Chapter 6 Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution

Advances in Genetics

Volumn 61, Issue , 2008, Pages 175-205

  Spitz, Francois ^a   Duboule, Denis ^b,c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c Physics Department   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; CHROMOSOME; DEVELOPMENTAL GENE; EVOLUTION; GENE EXPRESSION REGULATION; GENE ORDER; GENETIC DISORDER; GENETICS; GROWTH, DEVELOPMENT AND AGING; HOMEOBOX; HUMAN; MULTIGENE FAMILY; PHYSIOLOGY; PRENATAL DEVELOPMENT; REGULATORY SEQUENCE; REVIEW; VERTEBRATE;

ANIMALS; CHROMOSOMES; EVOLUTION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE ORDER; GENES, DEVELOPMENTAL; GENES, HOMEOBOX; GENETIC DISEASES, INBORN; HUMANS; MODELS, BIOLOGICAL; MULTIGENE FAMILY; REGULATORY SEQUENCES, NUCLEIC ACID; VERTEBRATES;

EID: 39049130281     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2660(07)00006-5     Document Type: Review

References (148)

1. Bastian H., Gruss P., Duboule D., and Izpisua-Belmonte J.C. The murine even-skipped-like gene Evx-2 is closely linked to the Hox-4 complex, but is transcribed in the opposite direction. Mamm. Genome 3 (1992) 241-243
2. Bellizzi D., Dato S., Cavalcante P., Covello G., Di Cianni F., Passarino G., Rose G., and De Benedictis G. Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13. Genomics 89 (2007) 143-150
3. Bernstein B.E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D.K., Huebert D.J., McMahon S., Karlsson E.K., Kulbokas III E.J., Gingeras T.R., Schreiber S.L., and Lander E.S. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120 (2005) 169-181
4. Blumenthal T., Evans D., Link C.D., Guffanti A., Lawson D., Thierry-Mieg J., Thierry-Mieg D., Chiu W.L., Duke K., Kiraly M., and Kim S.K. A global analysis of Caenorhabditis elegans operons. Nature 417 (2002) 851-854
5. Boutanaev A.M., Kalmykova A.I., Shevelyov Y.Y., and Nurminsky D.I. Large clusters of co-expressed genes in the Drosophila genome. Nature 420 (2002) 666-669
6. Brooke N.M., Garcia-Fernandez J., and Holland P.W. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature 392 (1998) 920-922
7. Bulger M., Bender M.A., van Doorninck J.H., Wertman B., Farrell C.M., Felsenfeld G., Groudine M., and Hardison R. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters. Proc. Natl. Acad. Sci. USA 97 (2000) 14560-14565
8. Bulger M., Schubeler D., Bender M.A., Hamilton J., Farrell C.M., Hardison R.C., and Groudine M. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus. Mol. Cell. Biol. 23 (2003) 5234-5244
9. Cajiao I., Zhang A., Yoo E.J., Cooke N.E., and Liebhaber S.A. Bystander gene activation by a locus control region. EMBO J. 23 (2004) 3854-3863
10. Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A., Taylor M.S., Engström M.S., Frith M.C., Forrest A.R., Alkema W.B., et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38 (2006) 626-635
11. Carroll S.B. Evolution at two levels: On genes and form. PLoS Biol. 3 (2005) e245
12. Carroll S.B. "Endless Forms Most Beautiful: The New Science of Evo Devo." (2006), W. W. Norton, New York
13. Carvajal J.J., Cox D., Summerbell D., and Rigby P.W. A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development. Development 128 (2001) 1857-1868
14. Chen P.Y., Chang W.S., Chou R.H., Lai Y.K., Lin S.C., Chi C.Y., and Wu C.W. Two non-homologous brain diseases-related genes, SERPINI1 and PDCD10, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner. BMC Mol. Biol. 8 (2007) 2
15. Chiu C.H., Amemiya C.T., Carr J.L., Bhargava J., Hwang J.K., Shashikant C.S., Ruddle F.H., and Wagner G.P. A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: Construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene. Dev. Genes Evol. 210 (2000) 105-109
