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  1. Article ; Online: Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

    Eberlein Annett / Goldammer Tom / Weikard Rosemarie / Kuehn Christa

    BMC Genomics, Vol 10, Iss 1, p

    2009  Volume 186

    Abstract: Abstract Background Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the ... ...

    Abstract Abstract Background Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC) clones mapped to the QTL intervals. Results Using the method of exon trapping, 92 unique exon trapping sequences (ETS) were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84%) displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome. Conclusion The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a distinctive tissue-specific expression profile. However, their definite regulatory function has to be analyzed in further studies. The novel transcripts will add new sequence information to annotate a complete bovine genome sequence assembly, contribute to establish a detailed transcription map for targeted BTA6 regions and will also be helpful to dissect of the molecular and regulatory background of the QTL detected on BTA6.
    Keywords Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
    Subject code 572
    Language English
    Publishing date 2009-04-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6.

    Weikard, Rosemarie / Goldammer, Tom / Eberlein, Annett / Kuehn, Christa

    BMC genomics

    2009  Volume 10, Page(s) 186

    Abstract: Background: Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the QTL and ...

    Abstract Background: Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC) clones mapped to the QTL intervals.
    Results: Using the method of exon trapping, 92 unique exon trapping sequences (ETS) were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84%) displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome.
    Conclusion: The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a distinctive tissue-specific expression profile. However, their definite regulatory function has to be analyzed in further studies. The novel transcripts will add new sequence information to annotate a complete bovine genome sequence assembly, contribute to establish a detailed transcription map for targeted BTA6 regions and will also be helpful to dissect of the molecular and regulatory background of the QTL detected on BTA6.
    MeSH term(s) Animals ; Cattle/genetics ; Chromosome Mapping/methods ; Chromosomes, Artificial, Bacterial/genetics ; Chromosomes, Human, Pair 4/genetics ; Chromosomes, Mammalian/genetics ; Cloning, Molecular ; DNA/genetics ; Gene Expression Profiling/methods ; Genome ; Genomics/methods ; Humans ; Kv Channel-Interacting Proteins/genetics ; Quantitative Trait Loci/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Synteny
    Chemical Substances Kv Channel-Interacting Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2009-04-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/1471-2164-10-186
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  3. Article: Annotation of novel transcripts putatively relevant for bovine fat metabolism

    Eberlein, Annett / Kalbe, Claudia / Goldammer, Tom / Brunner, Ronald M / Kuehn, Christa / Weikard, Rosemarie

    Molecular biology reports. 2011 June, v. 38, no. 5

    2011  

    Abstract: Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal ... ...

    Abstract Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal muscle containing different amount of intramuscular fat in a pilot screening experiment. However, for both loci any role in the regulation of energy or fat metabolism is not yet described. In this study, we validated and refined gene structure, screened for mRNA splice variants and analyzed the tissue-specific gene expression patterns of both loci as a prerequisite to elucidate their potential physiological function. Based on comparative sequence analysis, a new full-length gene model for the bovine IRAK1 gene was developed and confirmed experimentally. Expression of IRAK1 mRNA was found in a variety of tissues, and a splice variant was identified in skeletal muscle caused by an in-frame deleted segment of 210 bp affecting regions of intrinsic disorder in the respective protein. For the locus LOC618944, our data contributed to a revised gene model and its assignment to BTA23 (bovine chromosome 23) on the current bovine genome assembly supported by comparative similarity analysis between the bovine and human genomes and experimental data. Furthermore, we identified several splice variants in mammary gland, fat and skeletal muscle tissue and detected a highly similar processed pseudogene on BTA26. All transcript variants of LOC618944 detected in the analyzed tissues represent noncoding RNAs. For both loci, our results suggest yet undetected physiological functions in tissues relevant for fat or energy metabolism in cattle.
    Keywords cattle ; energy metabolism ; gene expression ; genome assembly ; intramuscular fat ; lipid metabolism ; loci ; messenger RNA ; open reading frames ; pseudogenes ; skeletal muscle
    Language English
    Dates of publication 2011-06
    Size p. 2975-2986.
    Publisher Springer Netherlands
    Publishing place Dordrecht
    Document type Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-010-9962-z
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  4. Article ; Online: Annotation of novel transcripts putatively relevant for bovine fat metabolism.

