메뉴 건너뛰기




Volumn 2, Issue JAN, 2012, Pages

Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek's disease virus infection via analysis of allele-specific expression

Author keywords

Allelic imbalance; Genetic resistance; Marek's disease; RNA sequencing

Indexed keywords

ANIMALIA; GALLID HERPESVIRUS 2; GALLUS GALLUS; MARDIVIRUS;

EID: 84876040948     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00113     Document Type: Article
Times cited : (23)

References (42)
  • 1
    • 77955504378 scopus 로고    scopus 로고
    • Statistical design and analysis of RNA sequencing data
    • Auer, P. L., and Doerge, R. W. (2010). Statistical design and analysis of RNA sequencing data. Genetics 185, 405-416.
    • (2010) Genetics , vol.185 , pp. 405-416
    • Auer, P.L.1    Doerge, R.W.2
  • 2
    • 0034243928 scopus 로고    scopus 로고
    • A review of the development of chicken lines to resolve genes determining resistance to diseases
    • Bacon, L. D., Hunt, H. D., and Cheng, H. H. (2000). A review of the development of chicken lines to resolve genes determining resistance to diseases. Poult. Sci. 79, 1082-1093.
    • (2000) Poult. Sci. , vol.79 , pp. 1082-1093
    • Bacon, L.D.1    Hunt, H.D.2    Cheng, H.H.3
  • 3
    • 0028411397 scopus 로고
    • B haplotype influence on the relative efficacy of Mareks disease vaccines in commercial chickens
    • Bacon, L. D., and Witter, R. L. (1994). B haplotype influence on the relative efficacy of Mareks disease vaccines in commercial chickens. Poult. Sci. 73, 481-487.
    • (1994) Poult. Sci. , vol.73 , pp. 481-487
    • Bacon, L.D.1    Witter, R.L.2
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing.J. R. Stat. Soc. Series B Stat. Methodol. 57, 289-300.
    • (1995) J. R. Stat. Soc. Series B Stat. Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 0037177625 scopus 로고    scopus 로고
    • Genetic dissection of transcriptional regulation in budding yeast
    • Brem, R. B., Yvert, G., Clinton, R., and Kruglyak, L. (2002). Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755.
    • (2002) Science , vol.296 , pp. 752-755
    • Brem, R.B.1    Yvert, G.2    Clinton, R.3    Kruglyak, L.4
  • 9
    • 34547616453 scopus 로고    scopus 로고
    • Evidence for widespread epistatic interactions influencing Mareks disease virus viremia levels in chicken
    • Cheng, H. H., Zhang, Y., and Muir, W. M. (2007). Evidence for widespread epistatic interactions influencing Mareks disease virus viremia levels in chicken. Cytogenet. Genome Res. 117, 313-318.
    • (2007) Cytogenet. Genome Res. , vol.117 , pp. 313-318
    • Cheng, H.H.1    Zhang, Y.2    Muir, W.M.3
  • 12
    • 38549084066 scopus 로고    scopus 로고
    • Evaluating the role of natural selection in the evolution of gene regulation
    • Fay, J. C., and Wittkopp, P. J. (2008). Evaluating the role of natural selection in the evolution of gene regulation. Heredity 100,191-199.
    • (2008) Heredity , vol.100 , pp. 191-199
    • Fay, J.C.1    Wittkopp, P.J.2
  • 13
    • 0043237970 scopus 로고    scopus 로고
    • Early cell-mediated immune responses to Mareks disease virus in two chicken lines with defined major histocom-patibility complex antigens Vet
    • Garcia-Camacho, L., Schat, K. A., Brooks, R. Jr., and Bonous, D. I. (2003). Early cell-mediated immune responses to Mareks disease virus in two chicken lines with defined major histocom-patibility complex antigens. Vet. Immunol. Immunopathol. 95, 145-153.
    • (2003) Immunol. Immunopathol. , vol.95 , pp. 145-153
    • Garcia-Camacho, L.1    Schat, K.A.2    Brooks Jr, R.3    Bonous, D.I.4
  • 14
    • 38349171595 scopus 로고    scopus 로고
    • Cisand trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster
    • Genissel, A., McIntyre, L. M., Wayne, M. L.,andNuzhdin,S.V. (2008). Cisand trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster. Mol. Biol. Evol. 25, 101-110.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 101-110
    • Genissel, A.1    McIntyre, L.M.2    Wayne, M.L.3    Nuzhdin, S.V.4
  • 15
    • 66249122107 scopus 로고    scopus 로고
    • Mapping genes for complex traits in domestic animals and their use in breeding programmes
    • Goddard, M. E., and Hayes, B. J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10, 381-391.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 381-391