16. Christoffels V.M., Keijser A.G., Houweling A.C., Clout D.E., and Moorman A.F. Patterning the embryonic heart: Identification of five mouse Iroquois homeobox genes in the developing heart. Dev. Biol. 224 (2000) 263-274
17. Crackower M.A., Scherer S.W., Rommens J.M., Hui C.C., Poorkaj P., Soder S., Cobben J.M., Hudgins L., Evans L., and Tsui L.C. Characterization of the split hand/split foot malformation locus SHFM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. Hum. Mol. Genet. 5 (1996) 571-579
18. Davidson E.H. "The Regulatory Genome: Gene Regulatory Networks in Development and Evolution" (2006), Academic Press/Elsevier, San Diego
19. Davis A.P., and Capecchi M.R. Axial homeosis and appendicular skeleton defects in mice with a targeted disruption of hoxd-11. Development 120 (1994) 2187-2198
20. Davisson M.T., and Cattanach B.M. The mouse mutation ulnaless on chromosome 2. J. Hered. 81 (1990) 151-153
21. de la Calle-Mustienes E., Feijoo C.G., Manzanares M., Tena J.J., Rodriguez-Seguel E., Letizia A., Allende M.L., and Gomez-Skarmeta J.L. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res. 15 (2005) 1061-1072
22. Dillon N., Trimborn T., Strouboulis J., Fraser P., and Grosveld F. The effect of distance on long-range chromatin interactions. Mol. Cell 1 (1997) 131-139
23. Dolle P., Izpisua-Belmonte J.C., Falkenstein H., Renucci A., and Duboule D. Coordinate expression of the murine Hox-5 complex homoeobox-containing genes during limb pattern formation. Nature 342 (1989) 767-772
24. Dolle P., Dierich A., LeMeur M., Schimmang T., Schuhbaur B., Chambon P., and Duboule D. Disruption of the Hoxd-13 gene induces localized heterochrony leading to mice with neotenic limbs. Cell 75 (1993) 431-441
25. Dolle P., Fraulob V., and Duboule D. Developmental expression of the mouse Evx-2 gene: Relationship with the evolution of the HOM/Hox complex. Dev Suppl. (1994) 143-153
26. Duboule D. Vertebrate hox gene regulation: Clustering and/or colinearity?. Curr. Opin. Genet. Dev. 8 (1998) 514-518
27. Duboule D., and Wilkins A.S. The evolution of 'bricolage'. Trends. Genet. 14 (1998) 54-59
28. Duboule D., Baron A., Mahl P., and Galliot B. A new homeo-box is present in overlapping cosmid clones which define the mouse Hox-1 locus. EMBO J. 5 (1986) 1973-1980
29. Engstrom P.G., Suzuki H., Ninomiya N., Akalin A., Sessa L., Lavorgna G., Brozzi A., Luzi L., Lam Tan S., Yang L., Kunarso G., Ng E.L.-C., et al. Complex loci in human and mouse genomes. PLoS Genet. 2 (2006) e47
30. Favier B., Le Meur M., Chambon P., and Dolle P. Axial skeleton homeosis and forelimb malformations in Hoxd-11 mutant mice. Proc. Natl. Acad. Sci. USA 92 (1995) 310-314
31. Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., and Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (1999) 1531-1545
32. Gallardo M.E., Lopez-Rios J., Fernaud-Espinosa I., Granadino B., Sanz R., Ramos C., Ayuso C., Seller M.J., Brunner H.G., Bovolenta P., and Rodríguez de Córdoba S. Genomic cloning and characterization of the human homeobox gene SIX6 reveals a cluster of SIX genes in chromosome 14 and associates SIX6 hemizygosity with bilateral anophthalmia and pituitary anomalies. Genomics 61 (1999) 82-91
33. Garcia-Fernandez J. The genesis and evolution of homeobox gene clusters. Nat. Rev. Genet. 6 (2005) 881-892
34. Gauchat D., Mazet F., Berney C., Schummer M., Kreger S., Pawlowski J., and Galliot B. Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning. Proc. Natl. Acad. Sci. USA 97 (2000) 4493-4498
35. Gerard M., Duboule D., and Zakany J. Structure and activity of regulatory elements involved in the activation of the Hoxd-11 gene during late gastrulation. EMBO J. 12 (1993) 3539-3550
