Human Gene Evolution

by Cooper

• ISBN13: 9780121878702
• ISBN10: 0121878708
• Edition: 1st
• Format: Hardcover
• Copyright: 1999-11-03
• Publisher: Elsevier Science

Summary

Presents the principles of human gene evolution in a concise and easy to understand fashion. Uses examples of how evolutionary processes have molded present day genes, drawn from the evolution of humans and other primates, as well as from more primitive organisms. With increasing attention in this expanding area, this review forms a timely publication of our current knowledge of this important field. Key Features * Structure and function in the human genome * The evolution of gene structure * Mutational mechanisms in evolution

Table of Contents

Preface	xi
Abbreviations	xv
PART 1 INTRODUCTION AND OVERVIEW
Structure and function in the human genome	3	(52)
Introduction	3	(1)
Chromosome structure and function	3	(4)
Chromatin structure	3	(1)
Centromeres	4	(1)
Telomeres	4	(1)
Sites of recombination	5	(1)
Gene distribution and density	6	(1)
Isochores	6	(1)
Matrix attachment regions	6	(1)
Origins of DNA replication	7	(1)
Gene organization and transcriptional regulation	7	(19)
Gene structure and regulation	7	(4)
Polymorphisms	11	(3)
Functional organization of human genes	14	(3)
Pseudogenes	17	(1)
Promoter elements	17	(2)
Enhancers	19	(1)
Negative regulatory elements	19	(1)
Locus control regions	20	(1)
Trans-acting protein factors	20	(1)
5' and 3' untranslated regions	21	(1)
Boundary elements	22	(1)
Sequence motifs involved in mRNA splicing and processing	23	(2)
Polycistronic and polyprotein genes	25	(1)
DNA methylation	26	(4)
CpG islands	27	(1)
CpG suppression in the vertebrate genome and its origin	28	(1)
The CpG dinucleotide as a mutation hotspot	29	(1)
Imprinting and imprinted genes	29	(1)
Repetitive sequence elements	30	(4)
Tandem repeats	30	(1)
Alu sequences and other SINEs	31	(2)
LINE elements	33	(1)
Endogenous retroviral sequences and transposons	34	(1)
Genes, mutations and disease	34	(21)
Single base-pair substitutions within the coding region	36	(1)
Single base-pair substitutions within splice sites	36	(1)
Single base-pair substitutions within promoter regions	37	(1)
Gross gene deletions	37	(1)
Microdeletions	37	(1)
Insertions	37	(1)
Inversions	37	(1)
Expansion of unstable repeat sequences	38	(17)
Evolution of the human genome	55	(52)
Ancient genome duplications at the dawn of vertebrate evolution	55	(8)
Evidence for an ancient genome duplication	55	(2)
Consequences of genome duplications for gene evolution	57	(6)
Mammalian genome evolution	63	(4)
Primate evolution	67	(21)
Adaptation and adaptive radiation	67	(1)
Primate phylogeny	68	(4)
Chromosome evolution in primates	72	(1)
Old World primates	72	(5)
New World primates	77	(1)
Evolution of the human sex chromosomes and the pseudoautosomal regions	77	(4)
Evolution of the mitochondrial genome	81	(3)
The evolution of human populations	84	(2)
The action of natural selection in human populations	86	(2)
Sequencing the genomes of model organisms and humans	88	(19)
PART 2 EVOLUTION OF GENE STRUCTURE
Introns, exons, and evolution	107	(32)
Intron structure, function and evolution	107	(4)
The evolution of alternative processing	111	(5)
Alternative splicing	111	(4)
Aberrant transcripts	115	(1)
mRNA surveilance	115	(1)
Ectopic transcripts	115	(1)
Exon structure and evolution	116	(1)
Introns early or introns late?	116	(4)
Mechanisms of intron insertion and deletion	120	(2)
Exon shuffling	122	(8)
Exon shuffling in the evolution of human genes	122	(1)
The phase compatibility of introns	123	(2)
The serine proteases of coagulation	125	(3)
Protein folds, primordial exons and the emergence of exon shuffling	128	(2)
Pseudoexons	130	(9)
Genes and gene families	139	(82)
The origins of human genes	139	(11)
Genes with a specifically human origin	139	(1)
Human genes which originated after the divergence of Old World monkeys and New World monkeys	140	(1)
Human genes which originated during primate evolution	141	(1)
Human genes whose origin preceded the divergence of mammals	142	(1)
Human genes whose origin preceded the divergence of the vertebrates	143	(1)
Human genes whose origin preceded the divergence of the metazoa	143	(2)
Human genes whose origin preceded the divergence of animals and fungi	145	(1)
Human genes whose origin preceded the divergence of plants and animals	146	(1)
Human genes whose origin preceded the divergence of prokaryotes and eukaryotes	146	(3)
The emergence of genes and gene families has paralleled organismal evolution	149	(1)
Multigene families	150	(46)
Gene families	150	(1)
Actin genes	150	(2)
Albumin genes	152	(1)
Apolipoprotein genes	152	(1)
