilly A Shah N Swearengen-Shahid S Snider J Strong JT Thompson J Yoakum M Leonard S Pearman C Trani L Radionenko M Waligorski JE Wang CY Rock SM Tin-Wollam AM Maupin R Latreille P Wendl MC Yang SP Pohl C Wallis JW Spieth J Bieri TA Berkowicz N Nelson JO Osborne J Ding L Meyer R Sabo A Shotland Y Sinha P Wohldmann PE Cook LL Hickenbotham MT Eldred J Williams D Jones TA She XW et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Nature 2005, 434:724-731. 10.1038/nature03466 15815621
35. Ovcharenko I Loots GG Nobrega MA Hardison RC Miller W Stubbs L Evolution and functional classification of vertebrate gene deserts Genome Res 2005, 15:137-145. 540279 15590943 10.1101/gr.3015505
36. Gerstein MB Bruce C Rozowsky JS Zheng DY Du J Korbel JO Emanuelsson O Zhang ZDD Weissman S Snyder M What is a gene, post-ENCODE? History and updated definition Genome Res 2007, 17:669-681. 10.1101/gr.6339607 17567988
37. Zheng DY Gerstein MB The ambiguous boundary between genes and pseudogenes: The dead rise up, or do they? Trends Genet 2007, 23:219-224. 10.1016/j.tig.2007.03.003 17382428
38. Seemann SE Gilchrist MJ Hofacker IL Stadler PF Gorodkin J Detection of RNA structures in porcine EST data and related mammals BMC Genomics 2007, 8:316. 2072958 17845718 10.1186/1471-2164-8-316
39. Choy KW Wang CC Ogura A Lau TK Rogers MS Ikeo K Gojobori T Lam DSC Pang CP Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes Physiol Genomics 2006, 25:9-15. 10.1152/ physiolgenomics.00121.2005 16368877
40. Peters BA Croix BS Sjoblom T Cummins JM Silliman N Ptak J Saha S Kinzler KW Hatzis C Velculescu VE Large-scale identification of novel transcripts in the human genome Genome Res 2007, 17:287-292. 1800919 17267814 10.1101/gr.5486607
41. Carninci P Hayashizaki Y Noncoding RNA transcription beyond annotated genes Current Opinion in Genetics & Development 2007, 17:139-144. 10.1016/j.gde.2007.02.008 17317145
42. Birney E Stamatoyannopoulos JA Dutta A Guigo R Gingeras TR Margulies EH Weng ZP Snyder M Dermitzakis ET Stamatoyannopoulos JA Thurman RE Kuehn MS Taylor CM Neph S Koch CM Asthana S Malhotra A Adzhubei I Greenbaum JA Andrews RM Flicek P Boyle PJ Cao H Carter NP Clelland GK Davis S Day N Dhami P Dillon SC Dorschner MO Fiegler H Giresi PG Goldy J Hawrylycz M Haydock A Humbert R James KD Johnson BE Johnson EM Frum TT Rosenzweig ER Karnani N Lee K Lefebvre GC Navas PA Neri F Parker SCJ Sabo PJ Sandstrom R Shafer A Vetrie D Weaver M Wilcox S Yu M Collins FS Dekker J Lieb JD Tullius TD Crawford GE Sunyaev S Noble WS Dunham I Dutta A Guigo R Denoeud F Reymond A Kapranov P Rozowsky J Zheng DY Castelo R Frankish A Harrow J Ghosh S Sandelin A Hofacker IL Baertsch R Keefe D Flicek P Dike S Cheng J Hirsch HA Sekinger EA Lagarde J Abril JF Shahab A Flamm C Fried C Hackermuller J Hertel J Lindemeyer M Missal K Tanzer A Washietl S Korbel J Emanuelsson O Pedersen JS Holroyd N Taylor R Swarbreck D et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447:799-816. 2212820 17571346 10.1038/nature05874
43. Pheasant M Mattick JS Raising the estimate of functional human sequences Genome Res 2007, 17:1245-1253. 10.1101/gr.6406307 17690206
44. Soares LMM Valcarcel J The expanding transcriptome: The genome as the 'Book of Sand' EMBO J 2006, 25:923-931. 1409726 16511566 10.1038/ sj.emboj.7601023
45. Cheng J Kapranov P Drenkow J Dike S Brubaker S Patel S Long J Stern D Tammana H Helt G Sementchenko V Piccolboni A Bekiranov S Bailey DK Ganesh M Ghosh S Bell I Gerhard DS Gingeras TR Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution Science 2005, 308:1149-1154. 10.1126/science.1108625 15790807
46. Gingeras TR Origin of phenotypes: Genes and transcripts Genome Res 2007, 17:682-6906. 10.1101/gr.6525007 17567989
47. Mattick JS Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms Bioessays 2003, 25:930-939. 10.1002/bies.10332 14505360
48. Mattick JS Makunin IV Non-coding RNA Hum Mol Genet 2006, 15:R17-R29. 10.1093/hmg/ddl046 16651366
49. Carninci P Constructing the landscape of the mammalian transcriptome J Exp Biol 2007, 210:1497-1506. 10.1242/jeb.000406 17449815
50. Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C Kodzius R Shimokawa K Bajic VB Brenner SE Batalov S Forrest ARR Zavolan M Davis MJ Wilming LG Aidinis V Allen JE mbesi-Impiombato X Apweiler R Aturaliya RN Bailey TL Bansal M Baxter L Beisel KW Bersano T Bono H Chalk AM Chiu KP Choudhary V Christoffels A Clutterbuck DR Crowe ML Dalla E Dalrymple BP de Bono B la Gatta G di Bernardo D Down T Engstrom P Fagiolini M Faulkner G Fletcher CF Fukushima T Furuno M Futaki S Gariboldi M Georgii-Hemming P Gingeras TR Gojobori T Green RE Gustincich S Harbers M Hayashi Y Hensch TK Hirokawa N Hill D Huminiecki L Iacono M Ikeo K Iwama A Ishikawa T Jakt M Kanapin A Katoh M Kawasawa Y Kelso J Kitamura H Kitano H Kollias G Krishnan SPT Kruger A Kummerfeld SK Kurochkin IV Lareau LF Lazarevic D Lipovich L Liu J Liuni S McWilliam S Babu MM Madera M Marchionni L Matsuda H Matsuzawa S Miki H Mignone F Miyake S Morris K Mottagui-Tabar S Mulder N Nakano N Nakauchi H Ng P Nilsson R Nishiguchi S et al. FANTOM Consortium, RIKEN Genome Explorat Res Grp The transcriptional landscape of the mammalian genome Science 2005, 309:1559-1563. 10.1126/science.1112014 16141072
51. Glazier AM Nadeau JH Aitman TJ Finding genes that underlie complex traits Science 2002, 298:2345-2349. 10.1126/science.1076641 12493905
52. Georges M Mapping, fine mapping, and molecular dissection of quantitative trait loci in domestic animals Annu Rev Genomics Hum Genet 2007, 8:131-62. 10.1146/annurev.genom.8.080706.092408 17477823
53. Stark A Lin MF Kheradpour P Pedersen JS Parts L Carlson JW Crosby MA Rasmussen MD Roy S Deoras AN Ruby JG Brennecke J Hodges E Hinrichs AS Caspi A Park SW Han MV Maeder ML Polansky BJ Robson BE Aerts S van Helden J Hassan B Gilbert DG Eastman DA Rice M Weir M Hahn MW Park Y Dewey CN Pachter L Kent WJ Haussler D Lai EC Bartel DP Hannon GJ Kaufman TC Eisen MB Clark AG Smith D Celniker SE Gelbart WM Kellis M Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures Nature 2007, 450:219-232. 2474711 17994088 10.1038/nature06340
54. Siepel A Diekhans M Brejova B Langton L Stevens M Comstock CLG Davis C Ewing B Oommen S Lau C Yu HC Li JF Roe BA Green P Gerhard DS Temple G Haussler D Brent MR Targeted discovery of novel human exons by comparative genomics Genome Res 2007, 17:1763-1773. 2099585 17989246 10.1101/gr.7128207
55. BovineGenome.Org http://genomes.arc.georgetown.edu/bovine/ annotation_information.html
56. ImaGenes http://www.imagenes-bio.de/
57. Weikard R Goldammer T Kühn C Barendse W Schwerin M Targeted development of microsatellite markers from the defined region of bovine chromosome 6q21-31 Mamm Genome 1997, 8:836-840. 10.1007/s003359900588 9337396
58. Brunner RM Sanftleben H Goldammer T Kühn C Weikard R Kata SR Womack JE Schwerin M The telomeric region of BTA18 containing a potential QTL region for health in cattle exhibits high similarity to the HSA19q region in humans Genomics 2003, 81:270-278. 10.1016/ S0888-7543(03)00019-3 12659811
59. Brennan MB Hochgeschwender U So Many Needles, So Much Hay Hum Mol Genet 1995, 4:153-156. 10.1093/hmg/4.2.153 7757061
60. Burn TC Connors TD VanRaay TJ Dackowski WR Millholland JM Klinger KW Landes GM Generation of a transcriptional map for a 700-kb region surrounding the polycystic kidney disease type 1 (PKD1) and tuberous sclerosis type 2 (TSC2) disease genes on human chromosome 16p13.3 Genome Res 1996, 6:525-537. 10.1101/gr.6.6.525 8828041
61. NCBI Bos taurus BLAST Search Home Page http://www.ncbi.nlm.nih.gov/ genome/seq/BlastGen/BlastGen.cgi?taxid=9913
62. NCBI Human BLAST Search Home Page http://www.ncbi.nlm.nih.gov/genome/seq/ BlastGen/BlastGen.cgi?taxid=9606
63. NCBI Mouse BLAST Search Home Page http://www.ncbi.nlm.nih.gov/genome/seq/ BlastGen/BlastGen.cgi?taxid=10090)
64. ORF Finder http://www.ncbi.nlm.nih.gov/gorf/
65. NCBI BLASTN Search Site http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi
66. Weikard R Kuhn C Goldammer T Freyer G Schwerin M The bovine PPARGC1A gene: Molecular characterization and association of an SNP with variation of milk fat synthesis Physiol Genomics 2005, 21:1-13. 10.1152/ physiolgenomics.00103.2004 15781588