36. Gerard M., Chen J.Y., Gronemeyer H., Chambon P., Duboule D., and Zakany J. In vivo targeted mutagenesis of a regulatory element required for positioning the Hoxd-11 and Hoxd-10 expression boundaries. Genes Dev. 10 (1996) 2326-2334
37. Glusman G., Yanai I., Rubin I., and Lancet D. The complete human olfactory subgenome. Genome Res. 11 (2001) 685-702
38. Gomez-Skarmeta J.L., and Modolell J. Iroquois genes: Genomic organization and function in vertebrate neural development. Curr. Opin. Genet. Dev. 12 (2002) 403-408
39. Gonzalez F., Duboule D., and Spitz F. Transgenic analysis of Hoxd gene regulation during digit development. Dev. Biol. 306 2 (2007) 847-859
40. Gould A., Morrison A., Sproat G., White R.A., and Krumlauf R. Positive cross-regulation and enhancer sharing: Two mechanisms for specifying overlapping Hox expression patterns. Genes Dev. 11 (1997) 900-913
41. Gray T.A., Saitoh S., and Nicholls R.D. An imprinted, mammalian bicistronic transcript encodes two independent proteins. Proc. Natl. Acad. Sci. USA 96 (1999) 5616-5621
42. Guris D.L., Duester G., Papaioannou V.E., and Imamoto A. Dose-dependent interaction of Tbx1 and Crkl and locally aberrant RA signaling in a model of del22q11 syndrome. Dev. Cell 10 (2006) 81-92
43. Hadchouel J., Tajbakhsh S., Primig M., Chang T.H., Daubas P., Rocancourt D., and Buckingham M. Modular long-range regulation of Myf5 reveals unexpected heterogeneity between skeletal muscles in the mouse embryo. Development 127 (2000) 4455-4467
44. Hayday A.C., Gillies S.D., Saito H., Wood C., Wiman K., Hayward W.S., and Tonegawa S. Activation of a translocated human c-myc gene by an enhancer in the immunoglobulin heavy-chain locus. Nature 307 (1984) 334-340
45. Herault Y., Hraba-Renevey S., van der Hoeven F., and Duboule D. Function of the Evx-2 gene in the morphogenesis of vertebrate limbs. EMBO J. 15 (1996) 6727-6738
46. Herault Y., Fraudeau N., Zakany J., and Duboule D. Ulnaless (Ul), a regulatory mutation inducing both loss-of-function and gain-of-function of posterior Hoxd genes. Development 124 (1997) 3493-3500
47. Herault Y., Beckers J., Kondo T., Fraudeau N., and Duboule D. Genetic analysis of a Hoxd-12 regulatory element reveals global versus local modes of controls in the HoxD complex. Development 125 (1998) 1669-1677
48. Herault Y., Beckers J., Gerard M., and Duboule D. Hox gene expression in limbs: Colinearity by opposite regulatory controls. Dev. Biol. 208 (1999) 157-165
49. Hesse M., Zimek A., Weber K., and Magin T.M. Comprehensive analysis of keratin gene clusters in humans and rodents. Eur. J. Cell Biol. 83 (2004) 19-26
50. Holmes G., Crooijmans R., Groenen M., and Niswander L. ALC (adjacent to LMX1 in chick) is a novel dorsal limb mesenchyme marker. Gene Expr. Patterns 3 (2003) 735-741
51. Houweling A.C., Dildrop R., Peters T., Mummenhoff J., Moorman A.F., Ruther U., and Christoffels V.M. Gene and cluster-specific expression of the Iroquois family members during mouse development. Mech. Dev. 107 (2001) 169-174
52. Hsu S.H., Noamani B., Abernethy D.E., Zhu H., Levi G., and Bendall A.J. Dlx5- and Dlx6-mediated chondrogenesis: Differential domain requirements for a conserved function. Mech. Dev. 123 (2006) 819-830
53. Huntley S., Baggott D.M., Hamilton A.T., Tran-Gyamfi M., Yang S., Kim J., Gordon L., Branscomb E., and Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 16 (2006) 669-677
54. Jacob F., Perrin D., Sanchez C., and Monod J. Operon: A group of genes with the expression coordinated by an operator. C. R. Hebd. Seances Acad. Sci. 250 (1960) 1727-1729
55. Jagla K., Bellard M., and Frasch M. A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs. Bioessays 23 (2001) 125-133
56. Ji Y., Eichler E.E., Schwartz S., and Nicholls R.D. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10 (2000) 597-610
