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Volumn 3, Issue 4, 2013, Pages 597-605

Genome-wide detection of gene coexpression domains showing linkage to regions enriched with polymorphic retrotransposons in recombinant inbred mouse strains

Author keywords

Clustering of; Coexpressed; Elements; Expression; Genes; Genetics of gene; Loci; Quantitative trait; Structural variants; Transposable

Indexed keywords

SPACER DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR GATA 4; TRANSCRIPTION FACTOR NKX2.5; TRANSCRIPTION FACTOR TBX5; CCCTC-BINDING FACTOR; REPRESSOR PROTEIN; RETROPOSON; TRANSPOSON;

EID: 84883240683     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.005546     Document Type: Article
Times cited : (8)

References (47)
  • 1
    • 44849120649 scopus 로고    scopus 로고
    • Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
    • Akagi, K., J. Li, R. M. Stephens, N. Volfovsky, and D. E. Symer, 2008 Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res. 18: 869-880.
    • (2008) Genome Res. , vol.18 , pp. 869-880
    • Akagi, K.1    Li, J.2    Stephens, R.M.3    Volfovsky, N.4    Symer, D.E.5
  • 2
    • 75549090942 scopus 로고    scopus 로고
    • MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains
    • Akagi, K., R. M. Stephens, J. Li, E. Evdokimov, M. R. Kuehn et al., 2010 MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains. Nucleic Acids Res. 38: D600-D606.
    • (2010) Nucleic Acids Res. , vol.38
    • Akagi, K.1    Stephens, R.M.2    Li, J.3    Evdokimov, E.4    Kuehn, M.R.5
  • 3
    • 77956641239 scopus 로고    scopus 로고
    • ChIPSeq identification of weakly conserved heart enhancers
    • Blow, M. J., D. J. McCulley, Z. Li, T. Zhang, J. A. Akiyama et al., 2010 ChIPSeq identification of weakly conserved heart enhancers. Nat. Genet. 42: 806-810.
    • (2010) Nat. Genet. , vol.42 , pp. 806-810
    • Blow, M.J.1    McCulley, D.J.2    Li, Z.3    Zhang, T.4    Akiyama, J.A.5
  • 4
    • 55549117831 scopus 로고    scopus 로고
    • Evolution of the mammalian transcription factor binding repertoire via transposable elements
    • Bourque, G., B. Leong, V. B. Vega, X. Chen, Y. L. Lee et al., 2008 Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 18: 1752-1762.
    • (2008) Genome Res. , vol.18 , pp. 1752-1762
    • Bourque, G.1    Leong, B.2    Vega, V.B.3    Chen, X.4    Lee, Y.L.5
  • 5
    • 84863879038 scopus 로고    scopus 로고
    • Fine-scale maps of recombination rates and hotspots in the mouse genome
    • Brunschwig, H., L. Levi, E. Ben-David, R. W. Williams, B. Yakir et al.,2012 Fine-scale maps of recombination rates and hotspots in the mouse genome. Genetics 191: 757-764.
    • (2012) Genetics , vol.191 , pp. 757-764
    • Brunschwig, H.1    Levi, L.2    Ben-David, E.3    Williams, R.W.4    Yakir, B.5
  • 6
    • 55549087533 scopus 로고    scopus 로고
    • B2 SINE retrotransposon causes polymorphic expression of mouse 5-aminolevulinic acid synthase 1 gene
    • Chernova, T., F. M. Higginson, R. Davies, and A. G. Smith, 2008 B2 SINE retrotransposon causes polymorphic expression of mouse 5-aminolevulinic acid synthase 1 gene. Biochem. Biophys. Res. Commun. 377: 515-520.
    • (2008) Biochem. Biophys. Res. Commun. , vol.377 , pp. 515-520
    • Chernova, T.1    Higginson, F.M.2    Davies, R.3    Smith, A.G.4
  • 7
    • 20144386111 scopus 로고    scopus 로고
    • Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function
    • Chesler, E. J., L. Lu, S. Shou, Y. Qu, J. Gu et al., 2005 Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet. 37: 233-242.
    • (2005) Nat. Genet. , vol.37 , pp. 233-242
    • Chesler, E.J.1    Lu, L.2    Shou, S.3    Qu, Y.4    Gu, J.5
  • 8
    • 84855886780 scopus 로고    scopus 로고
    • Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
    • Didion, J. P., H. Yang, K. Sheppard, C.-P. Fu, L. McMillan et al., 2012 Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics 13: 34.
    • (2012) BMC Genomics , vol.13 , pp. 34
    • Didion, J.P.1    Yang, H.2    Sheppard, K.3    Fu, C.-P.4    McMillan, L.5
  • 9
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J. R., S. Selvaraj, F. Yue, A. Kim, Y. Li et al., 2012 Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5
  • 10