    • Goddard, M.E.1    Hayes, B.J.2
  • 16
    • 0004104039 scopus 로고
    • The effect of MHC on resistance to Mareks disease by White Leghorn crosses
    • Amsterdam
    • Groot, A. J. C., and Albers, G. A. A. (1992). "The effect of MHC on resistance to Mareks disease by White Leghorn crosses," in Proceedings of the Worlds Poultry Congress, Amsterdam, 185-188.
    • (1992) Proceedings of the Worlds Poultry Congress , pp. 185-188
    • Groot, A.J.C.1    Albers, G.A.A.2
  • 19
    • 61949109206 scopus 로고    scopus 로고
    • Mapping QTL affecting resistance to Mareks disease in an F6 advanced intercross population of commercial layer chickens
    • doi:10.1186/1471-2164-10-20
    • Heifetz, E. M., Fulton, J. E., OSullivan, N. P, Arthur, J. A., Cheng, H., Wang, J., Soller, M., and Dekkers, J. C. M. (2009). Mapping QTL affecting resistance to Mareks disease in an F6 advanced intercross population of commercial layer chickens. BMC Genomics 10, 20. doi:10.1186/1471-2164-10-20
    • (2009) BMC Genomics 10, 20
    • Heifetz, E.M.1    Fulton, J.E.2    O'Sullivan, N.P.3    Arthur, J.A.4    Cheng, H.5    Wang, J.6    Soller, M.7    Dekkers, J.C.M.8
  • 20
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 21
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King, M. C., and Wilson, A. C. (1975). Evolution at two levels in humans and chimpanzees. Science 188, 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 22
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 23
    • 0035543327 scopus 로고    scopus 로고
    • A strategy to identify positional candidate genes conferring Mareks disease resistant by integrating DNA microarrays and genetic mapping
    • Liu, H.C., Cheng, H. H., Softer, L., and Burnside, J. (2001a). A strategy to identify positional candidate genes conferring Mareks disease resistant by integrating DNA microarrays and genetic mapping. Anim. Genet. 32, 351-359.
    • (2001) Anim. Genet. , vol.32 , pp. 351-359
    • Liu, H.C.1    Cheng, H.H.2    Softer, L.3    Burnside, J.4
  • 24
    • 0035979222 scopus 로고    scopus 로고
    • Growth hormone interacts with the Mareks disease virus SORF2 protein and is associated with disease resistance in chicken
    • Liu, H.C., Kung, H.J., Fulton, J. E., Morgan, R. W., and Cheng, H. H. (2001b). Growth hormone interacts with the Mareks disease virus SORF2 protein and is associated with disease resistance in chicken. Proc. Natl. Acad. Sci. U.S.A. 98, 9203-9208.
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 9203-9208
    • Liu, H.C.1    Kung, H.J.2    Fulton, J.E.3    Morgan, R.W.4    Cheng, H.H.5
  • 25
    • 1442348217 scopus 로고    scopus 로고
    • Identification of chicken stem lymphocyte antigen 6 complex, locus E (LY6E, alias SCA2) as a putative Mareks disease resistance gene via a virus-host protein interaction screen
    • Liu, H.C., Niikura, M., Fulton, J., and Cheng, H. H. (2003). Identification of chicken stem lymphocyte antigen 6 complex, locus E (LY6E, alias SCA2) as a putative Mareks disease resistance gene via a virus-host protein interaction screen. Cytogenet. Genome Res. 102, 304-308.
    • (2003) Cytogenet. Genome Res. , vol.102 , pp. 304-308
    • Liu, H.C.1    Niikura, M.2    Fulton, J.3    Cheng, H.H.4
  • 26
    • 65649140354 scopus 로고    scopus 로고
    • Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bov-inae)
    • doi:10.1186/1471-2164-10-177
    • MacEachern, S., McEwan, J., and Goddard, M. (2009). Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bov-inae). BMC Genomics 10, 177. doi:10.1186/1471-2164-10-177
    • (2009) BMC Genomics , vol.10 , pp. 177
    • MacEachern, S.1    McEwan, J.2    Goddard, M.3
  • 30
    • 33846807478 scopus 로고    scopus 로고
    • Mareks disease virus up-regulates major his-tocompatibility complex class II cell surface expression in infected cells
    • Niikura, M., Kim, T., Hunt, H. D., Burn-side, J., Morgan, R. W., Dodgson, J. B., and Cheng, H. H. (2007). Mareks disease virus up-regulates major his-tocompatibility complex class II cell surface expression in infected cells. Virology 359, 212-219.
    • (2007) Virology , vol.359 , pp. 212-219
    • Niikura, M.1    Kim, T.2    Hunt, H.D.3    Burn-side, J.4    Morgan, R.W.5    Dodgson, J.B.6    Cheng, H.H.7
  • 31
    • 33748085349 scopus 로고    scopus 로고