    Eberlein, Annett / Kalbe, Claudia / Goldammer, Tom / Brunner, Ronald M / Kuehn, Christa / Weikard, Rosemarie

    Molecular biology reports

    2010  Volume 38, Issue 5, Page(s) 2975–2986

    Abstract: Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal ... ...

    Abstract Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal muscle containing different amount of intramuscular fat in a pilot screening experiment. However, for both loci any role in the regulation of energy or fat metabolism is not yet described. In this study, we validated and refined gene structure, screened for mRNA splice variants and analyzed the tissue-specific gene expression patterns of both loci as a prerequisite to elucidate their potential physiological function. Based on comparative sequence analysis, a new full-length gene model for the bovine IRAK1 gene was developed and confirmed experimentally. Expression of IRAK1 mRNA was found in a variety of tissues, and a splice variant was identified in skeletal muscle caused by an in-frame deleted segment of 210 bp affecting regions of intrinsic disorder in the respective protein. For the locus LOC618944, our data contributed to a revised gene model and its assignment to BTA23 (bovine chromosome 23) on the current bovine genome assembly supported by comparative similarity analysis between the bovine and human genomes and experimental data. Furthermore, we identified several splice variants in mammary gland, fat and skeletal muscle tissue and detected a highly similar processed pseudogene on BTA26. All transcript variants of LOC618944 detected in the analyzed tissues represent noncoding RNAs. For both loci, our results suggest yet undetected physiological functions in tissues relevant for fat or energy metabolism in cattle.
    MeSH term(s) Alternative Splicing ; Animals ; Cattle ; Chromosome Mapping ; Energy Metabolism ; Gene Expression Profiling ; Humans ; Interleukin-1 Receptor-Associated Kinases/genetics ; Lipid Metabolism/genetics ; Models, Genetic ; Molecular Sequence Data ; Muscle, Skeletal/anatomy & histology ; Muscle, Skeletal/physiology ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances RNA, Messenger ; Interleukin-1 Receptor-Associated Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2010-02-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-010-9962-z
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  5. Article ; Online: Analysis of structure and gene expression of bovine CCDC3 gene indicates a function in fat metabolism.

    Eberlein, Annett / Kalbe, Claudia / Goldammer, Tom / Brunner, Ronald M / Kuehn, Christa / Weikard, Rosemarie

    Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology

    2010  Volume 156, Issue 1, Page(s) 19–25

    Abstract: Our study reports the molecular analysis of the bovine gene encoding the coiled-coil domain-containing protein 3 (CCDC3). Based on comparative sequence analysis and in silico sequence merging of predicted gene models, a new full-length gene model for the ...

    Abstract Our study reports the molecular analysis of the bovine gene encoding the coiled-coil domain-containing protein 3 (CCDC3). Based on comparative sequence analysis and in silico sequence merging of predicted gene models, a new full-length gene model for the bovine CCDC3 gene was predicted and confirmed experimentally. The CCDC3 gene was assigned to bovine chromosome 13. It consists of three exons comprising 2599bp encoding for a respective protein of 274 amino acids. The strong CCDC3 sequence homology on amino acid level between species suggests a conserved universal function of this protein. In mice, the CCDC3 gene had been found to be highly expressed in adipocytes and regulated by hormonal-nutritional alternations and in obesity. The tissue expression pattern of bovine CCDC3 mRNA indicates a ubiquitous physiological function of the gene. Significant differences in CCDC3 mRNA expression in skeletal muscle between individuals characterized by divergent intramuscular fat deposition support the potential function of the gene in fat or energy metabolism, which possibly could also be inferred for other mammalian species. This first report of structural analysis and molecular characterization of the CCDC3 gene in cattle will contribute to a better understanding of the yet unknown physiological role of the respective protein in mammals.
    MeSH term(s) Amino Acid Sequence ; Animals ; Cattle/genetics ; Cattle/metabolism ; Exons ; Gene Expression ; Lipid Metabolism/genetics ; Models, Genetic ; Molecular Sequence Data ; Proteins/genetics ; RNA, Messenger/metabolism ; Sequence Alignment
    Chemical Substances Proteins ; RNA, Messenger
    Language English
    Publishing date 2010-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 121247-3
    ISSN 1879-1107 ; 0305-0491 ; 1096-4959
    ISSN (online) 1879-1107
    ISSN 0305-0491 ; 1096-4959
    DOI 10.1016/j.cbpb.2010.01.013
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  6. Article ; Online: Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene.

