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Volumn 9, Issue 3, 2017, Pages 619-626

Allele-specific expression analysis does not support sex chromosome inactivation on the chicken Z chromosome

Author keywords

Allele specific expression; Dosage compensation; Transcription

Indexed keywords

ALLELE; ANIMAL; CHICKEN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; SEX CHROMOSOME; X CHROMOSOME; X CHROMOSOME INACTIVATION;

EID: 85029638527     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evx031     Document Type: Article
Times cited : (17)

References (44)
  • 1
    • 84872503128 scopus 로고    scopus 로고
    • Y-chromosome evolution: Emerging insights into processes of Y-chromosome degeneration
    • Bachtrog D. 2013. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat Rev Genet. 14:113–124.
    • (2013) Nat Rev Genet , vol.14 , pp. 113-124
    • Bachtrog, D.1
  • 3
    • 85016183703 scopus 로고    scopus 로고
    • The X to autosome expression ratio in haploid and diploid human embryonic stem cells
    • Chen X, Zhang J. 2016. The X to autosome expression ratio in haploid and diploid human embryonic stem cells. Mol Biol Evol. 33:3104–3107.
    • (2016) Mol Biol Evol , vol.33 , pp. 3104-3107
    • Chen, X.1    Zhang, J.2
  • 4
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and VCFtools
    • Danecek P, et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156–2158.
    • (2011) Bioinformatics , vol.27 , pp. 2156-2158
    • Danecek, P.1
  • 5
    • 84859256941 scopus 로고    scopus 로고
    • Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective
    • DeVeale B, van der Kooy D, Babak T. 2012. Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet. 8:e1002600.
    • (2012) PLoS Genet , vol.8
    • DeVeale, B.1    Van Der Kooy, D.2    Babak, T.3
  • 6
    • 84961755772 scopus 로고    scopus 로고
    • Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
    • Dozmorov MG, et al. 2015. Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinformatics 16 Suppl 13:S10.
    • (2015) BMC Bioinformatics , vol.16 , pp. S10
    • Dozmorov, M.G.1
  • 7
    • 36849094065 scopus 로고    scopus 로고
    • Faced with inequality: Chicken do not have a general dosage compensation of sex-linked genes
    • Ellegren H, et al. 2007. Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes. BMC Biol. 5:40.
    • (2007) BMC Biol , vol.5 , pp. 40
    • Ellegren, H.1
  • 8
    • 84899023759 scopus 로고    scopus 로고
    • Transcriptome-wide investigation of genomic imprinting in chicken
    • Fresard L, et al. 2014. Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Res. 42:3768–3782.
    • (2014) Nucleic Acids Res , vol.42 , pp. 3768-3782
    • Fresard, L.1
  • 9
    • 84900417384 scopus 로고    scopus 로고
    • Avian sex, sex chromosomes, and dosage compensation in the age of genomics
    • Graves JA. 2014. Avian sex, sex chromosomes, and dosage compensation in the age of genomics. Chromosome Res. 22:45–57.
    • (2014) Chromosome Res , vol.22 , pp. 45-57
    • Graves, J.A.1
  • 10
    • 77955285002 scopus 로고    scopus 로고
    • Sex-specific parent-of-origin allelic expression in the mouse brain
    • Gregg C, Zhang J, Butler JE, Haig D, Dulac C. 2010a. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329:682–685.
    • (2010) Science , vol.329 , pp. 682-685
    • Gregg, C.1    Zhang, J.2    Butler, J.E.3    Haig, D.4    Dulac, C.5
  • 11
    • 77955299096 scopus 로고    scopus 로고
    • High-resolution analysis of parent-of-origin allelic expression in the mouse brain
    • Gregg C, et al. 2010b. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329:643–648.
    • (2010) Science , vol.329 , pp. 643-648
    • Gregg, C.1
  • 12
    • 85016219024 scopus 로고    scopus 로고
    • X-Chromosome dosage compensation
    • Chichester: John Wiley & Sons, Ltd.
    • He X, Zhang J. 2016. X-Chromosome dosage compensation. In: eLS. Chichester: John Wiley & Sons, Ltd. p. 1–7.
    • (2016) eLS , pp. 1-7
    • He, X.1    Zhang, J.2
  • 13
    • 84901675746 scopus 로고    scopus 로고
    • Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus
    • Hough J, Hollister JD, Wang W, Barrett SC, Wright SI. 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. Proc Natl Acad Sci U S A. 111:7713–7718.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 7713-7718
