메뉴 건너뛰기




Volumn 116, Issue , 2016, Pages 299-314

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

Author keywords

Evolution of regulations; Hox gene function; Long range transcription; Pioneer enhancers; TADs

Indexed keywords

CHROMATIN; HOMEODOMAIN PROTEIN;

EID: 84955602762     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.ctdb.2015.11.022     Document Type: Chapter
Times cited : (27)

References (58)
  • 2
    • 0024592814 scopus 로고
    • Hox and HOM: Homologous gene clusters in insects and vertebrates
    • Akam M. Hox and HOM: Homologous gene clusters in insects and vertebrates. Cell 1989, 57:347-349.
    • (1989) Cell , vol.57 , pp. 347-349
    • Akam, M.1
  • 3
    • 84939497927 scopus 로고    scopus 로고
    • The octopus genome and the evolution of cephalopod neural and morphological novelties
    • Albertin C.B., Simakov O., Mitros T., Wang Z.Y., Pungor J.R., Edsinger-Gonzales E., et al. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature 2015, 524:220-224.
    • (2015) Nature , vol.524 , pp. 220-224
    • Albertin, C.B.1    Simakov, O.2    Mitros, T.3    Wang, Z.Y.4    Pungor, J.R.5    Edsinger-Gonzales, E.6
  • 4
    • 58149463874 scopus 로고    scopus 로고
    • Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription
    • Amano T., Sagai T., Tanabe H., Mizushina Y., Nakazawa H., Shiroishi T. Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription. Developmental Cell 2009, 16:47-57.
    • (2009) Developmental Cell , vol.16 , pp. 47-57
    • Amano, T.1    Sagai, T.2    Tanabe, H.3    Mizushina, Y.4    Nakazawa, H.5    Shiroishi, T.6
  • 5
    • 84878754528 scopus 로고    scopus 로고
    • A switch between topological domains underlies HoxD genes collinearity in mouse limbs
    • Andrey G., Montavon T., Mascrez B., Gonzalez F., Noordermeer D., Leleu M., et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 2013, 340:1234167.
    • (2013) Science , vol.340 , pp. 1234167
    • Andrey, G.1    Montavon, T.2    Mascrez, B.3    Gonzalez, F.4    Noordermeer, D.5    Leleu, M.6
  • 6
    • 37049188514 scopus 로고
    • Molecular genetics of the bithorax complex in Drosophila melanogaster
    • Bender W., Akam M., Karch F., Beachy P.A., Peifer M., Spierer P., et al. Molecular genetics of the bithorax complex in Drosophila melanogaster. Science 1983, 221:23-29.
    • (1983) Science , vol.221 , pp. 23-29
    • Bender, W.1    Akam, M.2    Karch, F.3    Beachy, P.A.4    Peifer, M.5    Spierer, P.6
  • 7
    • 84892715701 scopus 로고    scopus 로고
    • Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs
    • Berlivet S., Paquette D., Dumouchel A., Langlais D., Dostie J., Kmita M. Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genetics 2013, 9:e1004018.
    • (2013) PLoS Genetics , vol.9 , pp. e1004018
    • Berlivet, S.1    Paquette, D.2    Dumouchel, A.3    Langlais, D.4    Dostie, J.5    Kmita, M.6
  • 10
    • 84870317191 scopus 로고    scopus 로고
    • 3C-based technologies to study the shape of the genome
    • de Laat W., Dekker J. 3C-based technologies to study the shape of the genome. Methods 2012, 58:189-191.
    • (2012) Methods , vol.58 , pp. 189-191
    • de Laat, W.1    Dekker, J.2
  • 11
    • 84886853624 scopus 로고    scopus 로고
    • Topology of mammalian developmental enhancers and their regulatory landscapes
    • de Laat W., Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 2013, 502:499-506.
    • (2013) Nature , vol.502 , pp. 499-506
    • de Laat, W.1    Duboule, D.2
  • 12
    • 0042880630 scopus 로고    scopus 로고
    • Spatial organization of gene expression: The active chromatin hub
    • de Laat W., Grosveld F. Spatial organization of gene expression: The active chromatin hub. Chromosome Research 2003, 11:447-459.
    • (2003) Chromosome Research , vol.11 , pp. 447-459
    • de Laat, W.1    Grosveld, F.2
  • 13
    • 84885733377 scopus 로고    scopus 로고
    • Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding
    • Delpretti S., Montavon T., Leleu M., Joye E., Tzika A., Milinkovitch M., et al. Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Reports 2013, 5:137-150.
    • (2013) Cell Reports , vol.5 , pp. 137-150
    • Delpretti, S.1    Montavon, T.2    Leleu, M.3    Joye, E.4    Tzika, A.5    Milinkovitch, M.6
  • 14
    • 84858285503 scopus 로고    scopus 로고
    • A function for all posterior Hoxd genes during digit development?