Complement genes	153	(2)
Crystallin genes	155	(1)
Collagen genes	156	(2)
Genes for the fibroblast growth factors and their receptors	158	(1)
GABA receptor genes	159	(1)
G protein α subunit genes	160	(1)
Globin genes	160	(2)
Growth hormone and somatomammotropin genes	162	(2)
Glycophorin genes	164	(1)
Homeobox genes	165	(3)
Integrin genes	168	(1)
Keratin genes	168	(2)
Genes of the major histocompatibility complex	170	(5)
Mucin genes	175	(1)
Genes encoding RNA-binding proteins	175	(1)
Sulfatase genes	176	(1)
Genes encoding tRNAs and aminoacyl-tRNA synthetases	177	(1)
Ubiquitin genes	178	(1)
An overview of the evolution of multigene families in eukaryotes	179	(1)
Highly repetitive multigene families	180	(1)
Histone genes	180	(1)
Ribosomal RNA genes	181	(1)
5S ribosomal RNA genes	182	(1)
Small nuclear RNA genes	182	(1)
Gene superfamilies	183	(1)
Cadherin genes	183	(1)
Cytochrome P450 genes	183	(1)
Cystatin genes	184	(1)
G-protein-coupled receptor genes	184	(1)
Heat shock genes	185	(1)
Insulin and insulin-like growth factor genes	186	(1)
Interferon genes	186	(3)
Nuclear receptor genes	189	(1)
Protein kinase C genes	190	(1)
Serine protease genes	190	(1)
Serpin genes	191	(1)
Zinc finger genes	192	(1)
Olfactory receptor genes	193	(1)
Genes which undergo programmed rearrangement	194	(1)
Immunoglobulin genes	194	(2)
T-cell receptor genes	196	(1)
Convergent evolution	196	(2)
Coevolution	198	(23)
Promoters and transcription factors	221	(44)
Promoters and enhancers	221	(28)
Evolutionary conservation of cis-acting elements and `phylogenetic footprinting'	223	(2)
Nonhomologous genes containing similar regulatory elements	225	(1)
Paralogous genes containing dissimilar regulatory elements	225	(3)
Orthologous genes containing dissimilar regulatory elements	228	(3)
Bidirectional promoters	231	(2)
5' and 3' untranslated regions of genes	233	(1)
Inter-specific differences in promoter selection	234	(1)
Developmental changes in gene expression	235	(1)
Promoter polymorphisms	236	(2)
Promoter duplication	238	(1)
Functional redundancy of promoter elements	238	(1)
Recruitment of repetitive sequences as promoter and silencer elements	238	(1)
Alu sequences	238	(3)
Endogeneous retroviral elements	241	(3)
LINE elements	244	(1)
Minisatellites and microsatellites	245	(1)
mRNA editing	246	(1)
Coordinate regulation	247	(1)
Changes in expression of developmentally significant gene products	247	(2)
Transcription factors	249	(16)
Transcription factor families	250	(1)
Functional conservation of orthalogous transcription factors	251	(1)
Functional redundancy of paralogous transcription factors	251	(1)
Paralogus transcription factors	252	(1)
Orthologous transcription factors	253	(1)
Alternative splicing of transcription factor genes	253	(1)
Promoter shuffling in transcription factor genes	253	(1)
Transcription factor-binding site interactions	253	(1)
Exon shuffling in the evolution of transcription factors	254	(11)
Pseudogenes and their formation	265	(32)
Pseudogene formation	265	(14)
The generation of pseudogenes by duplication	265	(4)
The generation of pseudogenes by retrotransposition	269	(6)
The generation of pseudogenes by other means	275	(1)
Origin and age of pseudogenes	275	(1)
Patterns of mutation in pseudogenes	276	(1)
Pseudogenes and gene conversion	276	(2)
Pseudogene reactivation	278	(1)
Gene loss/inactivation in primates	279	(18)
Urate oxidase gene	280	(1)
α-1,3-Galactosyltransferase gene	280	(1)
Elastase 1 gene	281	(1)
L-gulono-γ-lactone oxidase gene	281	(1)
ADP-ribosyltransferase 1 gene	282	(1)
Haptoglobin gene	282	(1)
Fertilin-α gene	282	(1)
T-cell receptor γ V10 variable region gene	283	(1)
Cytidine monophospho-N-acetylneuramic acid hydroxylase gene	283	(1)
Flavin-containing monooxygenase 2 gene	283	(1)
Overview	284	(13)
PART 3 MUTATIONAL MECHANISMS IN EVOLUTION
Single base-pair substitutions	297	(32)
Single base-pair substitutions in evolution	297	(8)
The selectionist and neutralist perspectives	297	(2)
Synonymous and nonsynonymous substitutions	299	(1)
Positive and negative selection in protein evolution	300	(3)
Mutation rates and their evolution	303	(1)
The deleterious mutation rate in humans	304	(1)
Mutations in pathology and evolution; two sides of the same coin	305	(2)
The importance of evolutionary conservation in the study of pathological mutations at the protein level using human factor IX as a model	307	(4)
Equilibrium of synonymous codon substitutions	311	(1)
Single base-pair substitutions in gene regions	312	(1)
Neighboring-nucleotide effects on the rate of germline single base-pair substitutions in human genes	313	(2)