    • Genomic inference of cis- regulatory nucleotide polymorphism underlying gene expression differences between Drosophila melanogaster mating races
    • Osada, M., Kohn, M. H., and Wu, C.-I. (2006). Genomic inference of cis- regulatory nucleotide polymorphism underlying gene expression differences between Drosophila melanogaster mating races. Mol. Biol. Evol. 23, 1585-1591.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1585-1591
    • Osada, M.1    Kohn, M.H.2    Wu, C.I.3
  • 32
    • 77954763156 scopus 로고    scopus 로고
    • Genome-wide allele-specific analysis: insights into regulatory variation
    • Pastinen, T. (2010). Genome-wide allele-specific analysis: insights into regulatory variation. Nat. Rev. Genet. 11, 533-538.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 533-538
    • Pastinen, T.1
  • 34
    • 44049100817 scopus 로고    scopus 로고
    • Tran-scriptional analysis of host responses to Mareks disease virus infection in genetically resistant and susceptible chickens
    • Sarson, A. J., Parvizi, P., Lepp, D., Quin-ton, M., and Sharif, S. (2008). Tran-scriptional analysis of host responses to Mareks disease virus infection in genetically resistant and susceptible chickens. Anim. Genet. 32, 232-240.
    • (2008) Anim. Genet. , vol.32 , pp. 232-240
    • Sarson, A.J.1    Parvizi, P.2    Lepp, D.3    Quin-ton, M.4    Sharif, S.5
  • 36
    • 40149090710 scopus 로고    scopus 로고
    • Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression
    • e1000006 doi:10.1371/journal.pgen.1000006
    • Serre, D., Gurd, S., Ge, B., Sladek, R., Sinnett, D., Harmsen, E., Bibikova, M., Chudin, E., Barker, D. L., Dickinson, T., Fan, J. B., and Hudson, T. J. (2008). Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet. 4, e1000006. doi:10.1371/journal.pgen.1000006
    • (2008) PLoS Genet , vol.4
    • Serre, D.1    Gurd, S.2    Ge, B.3    Sladek, R.4    Sinnett, D.5    Harmsen, E.6    Bibikova, M.7    Chudin, E.8    Barker, D.L.9    Dickinson, T.10    Fan, J.B.11    Hudson, T.J.12
  • 37
    • 0031908528 scopus 로고    scopus 로고
    • Genetic mapping of quantitative trait loci affecting susceptibility to Mareks disease virus induced tumors in F2 intercross chickens
    • Vallejo, R. L., Bacon, L. D., Liu, H.-C., Witter, R. L., Groenen, M. A. M., Hillel, J., and Cheng, H. H. (1998). Genetic mapping of quantitative trait loci affecting susceptibility to Mareks disease virus induced tumors in F2 intercross chickens. Genetics 148, 349-360.
    • (1998) Genetics , vol.148 , pp. 349-360
    • Vallejo, R.L.1    Bacon, L.D.2    Liu, H.C.3    Witter, R.L.4    Groenen, M.A.M.5    Hillel, J.6    Cheng, H.H.7
  • 38
    • 0030936371 scopus 로고    scopus 로고
    • Increased virulence of Mareks disease field isolates
    • Witter, R. L. (1997). Increased virulence of Mareks disease field isolates. Avian Dis. 41, 149-163.
    • (1997) Avian Dis , vol.41 , pp. 149-163
    • Witter, R.L.1
  • 39
    • 3042722019 scopus 로고    scopus 로고
    • Evolutionary changes in cis and trans gene regulation
    • Wittkopp, P. J., Haerum, B. L., and Clark, A. G. (2004). Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88.
    • (2004) Nature , vol.430 , pp. 85-88
    • Wittkopp, P.J.1    Haerum, B.L.2    Clark, A.G.3
  • 40
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray, G. A. (2007). The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8, 206-216.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 206-216
    • Wray, G.A.1
  • 41
    • 0033121006 scopus 로고    scopus 로고
    • Higher resolution mapping and identification of quantitative trait loci (QTL) affecting susceptibility to Mareks disease
    • Yonash, N., Bacon, L. D., Witter, R. L., and Cheng, H. H. (1999). Higher resolution mapping and identification of quantitative trait loci (QTL) affecting susceptibility to Mareks disease. Anim. Genet. 30, 126-135.
    • (1999) Anim. Genet. , vol.30 , pp. 126-135
    • Yonash, N.1    Bacon, L.D.2    Witter, R.L.3    Cheng, H.H.4
  • 42
    • 70350142925 scopus 로고    scopus 로고
    • Global analysis of allele-specific expression in Arabidopsis thaliana
    • Zhang, X., and Borevitz, J. O. (2009). Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182, 943-954.
    • (2009) Genetics , vol.182 , pp. 943-954
    • Zhang, X.1    Borevitz, J.O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.