    • Delpretti S., Zakany J., Duboule D. A function for all posterior Hoxd genes during digit development?. Developmental Dynamics 2012, 241:792-802.
    • (2012) Developmental Dynamics , vol.241 , pp. 792-802
    • Delpretti, S.1    Zakany, J.2    Duboule, D.3
  • 15
    • 63849253211 scopus 로고    scopus 로고
    • Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard
    • Di-Poï N., Montoya-Burgos J., Duboule D. Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard. Genome Research 2009, 19(4):602-610.
    • (2009) Genome Research , vol.19 , Issue.4 , pp. 602-610
    • Di-Poï, N.1    Montoya-Burgos, J.2    Duboule, D.3
  • 18
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 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    Shen, Y.6
  • 19
    • 0026875503 scopus 로고
    • The vertebrate limb: A model system to study the Hox/HOM gene network during development and evolution
    • Duboule D. The vertebrate limb: A model system to study the Hox/HOM gene network during development and evolution. Bioessays 1992, 14:375-384.
    • (1992) Bioessays , vol.14 , pp. 375-384
    • Duboule, D.1
  • 20
    • 0028605603 scopus 로고
    • Temporal colinearity and the phylotypic progression: A basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony
    • Duboule D. Temporal colinearity and the phylotypic progression: A basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony. Development 1994, 135-142. (Suppl.).
    • (1994) Development , pp. 135-142
    • Duboule, D.1
  • 21
    • 34547819351 scopus 로고    scopus 로고
    • The rise and fall of Hox gene clusters
    • Duboule D. The rise and fall of Hox gene clusters. Development 2007, 134:2549-2560.
    • (2007) Development , vol.134 , pp. 2549-2560
    • Duboule, D.1
  • 22
    • 0022760992 scopus 로고
    • A new homeo-box is present in overlapping cosmid clones which define the mouse Hox-1 locus
    • Duboule D., Baron A., Mahl P., Galliot B. A new homeo-box is present in overlapping cosmid clones which define the mouse Hox-1 locus. The EMBO Journal 1986, 5:1973-1980.
    • (1986) The EMBO Journal , vol.5 , pp. 1973-1980
    • Duboule, D.1    Baron, A.2    Mahl, P.3    Galliot, B.4
  • 23
    • 0024341769 scopus 로고
    • The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes
    • Duboule D., Dolle P. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. The EMBO Journal 1989, 8:1497-1505.
    • (1989) The EMBO Journal , vol.8 , pp. 1497-1505
    • Duboule, D.1    Dolle, P.2
  • 24
    • 84900297485 scopus 로고    scopus 로고
    • Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription
    • Giorgetti L., Galupa R., Nora E.P., Piolot T., Lam F., Dekker J., et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 2014, 157:950-963.
    • (2014) Cell , vol.157 , pp. 950-963
    • Giorgetti, L.1    Galupa, R.2    Nora, E.P.3    Piolot, T.4    Lam, F.5    Dekker, J.6
  • 25
    • 34249943590 scopus 로고    scopus 로고
    • Transgenic analysis of Hoxd gene regulation during digit development
    • Gonzalez F., Duboule D., Spitz F. Transgenic analysis of Hoxd gene regulation during digit development. Developmental Biology 2007, 306:847-859.
    • (2007) Developmental Biology , vol.306 , pp. 847-859
    • Gonzalez, F.1    Duboule, D.2    Spitz, F.3
  • 26
    • 0024589805 scopus 로고
    • The murine and Drosophila homeobox gene complexes have common features of organization and expression
    • Graham A., Papalopulu N., Krumlauf R. The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 1989, 57:367-378.
    • (1989) Cell , vol.57 , pp. 367-378
    • Graham, A.1    Papalopulu, N.2    Krumlauf, R.3
  • 27
    • 0021804649 scopus 로고
    • Spatially regulated expression of homeotic genes in Drosophila
    • Harding K., Wedeen C., McGinnis W., Levine M. Spatially regulated expression of homeotic genes in Drosophila. Science 1985, 229:1236-1242.
    • (1985) Science , vol.229 , pp. 1236-1242
    • Harding, K.1    Wedeen, C.2    McGinnis, W.3    Levine, M.4
  • 28
    • 0023429380 scopus 로고
    • Sequence analysis of the murine Hox-2.2, -2.3, and -2.4 homeo boxes: Evolutionary and structural comparisons
    • Hart C.P., Fainsod A., Ruddle F.H. Sequence analysis of the murine Hox-2.2, -2.3, and -2.4 homeo boxes: Evolutionary and structural comparisons. Genomics 1987, 1:182-195.
    • (1987) Genomics , vol.1 , pp. 182-195
    • Hart, C.P.1    Fainsod, A.2    Ruddle, F.H.3