    • 68449101067 scopus 로고    scopus 로고
    • Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
    • Durinck, S., P. T. Spellman, E. Birney, and W. Huber, 2009 Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4: 1184-1191.
    • (2009) Nat. Protoc. , vol.4 , pp. 1184-1191
    • Durinck, S.1    Spellman, P.T.2    Birney, E.3    Huber, W.4
  • 12
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium, 2012 An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 13
    • 70849129445 scopus 로고    scopus 로고
    • Retroelements and their impact on genome evolution and functioning
    • Gogvadze, E., and A. Buzdin, 2009 Retroelements and their impact on genome evolution and functioning. Cell. Mol. Life Sci. 66: 3727-3742.
    • (2009) Cell. Mol. Life Sci. , vol.66 , pp. 3727-3742
    • Gogvadze, E.1    Buzdin, A.2
  • 14
    • 34548719076 scopus 로고    scopus 로고
    • Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes
    • Göring, H. H. H., J. E. Curran, M. P. Johnson, T. D. Dyer, J. Charlesworth et al., 2007 Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat. Genet. 39: 1208-1216.
    • (2007) Nat. Genet. , vol.39 , pp. 1208-1216
    • Göring, H.H.H.1    Curran, J.E.2    Johnson, M.P.3    Dyer, T.D.4    Charlesworth, J.5
  • 16
    • 8644284670 scopus 로고    scopus 로고
    • Clustering,duplication and chromosomal distribution of mouse SINE retrotransposons
    • Jurka, J., O. Kohany, A. Pavlicek, V. V. Kapitonov, and M. V. Jurka, 2005 Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenet. Genome Res. 110: 117-123.
    • (2005) Cytogenet. Genome Res. , vol.110 , pp. 117-123
    • Jurka, J.1    Kohany, O.2    Pavlicek, A.3    Kapitonov, V.V.4    Jurka, M.V.5
  • 17
    • 0030738774 scopus 로고    scopus 로고
    • Evolution of B2 repeats: the muroid explosion
    • Kass, D. H., J. Kim, A. Rao, and P. L. Deininger, 1997 Evolution of B2 repeats: the muroid explosion. Genetica 99: 1-13.
    • (1997) Genetica , vol.99 , pp. 1-13
    • Kass, D.H.1    Kim, J.2    Rao, A.3    Deininger, P.L.4
  • 18
    • 0028877463 scopus 로고
    • Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results
    • Lander, E., and L. Kruglyak, 1995 Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 11: 241-247.
    • (1995) Nat. Genet. , vol.11 , pp. 241-247
    • Lander, E.1    Kruglyak, L.2
  • 19
    • 0036613754 scopus 로고    scopus 로고
    • Clustering of housekeeping genes provides a unified model of gene order in the human genome
    • Lercher, M. J., A. O. Urrutia, and L. D. Hurst, 2002 Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31: 180-183.
    • (2002) Nat. Genet. , vol.31 , pp. 180-183
    • Lercher, M.J.1    Urrutia, A.O.2    Hurst, L.D.3
  • 20
    • 84858439844 scopus 로고    scopus 로고
    • Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
    • Li, J., K. Akagi, Y. Hu, A. L. Trivett, C. J. W. Hlynialuk et al., 2012 Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome Res. 22: 870-884.
    • (2012) Genome Res. , vol.22 , pp. 870-884
    • Li, J.1    Akagi, K.2    Hu, Y.3    Trivett, A.L.4    Hlynialuk, C.J.W.5
  • 21
    • 35548932508 scopus 로고    scopus 로고
    • Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice
    • Llamas, B., S. Bélanger, S. Picard, and C. F. Deschepper, 2007 Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice. Physiol. Genomics 31: 176-182.
    • (2007) Physiol. Genomics , vol.31 , pp. 176-182
    • Llamas, B.1    Bélanger, S.2    Picard, S.3    Deschepper, C.F.4
  • 22
    • 65549169430 scopus 로고    scopus 로고
    • Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
    • Llamas, B., R. A. Verdugo, G. A. Churchill, and C. F. Deschepper, 2009 Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone. BMC Genomics 10: 150.
    • (2009) BMC Genomics , vol.10 , pp. 150
    • Llamas, B.1    Verdugo, R.A.2    Churchill, G.A.3    Deschepper, C.F.4
  • 25
    • 39149119250 scopus 로고    scopus 로고
    • Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes
    • Michalak, P., 2008 Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91: 243-248.
    • (2008) Genomics , vol.91 , pp. 243-248
    • Michalak, P.1
  • 26
    • 84862203271 scopus 로고    scopus 로고
    • The genomic landscape shaped by selection on transposable elements across 18 mouse strains