57. Juan A.H., and Ruddle F.H. Enhancer timing of Hox gene expression: Deletion of the endogenous Hoxc8 early enhancer. Development 130 (2003) 4823-4834
58. Katoh M. WNT and FGF gene clusters (review). Int. J. Oncol. 21 (2002) 1269-1273
59. King M.C., and Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 188 (1975) 107-116
60. Kirschner M., and Gerhart J. Evolvability. Proc. Natl. Acad. Sci. USA 95 (1998) 8420-8427
61. Kleinjan D.A., Seawright A., Elgar G., and van Heyningen V. Characterization of a novel gene adjacent to PAX6, revealing synteny conservation with functional significance. Mamm. Genome 13 (2002) 102-107
62. Kmita M., and Duboule D. Organizing axes in time and space; 25 years of colinear tinkering. Science 301 (2003) 331-333
63. Kmita M., van Der Hoeven F., Zakany J., Krumlauf R., and Duboule D. Mechanisms of Hox gene colinearity: Transposition of the anterior Hoxb1 gene into the posterior HoxD complex. Genes Dev. 14 (2000) 198-211
64. Kmita M., Kondo T., and Duboule D. Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing. Nat. Genet. 26 (2000) 451-454
65. Kmita M., Fraudeau N., Herault Y., and Duboule D. Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420 (2002) 145-150
66. Kmita M., Tarchini B., Duboule D., and Herault Y. Evolutionary conserved sequences are required for the insulation of the vertebrate Hoxd complex in neural cells. Development 129 (2002) 5521-5528
67. Kokubu C., Wilm B., Kokubu T., Wahl M., Rodrigo I., Sakai N., Santagati F., Hayashizaki Y., Suzuki M., Yamamura M., Abe K., and Imai K. Undulated short-tail deletion mutation in the mouse ablates Pax1 and leads to ectopic activation of neighboring Nkx2-2 in domains that normally express Pax1. Genetics 165 (2003) 299-307
68. Kondo T., Dolle P., Zakany J., and Duboule D. Function of posterior HoxD genes in the morphogenesis of the anal sphincter. Development 122 (1996) 2651-2659
69. Kosak S.T., and Groudine M. Gene order and dynamic domains. Science 306 (2004) 644-647
70. Krumlauf R. Hox genes in vertebrate development. Cell 78 (1994) 191-201
71. Lecaudey V., Anselme I., Dildrop R., Ruther U., and Schneider-Maunoury S. Expression of the zebrafish Iroquois genes during early nervous system formation and patterning. J. Comp. Neurol. 492 (2005) 289-302
72. Lee E.C., Yu D., Martinez de Velasco J., Tessarollo L., Swing D.A., Court D.L., Jenkins N.A., and Copeland N.G. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73 (2001) 56-65
73. Lee S.J. Expression of growth/differentiation factor 1 in the nervous system: Conservation of a bicistronic structure. Proc. Natl. Acad. Sci. USA 88 (1991) 4250-4254
74. Lee K.Z., and Sommer R.J. Operon structure and trans-splicing in the nematode Pristionchus pacificus. Mol. Biol. Evol. 20 (2003) 2097-2103
75. Lemons D., and McGinnis W. Genomic evolution of Hox gene clusters. Science 313 (2006) 1918-1922
76. Lercher M.J., Urrutia A.O., and Hurst L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31 (2002) 180-183
77. Lercher M.J., Blumenthal T., and Hurst L.D. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res. 13 (2003) 238-243
78. Lettice L.A., Horikoshi T., Heaney S.J.H., van Baren M.J., van der Linde H.C., Breedveld G.J., Joosse M., Akarsu N., Oostra B.A., Endo N., Shibata M., Suzuki M., et al. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc. Natl. Acad. Sci. USA 99 (2002) 7548-7553
79. Lettice L.A., Heaney S.J.H., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., and de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12 (2003) 1725-1735
80. Levine M., and Tjian R. Transcription regulation and animal diversity. Nature 424 (2003) 147-151