    • Hough, J.1    Hollister, J.D.2    Wang, W.3    Barrett, S.C.4    Wright, S.I.5
  • 14
    • 33947528380 scopus 로고    scopus 로고
    • Dosage compensation is less effective in birds than in mammals
    • Itoh Y, et al. 2007. Dosage compensation is less effective in birds than in mammals. J Biol. 6:2.
    • (2007) J Biol , vol.6 , pp. 2
    • Itoh, Y.1
  • 15
    • 77950657563 scopus 로고    scopus 로고
    • Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds
    • Itoh Y, et al. 2010. Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res. 20:512–518.
    • (2010) Genome Res , vol.20 , pp. 512-518
    • Itoh, Y.1
  • 16
    • 38949090440 scopus 로고    scopus 로고
    • Large-scale population study of human cell lines indicates that dosage compensation is virtually complete
    • Johnston CM, et al. 2008. Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet. 4:e9.
    • (2008) PLoS Genet , vol.4
    • Johnston, C.M.1
  • 17
    • 84861541065 scopus 로고    scopus 로고
    • Mechanisms and evolutionary patterns of mammalian and avian dosage compensation
    • Julien P, et al. 2012. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10:e1001328.
    • (2012) PLoS Biol , vol.10
    • Julien, P.1
  • 18
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 19
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li H, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 20
    • 84863955476 scopus 로고    scopus 로고
    • Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation
    • Lin F, Xing K, Zhang J, He X. 2012. Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation. Proc Natl Acad Sci U S A. 109:11752–11757.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 11752-11757
    • Lin, F.1    Xing, K.2    Zhang, J.3    He, X.4
  • 21
    • 38749117957 scopus 로고    scopus 로고
    • Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes
    • Lin H, et al. 2007. Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol. 5:e326.
    • (2007) PLoS Biol , vol.5
    • Lin, H.1
  • 23
    • 0033535478 scopus 로고    scopus 로고
    • X-chromosome inactivation
    • Lyon MF. 1999. X-chromosome inactivation. Curr Biol. 9:R235–R237.
    • (1999) Curr Biol , vol.9 , pp. R235-R237
    • Lyon, M.F.1
  • 24
    • 84859934498 scopus 로고    scopus 로고
    • Mediation of Drosophila autosomal dosage effects and compensation by network interactions
    • Malone JH, et al. 2012. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol. 13:r28.
    • (2012) Genome Biol , vol.13 , pp. r28
    • Malone, J.H.1
  • 25
    • 85011854458 scopus 로고    scopus 로고
    • The transcriptional architecture of phenotypic dimorphism
    • Mank JE. 2017. The transcriptional architecture of phenotypic dimorphism. Nat Ecol Evol. 1:0006.
    • (2017) Nat Ecol Evol , vol.1 , pp. 0006
    • Mank, J.E.1
  • 26
    • 84888136375 scopus 로고    scopus 로고
    • Sex chromosome dosage compensation: Definitely not for everyone
    • Mank JE. 2013. Sex chromosome dosage compensation: definitely not for everyone. Trends Genet. 29:677–683.
    • (2013) Trends Genet , vol.29 , pp. 677-683
    • Mank, J.E.1
  • 27
    • 65349150546 scopus 로고    scopus 로고
    • The W, X, Y and Z of sex-chromosome dosage compensation
    • Mank JE. 2009. The W, X, Y and Z of sex-chromosome dosage compensation. Trends Genet. 25:226–233.
    • (2009) Trends Genet , vol.25 , pp. 226-233
    • Mank, J.E.1
  • 28
    • 60549110047 scopus 로고    scopus 로고
    • All dosage compensation is local: Gene-by-gene regulation of sex-biased expression on the chicken Z chromosome
    • Mank JE, Ellegren H. 2009. All dosage compensation is local: gene-by-gene regulation of sex-biased expression on the chicken Z chromosome. Heredity (Edinburgh) 102:312–320.
    • (2009) Heredity (Edinburgh) , vol.102 , pp. 312-320
    • Mank, J.E.1    Ellegren, H.2
  • 29
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, et al. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303.
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 30
    • 77955188336 scopus 로고    scopus 로고
    • Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome
    • Moreira de Mello JC, et al. 2010. Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome. PLoS One 5:e10947.
    • (2010) PLoS One , vol.5
    • Moreira De Mello, J.C.1
  • 31
    • 0001732966 scopus 로고