    • Nellåker, C., T. M. Keane, B. Yalcin, K. Wong, A. Agam et al., 2012 The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol. 13: R45.
    • (2012) Genome Biol. , vol.13
    • Nellåker, C.1    Keane, T.M.2    Yalcin, B.3    Wong, K.4    Agam, A.5
  • 27
    • 84857470719 scopus 로고    scopus 로고
    • Murine warriors or worriers: the saga of Comt1, B2 SINE elements, and the future of translational genetics
    • Palmer, A. A., and S. C. Dulawa, 2010 Murine warriors or worriers: the saga of Comt1, B2 SINE elements, and the future of translational genetics. Front. Neurosci. 4: 177.
    • (2010) Front. Neurosci. , vol.4 , pp. 177
    • Palmer, A.A.1    Dulawa, S.C.2
  • 28
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: master weaver of the genome
    • Phillips, J. E., and V. G. Corces, 2009 CTCF: master weaver of the genome. Cell 137: 1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 29
    • 78249277873 scopus 로고    scopus 로고
    • The structural complexity of the human BORIS gene in gametogenesis and cancer
    • Pugacheva, E. M., T. Suzuki, S. D. Pack, N. Kosaka-Suzuki, J. Yoon et al., 2010 The structural complexity of the human BORIS gene in gametogenesis and cancer. PLoS ONE 5: e13872.
    • (2010) PLoS ONE , vol.5
    • Pugacheva, E.M.1    Suzuki, T.2    Pack, S.D.3    Kosaka-Suzuki, N.4    Yoon, J.5
  • 30
    • 34247256762 scopus 로고    scopus 로고
    • Genomic organization of transcriptomes in mammals: coregulation and cofunctionality
    • Purmann, A., J. Toedling, M. Schueler, P. Carninci, H. Lehrach et al., 2007 Genomic organization of transcriptomes in mammals: coregulation and cofunctionality. Genomics 89: 580-587.
    • (2007) Genomics , vol.89 , pp. 580-587
    • Purmann, A.1    Toedling, J.2    Schueler, M.3    Carninci, P.4    Lehrach, H.5
  • 31
    • 0037456823 scopus 로고    scopus 로고
    • Genetics of gene expression surveyed in maize, mouse and man
    • Schadt, E. E., S. A. Monks, T. A. Drake, A. J. Lusis, N. Che et al., 2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
    • (2003) Nature , vol.422 , pp. 297-302
    • Schadt, E.E.1    Monks, S.A.2    Drake, T.A.3    Lusis, A.J.4    Che, N.5
  • 32
    • 79952275149 scopus 로고    scopus 로고
    • The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and MicroRNAs.
    • Schlesinger, J., M. Schueler, M. Grunert, J. J. Fischer, Q. Zhang et al., 2011 The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and MicroRNAs. PLoS Genet. 7: e1001313.
    • (2011) PLoS Genet. , vol.7
    • Schlesinger, J.1    Schueler, M.2    Grunert, M.3    Fischer, J.J.4    Zhang, Q.5
  • 33
    • 84863393570 scopus 로고    scopus 로고
    • Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
    • Schmidt, D., P. C. Schwalie, M. D. Wilson, B. Ballester, â. Gonçalves et al., 2012 Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335-348.
    • (2012) Cell , vol.148 , pp. 335-348
    • Schmidt, D.1    Schwalie, P.C.2    Wilson, M.D.3    Ballester, B.4    Gonçalves, â.5
  • 34
    • 84862969984 scopus 로고    scopus 로고
    • Dynamics of Srf, p300 and histone modifications during cardiac maturation in mouse
    • Schueler, M., Q. Zhang, J. Schlesinger, M. Tönjes, and S. R. Sperling, 2012 Dynamics of Srf, p300 and histone modifications during cardiac maturation in mouse. Mol. Biosyst. 8: 495.
    • (2012) Mol. Biosyst. , vol.8 , pp. 495
    • Schueler, M.1    Zhang, Q.2    Schlesinger, J.3    Tönjes, M.4    Sperling, S.R.5
  • 35
    • 84870895128 scopus 로고    scopus 로고
    • Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the MetaXpress consortium
    • Schurmann, C., K. Heim, A. Schillert, S. Blankenberg, M. Carstensen et al., 2012 Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the MetaXpress consortium. PLoS ONE 7: e50938.
    • (2012) PLoS ONE , vol.7
    • Schurmann, C.1    Heim, K.2    Schillert, A.3    Blankenberg, S.4    Carstensen, M.5
  • 36
    • 33748195447 scopus 로고    scopus 로고
    • Evolutionary origin and maintenance of coexpressed gene clusters in mammals
    • Sémon, M., and L. Duret, 2006 Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol. Biol. Evol. 23: 1715-1723.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1715-1723
    • Sémon, M.1    Duret, L.2