81. Li B., Carey M., and Workman J.L. The role of chromatin during transcription. Cell 128 (2007) 707-719
82. Lomvardas S., Barnea G., Pisapia D.J., Mendelsohn M., Kirkland J., and Axel R. Interchromosomal interactions and olfactory receptor choice. Cell 126 (2006) 403-413
83. Loots G.G., Locksley R.M., Blankespoor C.M., Wang Z.E., Miller W., Rubin E.M., and Frazer K.A. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288 (2000) 136-140
84. Luke G.N., Castro L.F., McLay K., Bird C., Coulson A., and Holland P.W. Dispersal of NK homeobox gene clusters in amphioxus and humans. Proc. Natl. Acad. Sci. USA 100 (2003) 5292-5295
85. Lunyak V.V., Burgess R., Prefontaine G.G., Nelson C., Sze S.-H., Chenoweth J., Schwartz P., Pevzner P.A., Glass C., Mandel G., and Rosenfeld M.G. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science 298 (2002) 1747-1752
86. Maas S.A., and Fallon J.F. Isolation of the chicken Lmbr1 coding sequence and characterization of its role during chick limb development. Dev. Dyn. 229 (2004) 520-528
87. Maclean J.A., Chen II M.A., Wayne C.M., Bruce S.R., Rao M., Meistrich M.L., Macleod C., and Wilkinson M.F. Rhox: A new homeobox gene cluster. Cell 120 (2005) 369-382
88. Maconochie M.K., Nonchev S., Studer M., Chan S.K., Popperl H., Sham M.H., Mann R.S., and Krumlauf R. Cross-regulation in the mouse HoxB complex: The expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1. Genes Dev. 11 (1997) 1885-1895
89. Mass R.L., Zeller R., Woychik R.P., Vogt T.F., and Leder P. Disruption of formin-encoding transcripts in two mutant limb deformity alleles. Nature 346 (1990) 853-855
90. McEwen G.K., Woolfe A., Goode D., Vavouri T., Callaway H., and Elgar G. Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis. Genome Res. 16 (2006) 451-465
91. McLysaght A., Hokamp K., and Wolfe K.H. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31 (2002) 200-204
92. Michos O., Panman L., Vintersten K., Beier K., Zeller R., and Zuniga A. Gremlin-mediated BMP antagonism induces the epithelial-mesenchymal feedback signaling controlling metanephric kidney and limb organogenesis. Development 131 (2004) 3401-3410
93. Miller D.J., and Miles A. Homeobox genes and the zootype. Nature 365 (1993) 215-216
94. Minguillon C., and Garcia-Fernandez J. Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters. Genome Biol. 4 (2003) R12
95. Monge I., Kondo T., and Duboule D. An enhancer-titration effect induces digit-specific regulatory alleles of the HoxD cluster. Dev. Biol. 256 (2003) 212-220
96. Moran-Rivard L., Kagawa T., Saueressig H., Gross M.K., Burrill J., and Goulding M. Evx1 is a postmitotic determinant of v0 interneuron identity in the spinal cord. Neuron 29 (2001) 385-399
97. Morey C., Da Silva N.R., Perry P., and Bickmore W.A. Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134 (2007) 909-919
98. Mummenhoff J., Houweling A.C., Peters T., Christoffels V.M., and Ruther U. Expression of Irx6 during mouse morphogenesis. Mech. Dev. 103 (2001) 193-195
99. Muyrers J.P., Zhang Y., Testa G., and Stewart A.F. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 27 (1999) 1555-1557
100. Nusse R. An ancient cluster of Wnt paralogues. Trends Genet. 17 (2001) 443
101. Olson E.N., Arnold H.H., Rigby P.W., and Wold B.J. Know your neighbors: Three phenotypes in null mutants of the myogenic bHLH gene MRF4. Cell 85 (1996) 1-4
102. Osborne C.S., Chakalova L., Brown K.E., Carter D., Horton A., Debrand E., Goyenechea B., Mitchell J.A., Lopes S., Reik W., and Fraser P. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36 (2004) 1065-1071
103. Papp B., and Muller J. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev. 20 (2006) 2041-2054
104. Peichel C.L., Prabhakaran B., and Vogt T.F. The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning. Development 124 (1997) 3481-3492
