Contents
English summary v
Nederlandse samenvatting vi
Resum ´e en francais vii
List of abbreviations x
IUPAC code for ambiguous nucleotides x
List of organisms names xi
Foreword xii
1 The Hox gene family 1
1.1 Hox genes: a hundred years’ story . . . 1
1.1.1 From fruitfly mutants to the bithorax complex . . . 1
1.1.2 Organisation in gene clusters and spatial colinearity . . . 3
1.1.3 1980s: The homeobox gene family . . . 4
1.1.4 Discovery of Hox genes in vertebrates . . . 4
1.1.5 1990s: Clustering and colinearity are a common rule . . . 5
1.1.6 2000s: Some exceptions to the cluster rule . . . 6
1.2 The homeobox superfamily of transcription factors . . . 8
1.2.1 Hox gene definition . . . 8
1.2.2 Homeodomain proteins are transcription factors . . . 8
1.2.3 Classification of homeobox genes . . . 10
1.3 The multiple roles of Hox proteins . . . 11
1.3.1 Roles during development . . . 11
1.3.2 Roles in adults . . . 13
1.3.3 Roles in cancers . . . 13
2 Evolution of Hox genes and clusters 15 2.1 The metazoan phylogeny . . . 15
2.2 Hox genes throughout the animal kingdom . . . 19
2.2.1 Classification in homology groups . . . 19
2.2.2 Hox genes and clusters in bilaterians . . . 20
2.2.3 Homeobox genes in non-bilaterian metazoans . . . 31
2.3 Models for the origin and evolution of the Hox genes . . . 33
2.3.1 Reconstructing the Hox content of the bilaterian ancestor . . . 33
2.3.2 The ProtoHox in the Cnidaria-Bilateria ancestor . . . 34
2.4 Methods to classify Hox sequences in homology groups . . . 35
2.4.1 Methods to produce Hox sequences: implications for further studies . . . 35
2.4.2 Phylogenetic tree reconstruction . . . 36
2.4.3 Sequence similarity and Hox ’signatures’ . . . 38
3 Transcriptional regulation by Hox proteins 41 3.1 Hox transcription factors and their cis-regulatory elements . . . 41
3.1.1 Hox target genes . . . 41
3.1.2 Hox cofactors . . . 44
3.2 Detecting cis-regulatory elements with pattern matching . . . 45
3.2.1 Building and describing a motif . . . 45
3.2.2 Pattern matching: scanning a sequence with a motif . . . 48
3.3 Computational approaches applied to search for Hox target genes . . . 50
4 Objectives of the thesis 53
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5 Classification of Hox proteins with HoxPred 55
5.1 HoxPred: a motif-based approach to classify Hox sequences . . . 55
5.2 HoxPred in action: annotation of teleost Hox sequences . . . 68
5.3 Insights into the evolution of Hox and ParaHox genes in metazoans . . . 73
5.3.1 Introduction . . . 73
5.3.2 Methods . . . 75
5.3.3 Results . . . 76
5.3.4 Discussion . . . 89
6 Detection of cis-regulatory elements with RSAT 93 6.1 RSAT: a suite of tools for regulatory sequence analysis . . . 93
6.2 matrix-scan: a comprehensive matrix-based pattern matching program . . . 103
6.3 A guide to detect cis-regulatory elements and modules with RSAT . . . 122
6.4 Application of cis-regulatory element detection to the HoxB1 study case . . . 135
6.4.1 PSSM construction . . . 135
6.4.2 PSSM quality . . . 136
6.4.3 Detecting the annotated PH and PM binding sites . . . 138
6.4.4 Random controls . . . 147
6.4.5 PH and PM site predictions upstream theMeis1gene . . . 148
6.4.6 Conclusions . . . 148
7 General discussion and Perspectives 151 7.1 Detection of cis-regulatory elements with pattern matching . . . 151
7.1.1 Analysis of the HoxB1 target genes . . . 151
7.1.2 Could this approach be used at the scale of a vertebrate genome ? . . . 152
7.1.3 Could this approach be extended to other Hox transcription factors ? . . . 153
7.2 Classification of Hox sequences with HoxPred . . . 154
7.2.1 Considerations for working with Hox sequences . . . 154
7.2.2 HoxPred: a program to classify Hox sequences . . . 155
7.2.3 Evolution of Hox genes . . . 156
7.2.4 Evolution of Hox clusters: hypothetical organisation of the Urbilateria Hox cluster . . . . 158
7.2.5 Xenoturbellida and Acoelomorpha: towards the origins of bilaterians ? . . . 160
References 164
Curriculum vitae 174
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