    • Why polyploidy is rare in animals than in plants
    • Muller HJ. 1925. Why polyploidy is rare in animals than in plants. Am Nat. 59:346–353.
    • (1925) Am Nat , vol.59 , pp. 346-353
    • Muller, H.J.1
  • 32
    • 84938379720 scopus 로고    scopus 로고
    • Evolution of dosage compensation under sexual selection differs between X and Z chromosomes
    • Mullon C, Wright AE, Reuter M, Pomiankowski A, Mank JE. 2015. Evolution of dosage compensation under sexual selection differs between X and Z chromosomes. Nat Commun. 6:7720.
    • (2015) Nat Commun , vol.6 , pp. 7720
    • Mullon, C.1    Wright, A.E.2    Reuter, M.3    Pomiankowski, A.4    Mank, J.E.5
  • 33
    • 29444455049 scopus 로고    scopus 로고
    • Dosage compensation of the active X chromosome in mammals
    • Nguyen DK, Disteche CM. 2006. Dosage compensation of the active X chromosome in mammals. Nat Genet. 38:47–53.
    • (2006) Nat Genet , vol.38 , pp. 47-53
    • Nguyen, D.K.1    Disteche, C.M.2
  • 35
    • 70349673635 scopus 로고    scopus 로고
    • Lessons from comparative analysis of X-chromosome inactivation in mammals
    • Okamoto I, Heard E. 2009. Lessons from comparative analysis of X-chromosome inactivation in mammals. Chromosome Res. 17:659–669.
    • (2009) Chromosome Res , vol.17 , pp. 659-669
    • Okamoto, I.1    Heard, E.2
  • 36
    • 0942268864 scopus 로고    scopus 로고
    • Epigenetic dynamics of imprinted X inactivation during early mouse development
    • Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E. 2004. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303:644–649.
    • (2004) Science , vol.303 , pp. 644-649
    • Okamoto, I.1    Otte, A.P.2    Allis, C.D.3    Reinberg, D.4    Heard, E.5
  • 37
    • 84859448442 scopus 로고    scopus 로고
    • Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome
    • Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA. 2012. Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proc Natl Acad Sci U S A. 109:5346–5351.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 5346-5351
    • Pessia, E.1    Makino, T.2    Bailly-Bechet, M.3    McLysaght, A.4    Marais, G.A.5
  • 38
    • 2942538192 scopus 로고    scopus 로고
    • Reduced variation on the chicken Z chromosome
    • Sundstrom H, Webster MT, Ellegren H. 2004. Reduced variation on the chicken Z chromosome. Genetics 167:377–385.
    • (2004) Genetics , vol.167 , pp. 377-385
    • Sundstrom, H.1    Webster, M.T.2    Ellegren, H.3
  • 39
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 40
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 7:562–578.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 41
    • 84891706153 scopus 로고    scopus 로고
    • Chromosome-wide profiling of X-chromosome inactivation and epi-genetic states in fetal brain and placenta of the opossum, Monodelphis domestica
    • Wang X, Douglas KC, Vandeberg JL, Clark AG, Samollow PB. 2014. Chromosome-wide profiling of X-chromosome inactivation and epi-genetic states in fetal brain and placenta of the opossum, Monodelphis domestica. Genome Res. 24:70–83.
    • (2014) Genome Res , vol.24 , pp. 70-83
    • Wang, X.1    Douglas, K.C.2    Vandeberg, J.L.3    Clark, A.G.4    Samollow, P.B.5
  • 42
    • 84924872784 scopus 로고    scopus 로고
    • Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution
    • Wright AE, et al. 2015a. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Mol Ecol. 24:1218–1235.
    • (2015) Mol Ecol , vol.24 , pp. 1218-1235
    • Wright, A.E.1
  • 43
    • 84943650369 scopus 로고    scopus 로고
    • Conservation of regional variation in sex-specific sex chromosome regulation
    • Wright AE, Zimmer F, Harrison PW, Mank JE. 2015b. Conservation of regional variation in sex-specific sex chromosome regulation. Genetics 201:587–598.
    • (2015) Genetics , vol.201 , pp. 587-598
    • Wright, A.E.1    Zimmer, F.2    Harrison, P.W.3    Mank, J.E.4
  • 44
    • 85015353251 scopus 로고    scopus 로고
    • Compensation of dosage-sensitive genes on the chicken Z chromosome
    • Zimmer F, Harrison PW, Dessimoz C, Mank JE. 2016. Compensation of dosage-sensitive genes on the chicken Z chromosome. Genome Biol Evol. 8:1233–1242.
    • (2016) Genome Biol Evol , vol.8 , pp. 1233-1242
    • Zimmer, F.1    Harrison, P.W.2    Dessimoz, C.3    Mank, J.E.4


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