Molecular evolution of the homeodomain family of transcription factors

Nucleic Acids Research

Volumn 29, Issue 15, 2001, Pages 3258-3269

  Banerjee Basu, S ^a   Baxevanis, A D ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HELIX LOOP HELIX PROTEIN; HOMEODOMAIN PROTEIN; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CELL ACTIVITY; CELL FATE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DEVELOPMENTAL BIOLOGY; DNA BINDING; DNA STRUCTURE; EMBRYO; EMBRYO PATTERN FORMATION; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; GENETIC PROCEDURES; HUMAN; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PHYSICAL DEVELOPMENT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FAMILY; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE;

ANIMALIA; METAZOA;

EID: 0035420653     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.15.3258     Document Type: Article

References (85)

1. Structural relationships among genes that control development: Sequence homology between the Antennapedia, Ultrabithorax and fushi tarazu loci of Drosophila
2. A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes
3. Homeodomain proteins
4. The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding
5. Solution structure of the POU-specific DNA-binding domain of Oct-1
6. Structure of the rat thyroid transcription factor-1 (TTF-1) gene
7. Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: Basis of binding specificity
8. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions
9. Crystallization and preliminary X-ray diffraction studies of the engrailed homeodomain and of an engrailed homeodomain/DNA complex
10. The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: Comparison with prokaryotic repressors
11. Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain
12. Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions
13. Homeodomain-DNA recognition
14. Comprehensive classification of homeobox genes
15. Threading analysis of Prospero-type homeodomains
16. Origin of the paired domain
17. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster
18. The function and evolution of Msx genes: Pointers and paradoxes
19. Ancient origin of the HOX gene cluster
20. Analysis of a complete homeobox gene repertoire: Implications for the evolution of diversity
21. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
22. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
23. The neighbor-joining method: A new method for reconstructing phylogenetic trees
24. Engrailed (Gln50→Lys) homeodomain-DNA complex at 1.9 Å resolution: Structural basis for enhanced affinity and altered specificity
25. Developmental genetics of homoeosis
26. A gene complex controlling segmentation in Drosophila
27. Two steps in the evolution of Antennapedia-class vertebrate homeobox genes
28. Phylogenetic reconstruction of vertebrate Hox cluster duplications
29. A rational nomenclature for vertebrate homeobox (HOX) genes
30. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes
31. DNA binding specificity of homeodomains
32. Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation
33. Absence of radius and ulna in mice lacking hoxa-11 and hoxd-11
34. Amegakaryocytic thrombocytopenia and radio-ulnar synostosis are associated with HOXA11 mutation
35. Axial homeosis and appendicular skeleton defects in mice with a targeted disruption of hoxd-11
36. Deletions in HOXD13 segregate with an identical, novel foot malformation in two unrelated families
37. Mutation of HOXA13 in hand-foot-genital syndrome
38. Novel HOXA13 mutations and the phenotypic spectrum of hand-foot-genital syndrome
39. Disruption of the murine homeobox gene Cdx1 affects axial skeletal identities by altering the mesodermal expression domains of Hox genes
40. Cdx1 and cdx2 expression during intestinal development
41. Combined-method phylogenetic analysis of Hox and ParaHox genes of the metazoa
42. Isolation and mapping of EVX1, a human homeobox gene homologous to even-skipped, localized at the 5′ end of HOX1 locus on chromosome 7
43. EVX2, a human homeobox gene homologous to the even-skipped segmentation gene, is localized at the 5′ end of HOX4 locus on chromosome 2
44. Evidence for 14 homeobox gene clusters in human genome ancestry
45. The HOX complex neighbored by the EVX gene, as well as two other homeobox-containing genes, the GBX-class and the EN-class, are located on the same chromosomes 2 and 7 in humans
46. Structural basis of an embryonically lethal single Ala → The mutation in the vnd/NK-2 homeodomain
47. The cardiac homeobox gene Csx/Nkx2.5 lies genetically upstream of multiple genes essential for heart development
48. Vertebrate homologs of tinman and bagpipe: Roles of the homeobox genes in cardiovascular development
49. Congenital heart disease caused by mutations in the transcription factor NKX2-5
50. Functional analyses of three Csx/Nkx-2.5 mutations that cause human congenital heart disease
51. The gene tinman is required for specification of the heart and visceral muscles in Drosophila
52. Epithelial-mesenchymal interactions are required for msx 1 and msx 2 gene expression in the developing murine molar tooth
53. Role of the Dlx homeobox genes in proximodistal patterning of the branchial arches: Mutations of Dlx-1, Dlx-2 and Dlx-1 and -2 alter morphogenesis of proximal skeletal and soft tissue structures derived and second arches
54. Msx2 deficiency in mice causes pleiotropic defects in bone growth and ectodermal organ formation
55. Msx1 deficient mice exhibit cleft palate and abnormalities of craniofacial and tooth development
56. MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans
57. A mutation in the homeodomain of the human MSX2 gene in a family affected with autosomal dominant craniosynostosis
58. Functional haploinsufficiency of the human homeobox gene MSX2 causes defects in skull ossification
59. Identification of a mutation in DLX3 associated with trichodento-osseous (TDO) syndrome
60. Cloning and characterization of two members of the vertebrate Dlx gene family
61. Assignment of the human homolog of mouse Dlx3 to chromosome 17q21.3-q22 by analysis of somatic cell hybrids and fluorescence in situ hybridization
62. Genomic analysis of a new mammalian distal-less gene: Dlx7
63. Mutations at the PAX6 locus are found in heterogeneous anterior segment malformations including Peters' anomaly
64. Pax6 and the genetic control of early eye development
65. Specification of pituitary cell lineages by the LIM homeobox gene Lhx3
66. Mutations in LHX3 result in a new syndrome revealed by combined pituitary hormone deficiency
67. Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome
68. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules
69. Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans
70. Association between X-linked mixed deafness and mutations in the POU domain gene POU3F4
71. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals
72. Mutations in the homeodomain of the human SIX3 gene cause holoprosencephaly
73. Expression of a novel murine homeobox gene in the developing cerebellar external granular layer during its proliferation
74. Mutations in TGIF cause holoprosencephaly and link NODAL signalling to human neural axis determination
75. Initial sequencing and analysis of the human genome
76. Structure of chromosomal duplicons and their role in mediating human genomic disorders
77. Masquerading repeats: Paralogous pitfalls of the human genome
78. Pathological consequences of sequence duplications in the human genome
79. Molecular phylogeny
80. A molecular evolutionary framework for eukaryotic model organisms
81. Gen(om)e duplications in the evolution of early vertebrates
82. ALSCRIPT: A tool to format multiple sequence alignments