    Eberlein, Annett / Takasuga, Akiko / Setoguchi, Kouji / Pfuhl, Ralf / Flisikowski, Krzysztof / Fries, Ruedi / Klopp, Norman / Fürbass, Rainer / Weikard, Rosemarie / Kühn, Christa

    Genetics

    2009  Volume 183, Issue 3, Page(s) 951–964

    Abstract: The increasing evidence of fetal developmental effects on postnatal life, the still unknown fetal growth mechanisms impairing offspring generated by somatic nuclear transfer techniques, and the impact on stillbirth and dystocia in conventional ... ...

    Abstract The increasing evidence of fetal developmental effects on postnatal life, the still unknown fetal growth mechanisms impairing offspring generated by somatic nuclear transfer techniques, and the impact on stillbirth and dystocia in conventional reproduction have generated increasing attention toward mammalian fetal growth. We identified a highly significant quantitative trait locus (QTL) affecting fetal growth on bovine chromosome 6 in a specific resource population, which was set up by consistent use of embryo transfer and foster mothers and, thus, enabled dissection of fetal-specific genetic components of fetal growth. Merging our data with results from other cattle populations differing in historical and geographical origin and with comparative data from human whole-genome association mapping suggests that a nonsynonymous polymorphism in the non-SMC condensin I complex, subunit G (NCAPG) gene, NCAPG c.1326T>G, is the potential cause of the identified QTL resulting in divergent bovine fetal growth. NCAPG gene expression data in fetal placentomes with different NCAPG c.1326T>G genotypes, which are in line with recent results about differential NCAPG expression in placentomes from studies on assisted reproduction techniques, indicate that the NCAPG locus may give valuable information on the specific mechanisms regulating fetal growth in mammals.
    MeSH term(s) Algorithms ; Animals ; Animals, Newborn ; Cattle/embryology ; Cattle/genetics ; Cell Cycle Proteins/genetics ; Chromosome Mapping/methods ; Female ; Fetal Development/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genotype ; Haplotypes ; Humans ; Male ; Models, Genetic ; Polymorphism, Single Nucleotide ; Pregnancy ; Quantitative Trait Loci/genetics ; Reverse Transcriptase Polymerase Chain Reaction
    Chemical Substances Cell Cycle Proteins
    Language English
    Publishing date 2009-08-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.109.106476
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  7. Article ; Online: The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    Elsik, Christine G / Tellam, Ross L / Worley, Kim C / Gibbs, Richard A / Muzny, Donna M / Weinstock, George M / Adelson, David L / Eichler, Evan E / Elnitski, Laura / Guigó, Roderic / Hamernik, Debora L / Kappes, Steve M / Lewin, Harris A / Lynn, David J / Nicholas, Frank W / Reymond, Alexandre / Rijnkels, Monique / Skow, Loren C / Zdobnov, Evgeny M /
    Schook, Lawrence / Womack, James / Alioto, Tyler / Antonarakis, Stylianos E / Astashyn, Alex / Chapple, Charles E / Chen, Hsiu-Chuan / Chrast, Jacqueline / Câmara, Francisco / Ermolaeva, Olga / Henrichsen, Charlotte N / Hlavina, Wratko / Kapustin, Yuri / Kiryutin, Boris / Kitts, Paul / Kokocinski, Felix / Landrum, Melissa / Maglott, Donna / Pruitt, Kim / Sapojnikov, Victor / Searle, Stephen M / Solovyev, Victor / Souvorov, Alexandre / Ucla, Catherine / Wyss, Carine / Anzola, Juan M / Gerlach, Daniel / Elhaik, Eran / Graur, Dan / Reese, Justin T / Edgar, Robert C / McEwan, John C / Payne, Gemma M / Raison, Joy M / Junier, Thomas / Kriventseva, Evgenia V / Eyras, Eduardo / Plass, Mireya / Donthu, Ravikiran / Larkin, Denis M / Reecy, James / Yang, Mary Q / Chen, Lin / Cheng, Ze / Chitko-McKown, Carol G / Liu, George E / Matukumalli, Lakshmi K / Song, Jiuzhou / Zhu, Bin / Bradley, Daniel G / Brinkman, Fiona S L / Lau, Lilian P L / Whiteside, Matthew D / Walker, Angela / Wheeler, Thomas T / Casey, Theresa / German, J Bruce / Lemay, Danielle G / Maqbool, Nauman J / Molenaar, Adrian J / Seo, Seongwon / Stothard, Paul / Baldwin, Cynthia L / Baxter, Rebecca / Brinkmeyer-Langford, Candice L / Brown, Wendy C / Childers, Christopher P / Connelley, Timothy / Ellis, Shirley A / Fritz, Krista / Glass, Elizabeth J / Herzig, Carolyn T A / Iivanainen, Antti / Lahmers, Kevin K / Bennett, Anna K / Dickens, C Michael / Gilbert, James G R / Hagen, Darren E / Salih, Hanni / Aerts, Jan / Caetano, Alexandre R / Dalrymple, Brian / Garcia, Jose Fernando / Gill, Clare A / Hiendleder, Stefan G / Memili, Erdogan / Spurlock, Diane / Williams, John L / Alexander, Lee / Brownstein, Michael J / Guan, Leluo / Holt, Robert A / Jones, Steven J M / Marra, Marco A / Moore, Richard / Moore, Stephen S / Roberts, Andy / Taniguchi, Masaaki / Waterman, Richard C / Chacko, Joseph / Chandrabose, Mimi M / Cree, Andy / Dao, Marvin Diep / Dinh, Huyen H / Gabisi, Ramatu Ayiesha / Hines, Sandra / Hume, Jennifer / Jhangiani, Shalini N / Joshi, Vandita / Kovar, Christie L / Lewis, Lora R / Liu, Yih-Shin / Lopez, John / Morgan, Margaret B / Nguyen, Ngoc Bich / Okwuonu, Geoffrey O / Ruiz, San Juana / Santibanez, Jireh / Wright, Rita A / Buhay, Christian / Ding, Yan / Dugan-Rocha, Shannon / Herdandez, Judith / Holder, Michael / Sabo, Aniko / Egan, Amy / Goodell, Jason / Wilczek-Boney, Katarzyna / Fowler, Gerald R / Hitchens, Matthew Edward / Lozado, Ryan J / Moen, Charles / Steffen, David / Warren, James T / Zhang, Jingkun / Chiu, Readman / Schein, Jacqueline E / Durbin, K James / Havlak, Paul / Jiang, Huaiyang / Liu, Yue / Qin, Xiang / Ren, Yanru / Shen, Yufeng / Song, Henry / Bell, Stephanie Nicole / Davis, Clay / Johnson, Angela Jolivet / Lee, Sandra / Nazareth, Lynne V / Patel, Bella Mayurkumar / Pu, Ling-Ling / Vattathil, Selina / Williams, Rex Lee / Curry, Stacey / Hamilton, Cerissa / Sodergren, Erica / Wheeler, David A / Barris, Wes / Bennett, Gary L / Eggen, André / Green, Ronnie D / Harhay, Gregory P / Hobbs, Matthew / Jann, Oliver / Keele, John W / Kent, Matthew P / Lien, Sigbjørn / McKay, Stephanie D / McWilliam, Sean / Ratnakumar, Abhirami / Schnabel, Robert D / Smith, Timothy / Snelling, Warren M / Sonstegard, Tad S / Stone, Roger T / Sugimoto, Yoshikazu / Takasuga, Akiko / Taylor, Jeremy F / Van Tassell, Curtis P / Macneil, Michael D / Abatepaulo, Antonio R R / Abbey, Colette A / Ahola, Virpi / Almeida, Iassudara G / Amadio, Ariel F / Anatriello, Elen / Bahadue, Suria M / Biase, Fernando H / Boldt, Clayton R / Carroll, Jeffery A / Carvalho, Wanessa A / Cervelatti, Eliane P / Chacko, Elsa / Chapin, Jennifer E / Cheng, Ye / Choi, Jungwoo / Colley, Adam J / de Campos, Tatiana A / De Donato, Marcos / Santos, Isabel K F de Miranda / de Oliveira, Carlo J F / Deobald, Heather / Devinoy, Eve / Donohue, Kaitlin E / Dovc, Peter / Eberlein, Annett / Fitzsimmons, Carolyn J / Franzin, Alessandra M / Garcia, Gustavo R / Genini, Sem / Gladney, Cody J / Grant, Jason R / Greaser, Marion L / Green, Jonathan A / Hadsell, Darryl L / Hakimov, Hatam A / Halgren, Rob / Harrow, Jennifer L / Hart, Elizabeth A / Hastings, Nicola / Hernandez, Marta / Hu, Zhi-Liang / Ingham, Aaron / Iso-Touru, Terhi / Jamis, Catherine / Jensen, Kirsty / Kapetis, Dimos / Kerr, Tovah / Khalil, Sari S / Khatib, Hasan / Kolbehdari, Davood / Kumar, Charu G / Kumar, Dinesh / Leach, Richard / Lee, Justin C-M / Li, Changxi / Logan, Krystin M / Malinverni, Roberto / Marques, Elisa / Martin, William F / Martins, Natalia F / Maruyama, Sandra R / Mazza, Raffaele / McLean, Kim L / Medrano, Juan F / Moreno, Barbara T / Moré, Daniela D / Muntean, Carl T / Nandakumar, Hari P / Nogueira, Marcelo F G / Olsaker, Ingrid / Pant, Sameer D / Panzitta, Francesca / Pastor, Rosemeire C P / Poli, Mario A / Poslusny, Nathan / Rachagani, Satyanarayana / Ranganathan, Shoba / Razpet, Andrej / Riggs, Penny K / Rincon, Gonzalo / Rodriguez-Osorio, Nelida / Rodriguez-Zas, Sandra L / Romero, Natasha E / Rosenwald, Anne / Sando, Lillian / Schmutz, Sheila M / Shen, Libing / Sherman, Laura / Southey, Bruce R / Lutzow, Ylva Strandberg / Sweedler, Jonathan V / Tammen, Imke / Telugu, Bhanu Prakash V L / Urbanski, Jennifer M / Utsunomiya, Yuri T / Verschoor, Chris P / Waardenberg, Ashley J / Wang, Zhiquan / Ward, Robert / Weikard, Rosemarie / Welsh, Thomas H / White, Stephen N / Wilming, Laurens G / Wunderlich, Kris R / Yang, Jianqi / Zhao, Feng-Qi