  • 37
    • 84883245014 scopus 로고    scopus 로고
    • High resolution genomic architecture of genetic reference populations: chromosome substitution panels and recombinant inbred strains
    • Abstracts of the Meeting of the Genetics Society of America, June 22-25, 2011, Washington, DC
    • Simecek, P., J. Forejt, R. W. Williams, L. Lu, T. E. Johnson et al., 2011 High resolution genomic architecture of genetic reference populations: chromosome substitution panels and recombinant inbred strains. Abstracts of the Meeting of the Genetics Society of America, June 22-25, 2011, Washington, DC.
    • (2011)
    • Simecek, P.1    Forejt, J.2    Williams, R.W.3    Lu, L.4    Johnson, T.E.5
  • 38
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • Smyth, G. K., 2004 Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3: Article 3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 39
    • 0003328368 scopus 로고    scopus 로고
    • Evidence for large domains of similarly expressed genes in the Drosophila genome
    • Spellman, P. T., and G. M. Rubin, 2002 Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1: 5.
    • (2002) J. Biol. , vol.1 , pp. 5
    • Spellman, P.T.1    Rubin, G.M.2
  • 40
    • 80053188808 scopus 로고    scopus 로고
    • Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers
    • Teng, L., H. A. Firpi, and K. Tan, 2011 Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. Nucleic Acids Res. 39: 7371-7379.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 7371-7379
    • Teng, L.1    Firpi, H.A.2    Tan, K.3
  • 41
    • 0141561907 scopus 로고    scopus 로고
    • Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions
    • van de Lagemaat, L. N., J.-R. Landry, D. L. Mager, and P. Medstrand, 2003 Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 19: 530-536.
    • (2003) Trends Genet. , vol.19 , pp. 530-536
    • van de Lagemaat, L.N.1    Landry, J.-R.2    Mager, D.L.3    Medstrand, P.4
  • 42
    • 70249088327 scopus 로고    scopus 로고
    • Genomic views of distant-acting enhancers
    • Visel, A., E. M. Rubin, and L. A. Pennacchio, 2009 Genomic views of distant-acting enhancers. Nature 461: 199-205.
    • (2009) Nature , vol.461 , pp. 199-205
    • Visel, A.1    Rubin, E.M.2    Pennacchio, L.A.3
  • 43
    • 77957891169 scopus 로고    scopus 로고
    • Coordinated expression domains in mammalian genomes
    • Woo, Y. H., M. Walker, and G. A. Churchill, 2010 Coordinated expression domains in mammalian genomes. PLoS ONE 5: e12158.
    • (2010) PLoS ONE , vol.5
    • Woo, Y.H.1    Walker, M.2    Churchill, G.A.3
  • 44
    • 44949147109 scopus 로고    scopus 로고
    • Gene set enrichment in eQTL data identifies novel annotations and pathway regulators
    • Wu, C., D. L. Delano, N. Mitro, S. V. Su, J. Janes et al., 2008 Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 4: e1000070.
    • (2008) PLoS Genet. , vol.4
    • Wu, C.1    Delano, D.L.2    Mitro, N.3    Su, S.V.4    Janes, J.5
  • 45
    • 80052851948 scopus 로고    scopus 로고
    • Sequence-based characterization of structural variation in the mouse genome
    • Yalcin, B., K. Wong, A. Agam, M. Goodson, T. M. Keane et al., 2011 Sequence-based characterization of structural variation in the mouse genome. Nature 477: 326-329.
    • (2011) Nature , vol.477 , pp. 326-329
    • Yalcin, B.1    Wong, K.2    Agam, A.3    Goodson, M.4    Keane, T.M.5
  • 46
    • 69549102945 scopus 로고    scopus 로고
    • A customized and versatile high-density genotyping array for the mouse
    • Yang, H., Y. Ding, L. N. Hutchins, J. Szatkiewicz, T. A. Bell et al., 2009 A customized and versatile high-density genotyping array for the mouse. Nat. Methods 6: 663-666.
    • (2009) Nat. Methods , vol.6 , pp. 663-666
    • Yang, H.1    Ding, Y.2    Hutchins, L.N.3    Szatkiewicz, J.4    Bell, T.A.5
  • 47
    • 0037452888 scopus 로고    scopus 로고
    • Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci
    • USA
    • Zhang, H., K.-H. Pan, and S. N. Cohen, 2003 Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci. Proc. Natl. Acad. Sci. USA 100: 3251-3256.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 3251-3256
    • Zhang, H.1    Pan, K.-H.2    Cohen, S.N.3


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