105. Pennacchio L.A., Ahituv N., Moses A.M., Prabhakar S., Nobrega M.A., Shoukry M., Minovitsky S., Dubchak I., Holt A., Lewis K.D., Plajzer-Frick I., Akiyama J., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444 (2006) 499-502
106. Peters T., Dildrop R., Ausmeier K., and Ruther U. Organization of mouse Iroquois homeobox genes in two clusters suggests a conserved regulation and function in vertebrate development. Genome Res. 10 (2000) 1453-1462
107. Popperl H., and Featherstone M.S. An autoregulatory element of the murine Hox-4.2 gene. EMBO J. 11 (1992) 3673-3680
108. Qin Y., Kong L.K., Poirier C., Truong C., Overbeek P.A., and Bishop C.E. Long-range activation of Sox9 in Odd Sex (Ods) mice. Hum. Mol. Genet. 13 (2004) 1213-1218
109. Renucci A., Zappavigna V., Zakany J., Izpisua-Belmonte J.C., Burki K., and Duboule D. Comparison of mouse and human HOX-4 complexes defines conserved sequences involved in the regulation of Hox-4.4. EMBO J. 11 (1992) 1459-1468
110. Roberts D.J., Johnson R.L., Burke A.C., Nelson C.E., Morgan B.A., and Tabin C. Sonic hedgehog is an endodermal signal inducing Bmp-4 and Hox genes during induction and regionalization of the chick hindgut. Development 121 (1995) 3163-3174
111. Robledo R.F., Rajan L., Li X., and Lufkin T. The Dlx5 and Dlx6 homeobox genes are essential for craniofacial, axial, and appendicular skeletal development. Genes Dev. 16 (2002) 1089-1101
112. Rodriguez I. Remarkable diversity of mammalian pheromone receptor repertoires. Proc. Natl. Acad. Sci. USA 102 (2005) 6639-6640
113. Roy P.J., Stuart J.M., Lund J., and Kim S.K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418 (2002) 975-979
114. Ruiz-Perez V.L., Tompson S.W.J., Blair H.J., Espinoza-Valdez C., Lapunzina P., Silva E.O., Hamel B., Gibbs J.L., Young I.D., Wright M.J., and Goodship J.A. Mutations in two nonhomologous genes in a head-to-head configuration cause Ellis-van Creveld syndrome. Am. J. Hum. Genet. 72 (2003) 728-732
115. Sagai T., Hosoya M., Mizushina Y., Tamura M., and Shiroishi T. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132 (2005) 797-803
116. Schwartz Y.B., and Pirrotta V. Polycomb silencing mechanisms and the management of genomic programmes. Nat. Rev. Genet. 8 (2007) 9-22
117. Semon M., and Duret L. Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol. Biol. Evol. 23 (2006) 1715-1723
118. Sessa L., Breiling A., Lavorgna G., Silvestri L., Casari G., and Orlando V. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 13 (2007) 223-239
119. Shannon M., Hamilton A.T., Gordon L., Branscomb E., and Stubbs L. Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Res. 13 (2003) 1097-1110
120. Sharpe J., Nonchev S., Gould A., Whiting J., and Krumlauf R. Selectivity, sharing and competitive interactions in the regulation of Hoxb genes. EMBO J. 17 (1998) 1788-1798
121. Sharpe J., Lettice L., Hecksher-Sorensen J., Fox M., Hill R., and Krumlauf R. Identification of sonic hedgehog as a candidate gene responsible for the polydactylous mouse mutant Sasquatch. Curr. Biol. 9 (1999) 97-100
122. Shiga Y., Sagawa K., Takai R., Sakaguchi H., Yamagata H., and Hayashi S. Transcriptional read-through of Hox genes Ubx and Antp and their divergent post-transcriptional control during crustacean evolution. Evol. Dev. 8 (2006) 407-414
123. Singer G.A., Lloyd A.T., Huminiecki L.B., and Wolfe K.H. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol. Biol. Evol. 22 (2005) 767-775
124. Slager R.E., Newton T.L., Vlangos C.N., Finucane B., and Elsea S.H. Mutations in RAI1 associated with Smith-Magenis syndrome. Nat. Genet. 33 (2003) 466-468
125. Spellman P.T., and Rubin G.M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1 (2002) 5