Single base-pair substitutions in evolution which have altered the function of specific amino acid residues	315	(4)
The visual pigments	316	(2)
The kringle domains of apolipoprotein(a)	318	(1)
The DNA-binding specificity of steroid receptors	318	(1)
The calcium-dependent and -independent synaptotagmins	319	(1)
Olfactory receptor-ligand interactions	319	(1)
Single base-pair substitutions in evolution which have affected mRNA splicing	319	(10)
Splicing mutation and gene inactivation	320	(1)
Splice site difference between orthologous genes	321	(1)
Splice site differences between paralogous genes	321	(8)
Contractions and expansions in gene size and number	329	(60)
Gross gene deletions in evolution	329	(2)
Gross gene deletions during primate evolution	329	(1)
Gross deletional polymorphisms	330	(1)
Microdeletions in evolution	331	(3)
Microdeletions in pathology	331	(1)
Microdeletions mediated by direct repeats	332	(1)
Microdeletions mediated by inverted repeats	333	(1)
Microdeletions in vertebrate evolution	334	(1)
Microinsertions in evolution	334	(2)
Gene coding region microinsertions	334	(1)
Microinsertion polymorphisms	335	(1)
Indels	335	(1)
Insertion of transposable elements in evolution	336	(8)
Endogenous retroviral sequences and transposable elements	337	(1)
Retrotransposons	337	(1)
Transposons	338	(1)
LINE elements	339	(1)
Alu sequences	340	(1)
Evolution of Alu sequences	340	(2)
Alu sequence polymorphisms	342	(1)
Alu sequences target sites	342	(1)
Alu sequences within protein-coding sequences	342	(1)
Splice-mediated insertion of Alu sequences	342	(2)
Alu sequence incorporation by intron sliding	344	(1)
Gross gene duplications in evolution	344	(8)
Duplications and the emergence of paralogous genes	346	(1)
Intra-chromosomal regional duplication	346	(1)
Tandem duplications	346	(1)
Translocation of duplicated genes	347	(1)
Duplication of translocated genes	347	(1)
Syntenic relationships and gene dispersal	348	(1)
Functional redundancy and post-duplication diversification	349	(1)
Truncated gene copies	350	(1)
Duplicational polymorphisms	351	(1)
Intragenic gene duplications in evolution	352	(5)
Multi-exon duplications	352	(1)
Exon duplication	353	(2)
Intra-exonic duplications	355	(1)
The emergence of primordial genes by oligomer duplication	356	(1)
Intragenic duplicational polymorphisms	357	(1)
Coding sequence expansion and contraction resulting from the introduction or removal of inititation and termination codons	357	(1)
Minisatellites, microsatellites and telomeric repeats	358	(2)
Minisatellite DNA sequences	358	(1)
Microsatellite DNA sequences	359	(1)
Telomeric and centromeric repetitive DNA	360	(1)
Expansion of unstable repeat sequences	360	(29)
Triplet repeat expansion disorders	360	(3)
Nature and distribution of triplet repeats in the human genome	363	(1)
Origin of expanded triplet repeats	363	(1)
Evolution of repeat number in the genes underlying disorders of triplet repeat expansion	364	(3)
The unique case of involucrin	367	(22)
Gross gene rearrangements	389	(34)
Inversions	389	(3)
Pericentric inversions	389	(1)
Paracentric inversions	390	(1)
Physiological and pathological inversions	391	(1)
Intragenic inversions	391	(1)
Common sites for inversions in pathology and evolution	392	(1)
Translocations and transpositions	392	(5)
Pericentromeric-directed transposition	394	(2)
Sub-telomeric transposition	396	(1)
Translocations and chromosome associations	397	(1)
Translocations in pathology and evolution	397	(1)
Gene fusion	397	(6)
Gene fusion during evolution	398	(3)
Internal methionines as evidence for ancient gene fusion events	401	(1)
Fusion gene polymorphisms	402	(1)
Fusion splicing	402	(1)
Recombination	403	(5)
Homologous recombination	403	(3)
V(D)J recombination	406	(2)
Gene conversion	408	(3)
Gene creation by retrotransposition	411	(12)
Molecular reconstruction of ancient genes/proteins	423	(16)
Introduction	423	(1)
Molecular reconstruction and homology modelling of the catalytic domain of the common ancestor of the hemostatic vitamin K-dependent serine proteases	424	(15)
The evolution of the vitamin K-dependent coagulation factors	424	(1)
Reconstruction of mammalian ancestral cDNAs	425	(1)
Evolutionary divergence of the vitamin K-dependent coagulation factors	426	(2)
Reconstruction of a common ancestor of the vitamin K-dependent coagulation factors	428	(3)
The evolution of human protein C	431	(1)
Comparison of the functional architecture of early mammalian protein C with the putative ancestor of all vitamin K-dependent factors	432	(3)
Comparative geometry of the active sites of early mammalian and extant protein C	435	(4)
Indices of Human Gene Symbols used in the text	439	(36)
Index	475