  • 31
    • 84918527386 scopus 로고    scopus 로고
    • Pioneer transcription factors in cell reprogramming
    • Iwafuchi-Doi M., Zaret K.S. Pioneer transcription factors in cell reprogramming. Genes & Development 2014, 28:2679-2692.
    • (2014) Genes & Development , vol.28 , pp. 2679-2692
    • Iwafuchi-Doi, M.1    Zaret, K.S.2
  • 32
    • 0038115063 scopus 로고    scopus 로고
    • Organizing axes in time and space; 25 years of colinear tinkering
    • Kmita M., Duboule D. Organizing axes in time and space; 25 years of colinear tinkering. Science 2003, 301:331-333.
    • (2003) Science , vol.301 , pp. 331-333
    • Kmita, M.1    Duboule, D.2
  • 33
    • 21344455343 scopus 로고    scopus 로고
    • Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function
    • Kmita M., Tarchini B., Zakany J., Logan M., Tabin C.J., Duboule D. Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function. Nature 2005, 435:1113-1116.
    • (2005) Nature , vol.435 , pp. 1113-1116
    • Kmita, M.1    Tarchini, B.2    Zakany, J.3    Logan, M.4    Tabin, C.J.5    Duboule, D.6
  • 34
    • 57749184792 scopus 로고    scopus 로고
    • Timing of genome duplications relative to the origin of the vertebrates: Did cyclostomes diverge before or after?
    • Kuraku S., Meyer A., Kuratani S. Timing of genome duplications relative to the origin of the vertebrates: Did cyclostomes diverge before or after?. Molecular Biology and Evolution 2009, 26:47-59.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 47-59
    • Kuraku, S.1    Meyer, A.2    Kuratani, S.3
  • 35
    • 0042810698 scopus 로고    scopus 로고
    • A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
    • Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Human Molecular Genetics 2003, 12:1725-1735.
    • (2003) Human Molecular Genetics , vol.12 , pp. 1725-1735
    • Lettice, L.A.1    Heaney, S.J.2    Purdie, L.A.3    Li, L.4    de Beer, P.5    Oostra, B.A.6
  • 36
    • 0018240421 scopus 로고
    • A gene complex controlling segmentation in Drosophila
    • Lewis E.B. A gene complex controlling segmentation in Drosophila. Nature 1978, 276:565-570.
    • (1978) Nature , vol.276 , pp. 565-570
    • Lewis, E.B.1
  • 37
    • 84943348158 scopus 로고    scopus 로고
    • Structure, function and evolution of topologically associating domains (TADs) at HOX loci
    • (review)
    • Lonfat N., Duboule D. Structure, function and evolution of topologically associating domains (TADs) at HOX loci. FEBS Letters 2015, 589(20 Pt. A):2869-2876. (review). 10.1016/j.febslet.2015.04.024.
    • (2015) FEBS Letters , vol.589 , Issue.20 , pp. 2869-2876
    • Lonfat, N.1    Duboule, D.2
  • 38
    • 84911895715 scopus 로고    scopus 로고
    • Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci
    • Lonfat N., Montavon T., Darbellay F., Gitto S., Duboule D. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science 2014, 346:1004-1006.
    • (2014) Science , vol.346 , pp. 1004-1006
    • Lonfat, N.1    Montavon, T.2    Darbellay, F.3    Gitto, S.4    Duboule, D.5
  • 41
    • 84862755561 scopus 로고    scopus 로고
    • Landscapes and archipelagos: Spatial organization of gene regulation in vertebrates
    • Montavon T., Duboule D. Landscapes and archipelagos: Spatial organization of gene regulation in vertebrates. Trends in Cell Biology 2012, 22(7):347-354.
    • (2012) Trends in Cell Biology , vol.22 , Issue.7 , pp. 347-354
    • Montavon, T.1    Duboule, D.2
  • 42
    • 81855227640 scopus 로고    scopus 로고
    • A regulatory archipelago controls Hox genes transcription in digits
    • Montavon T., Soshnikova N., Mascrez B., Joye E., Thevenet L., Splinter E., et al. A regulatory archipelago controls Hox genes transcription in digits. Cell 2011, 147:1132-1145.
    • (2011) Cell , vol.147 , pp. 1132-1145
    • Montavon, T.1    Soshnikova, N.2    Mascrez, B.3    Joye, E.4    Thevenet, L.5    Splinter, E.6
  • 43
    • 84881613036 scopus 로고    scopus 로고
    • Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?
    • Nora E.P., Dekker J., Heard E. Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?. Bioessays 2013, 35:818-828.
    • (2013) Bioessays , vol.35 , pp. 818-828
    • Nora, E.P.1    Dekker, J.2    Heard, E.3
  • 44
    • 84861100147 scopus 로고    scopus 로고
    • Spatial partitioning of the regulatory landscape of the X-inactivation centre