126. Spitz F., Gonzalez F., Peichel C., Vogt T.F., Duboule D., and Zakany J. Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev. 15 (2001) 2209-2214
127. Spitz F., Gonzalez F., and Duboule D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113 (2003) 405-417
128. Spitz F., Herkenne C., Morris M.A., and Duboule D. Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat. Genet. 37 (2005) 889-893
129. Sproul D., Gilbert N., and Bickmore W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet. 6 (2005) 775-781
130. Su A.I., Wiltshire T., Batalov S., Lapp H., Ching K.A., Block D., Zhang J., Soden R., Hayakawa M., Kreiman G., Cooke M.P., Walker J.R., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101 (2004) 6062-6067
131. Sumiyama K., Irvine S.Q., Stock D.W., Weiss K.M., Kawasaki K., Shimizu N., Shashikant C.S., Miller W., and Ruddle F.H. Genomic structure and functional control of the Dlx3-7 bigene cluster. Proc. Natl. Acad. Sci. USA 99 (2002) 780-785
132. Tarchini B., and Duboule D. Control of Hoxd genes' collinearity during early limb development. Dev. Cell 10 (2006) 93-103
133. Tarchini B., Duboule D., and Kmita M. Regulatory constraints in the evolution of the tetrapod limb anterior-posterior polarity. Nature 443 (2006) 985-988
134. Trumpp A., Blundell P.A., de la Pompa J.L., and Zeller R. The chicken limb deformity gene encodes nuclear proteins expressed in specific cell types during morphogenesis. Genes Dev. 6 (1992) 14-28
135. Tumpel S., Cambronero F., Ferretti E., Blasi F., Wiedemann L.M., and Krumlauf R. Expression of Hoxa2 in rhombomere 4 is regulated by a conserved cross-regulatory mechanism dependent upon Hoxb1. Dev. Biol. 302 (2007) 646-660
136. van der Hoeven F., Zakany J., and Duboule D. Gene transpositions in the HoxD complex reveal a hierarchy of regulatory controls. Cell 85 (1996) 1025-1035
137. Warming S., Costantino N., Court D.L., Jenkins N.A., and Copeland N.G. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res. 33 (2005) e36
138. Wijgerde M., Grosveld F., and Fraser P. Transcription complex stability and chromatin dynamics in vivo. Nature 377 (1995) 209-213
139. Wotton K.R., and Shimeld S.M. Comparative genomics of vertebrate Fox cluster loci. BMC Genomics 7 (2006) 271
140. Woychik R.P., Stewart T.A., Davis L.G., D'Eustachio P., and Leder P. An inherited limb deformity created by insertional mutagenesis in a transgenic mouse. Nature 318 (1985) 36-40
141. Wu Q., and Maniatis T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell 97 (1999) 779-790
142. Zakany J., and Duboule D. Hox genes and the making of sphincters. Nature 401 (1999) 761-762
143. Zakany J., Gerard M., Favier B., and Duboule D. Deletion of a HoxD enhancer induces transcriptional heterochrony leading to transposition of the sacrum. EMBO J. 16 (1997) 4393-4402
144. Zakany J., Kmita M., and Duboule D. A dual role for Hox genes in limb anterior-posterior asymmetry. Science 304 (2004) 1669-1672
145. Zeller R., Jackson-Grusby L., and Leder P. The limb deformity gene is required for apical ectodermal ridge differentiation and anteroposterior limb pattern formation. Genes Dev. 3 (1989) 1481-1492
146. Zulch A., Becker M.B., and Gruss P. Expression pattern of Irx1 and Irx2 during mouse digit development. Mech. Dev. 106 (2001) 159-162
147. Zuniga A., Haramis A.P., McMahon A.P., and Zeller R. Signal relay by BMP antagonism controls the SHH/FGF4 feedback loop in vertebrate limb buds. Nature 401 (1999) 598-602
148. Zuniga A., Michos O., Spitz F., Haramis A.-P.G., Panman L., Galli A., Vintersten K., Klasen C., Mansfield W., Kuc S., Duboule D., Dono R., et al. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 18 (2004) 1553-1564