    Science (New York, N.Y.)

    2009  Volume 324, Issue 5926, Page(s) 522–528

    Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which ... ...

    Abstract To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
    MeSH term(s) Alternative Splicing ; Animals ; Animals, Domestic ; Biological Evolution ; Cattle ; Evolution, Molecular ; Female ; Genetic Variation ; Genome ; Humans ; Male ; MicroRNAs/genetics ; Molecular Sequence Data ; Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Synteny
    Chemical Substances MicroRNAs ; Proteins
    Language English
    Publishing date 2009-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1169588
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  8. Article: Annotation of novel transcripts putatively relevant for bovine fat metabolism

    Eberlein, Annett / Kalbe, Claudia / Goldammer, Tom / Brunner, Ronald M. / Kuehn, Christa / Weikard, Rosemarie

    Molecular biology reports

    Volume v. 38,, Issue no. 5

    Abstract: Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal ... ...

    Abstract Two bovine transcripts encoded by the interleukin-1 receptor-associated kinase 1 (IRAK1) gene and the locus LOC618944 predicted as similar to human chromosome 6 open reading frame 52 (C6orf52) gene had indicated divergent expression in bovine skeletal muscle containing different amount of intramuscular fat in a pilot screening experiment. However, for both loci any role in the regulation of energy or fat metabolism is not yet described. In this study, we validated and refined gene structure, screened for mRNA splice variants and analyzed the tissue-specific gene expression patterns of both loci as a prerequisite to elucidate their potential physiological function. Based on comparative sequence analysis, a new full-length gene model for the bovine IRAK1 gene was developed and confirmed experimentally. Expression of IRAK1 mRNA was found in a variety of tissues, and a splice variant was identified in skeletal muscle caused by an in-frame deleted segment of 210 bp affecting regions of intrinsic disorder in the respective protein. For the locus LOC618944, our data contributed to a revised gene model and its assignment to BTA23 (bovine chromosome 23) on the current bovine genome assembly supported by comparative similarity analysis between the bovine and human genomes and experimental data. Furthermore, we identified several splice variants in mammary gland, fat and skeletal muscle tissue and detected a highly similar processed pseudogene on BTA26. All transcript variants of LOC618944 detected in the analyzed tissues represent noncoding RNAs. For both loci, our results suggest yet undetected physiological functions in tissues relevant for fat or energy metabolism in cattle.
    Keywords open reading frames ; messenger RNA ; intramuscular fat ; genome assembly ; energy metabolism ; loci ; gene expression ; lipid metabolism ; cattle ; pseudogenes ; skeletal muscle
    Language English
    Document type Article
    ISSN 0301-4851
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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