    • Nora E.P., Lajoie B.R., Schulz E.G., Giorgetti L., Okamoto I., Servant N., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012, 485:381-385.
    • (2012) Nature , vol.485 , pp. 381-385
    • Nora, E.P.1    Lajoie, B.R.2    Schulz, E.G.3    Giorgetti, L.4    Okamoto, I.5    Servant, N.6
  • 45
    • 27844575145 scopus 로고    scopus 로고
    • Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni
    • Pierce R.J., Wu W., Hirai H., Ivens A., Murphy L.D., Noel C., et al. Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni. Molecular Biology and Evolution 2005, 22:2491-2503.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 2491-2503
    • Pierce, R.J.1    Wu, W.2    Hirai, H.3    Ivens, A.4    Murphy, L.D.5    Noel, C.6
  • 47
    • 79953176250 scopus 로고    scopus 로고
    • Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor
    • Ruf S., Symmons O., Uslu V.V., Dolle D., Hot C., Ettwiller L., et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nature Genetics 2011, 43:379-386.
    • (2011) Nature Genetics , vol.43 , pp. 379-386
    • Ruf, S.1    Symmons, O.2    Uslu, V.V.3    Dolle, D.4    Hot, C.5    Ettwiller, L.6
  • 48
    • 0021984643 scopus 로고
    • Genetic organization of Drosophila bithorax complex
    • Sanchez-Herrero E., Vernos I., Marco R., Morata G. Genetic organization of Drosophila bithorax complex. Nature 1985, 313:108-113.
    • (1985) Nature , vol.313 , pp. 108-113
    • Sanchez-Herrero, E.1    Vernos, I.2    Marco, R.3    Morata, G.4
  • 49
    • 4544320630 scopus 로고    scopus 로고
    • Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica
    • Seo H.C., Edvardsen R.B., Maeland A.D., Bjordal M., Jensen M.F., Hansen A., et al. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 2004, 431:67-71.
    • (2004) Nature , vol.431 , pp. 67-71
    • Seo, H.C.1    Edvardsen, R.B.2    Maeland, A.D.3    Bjordal, M.4    Jensen, M.F.5    Hansen, A.6
  • 50
    • 39149144816 scopus 로고    scopus 로고
    • Maintenance of transposon-free regions throughout vertebrate evolution
    • Simons C., Makunin I.V., Pheasant M., Mattick J.S. Maintenance of transposon-free regions throughout vertebrate evolution. BMC Genomics 2007, 8:470.
    • (2007) BMC Genomics , vol.8 , pp. 470
    • Simons, C.1    Makunin, I.V.2    Pheasant, M.3    Mattick, J.S.4
  • 51
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: From enhancer binding to developmental control
    • Spitz F., Furlong E.E. Transcription factors: From enhancer binding to developmental control. Nature Reviews. Genetics 2012, 13:613-626.
    • (2012) Nature Reviews. Genetics , vol.13 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.2
  • 52
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • Spitz F., Gonzalez F., Duboule D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 2003, 113:405-417.
    • (2003) Cell , vol.113 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 53
    • 23044477774 scopus 로고    scopus 로고
    • Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes
    • Spitz F., Herkenne C., Morris M.A., Duboule D. Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nature Genetics 2005, 37:889-893.
    • (2005) Nature Genetics , vol.37 , pp. 889-893
    • Spitz, F.1    Herkenne, C.2    Morris, M.A.3    Duboule, D.4
  • 55
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active beta-globin locus
    • Tolhuis B., Palstra R.J., Splinter E., Grosveld F., De Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Molecular Cell 2002, 10:1453-1465.
    • (2002) Molecular Cell , vol.10 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.J.2    Splinter, E.3    Grosveld, F.4    De Laat, W.5
  • 57
    • 84893777034 scopus 로고    scopus 로고
    • Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits
    • Woltering J.M., Noordermeer D., Leleu M., Duboule D. Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits. PLoS Biology 2014, 12:e1001773.
    • (2014) PLoS Biology , vol.12
    • Woltering, J.M.1    Noordermeer, D.2    Leleu, M.3    Duboule, D.4
  • 58
    • 80455144479 scopus 로고    scopus 로고
    • Pioneer transcription factors: Establishing competence for gene expression
    • Zaret K.S., Carroll J.S. Pioneer transcription factors: Establishing competence for gene expression. Genes & Development 2011, 25:2227-2241.
    • (2011) Genes & Development , vol.25 , pp. 2227-2241
    • Zaret, K.S.1    Carroll, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.