Human adaptation and evolution by segmental duplication

Current Opinion in Genetics & Development - Tập 41 - Trang 44-52 - 2016
Megan Y Dennis1, Evan E Eichler2,3
1Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
2Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
3Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA

Tài liệu tham khảo

Bailey, 2001, Segmental duplications: organization and impact within the current human genome project assembly, Genome Res, 11, 1005, 10.1101/gr.GR-1871R Haldane, 1932 Ohno, 1970 Lynch, 2000, The evolutionary fate and consequences of duplicate genes, Science, 290, 1151, 10.1126/science.290.5494.1151 Carvalho, 2016, Mechanisms underlying structural variant formation in genomic disorders, Nat Rev Genet, 17, 224, 10.1038/nrg.2015.25 Lewis, 1951, Pseudoallelism and gene evolution, Cold Spring Harb Symp Quant Biol, 16, 159, 10.1101/SQB.1951.016.01.014 Sturtevant, 1925, The effects of unequal crossing over at the bar locus in Drosophila, Genetics, 10, 117, 10.1093/genetics/10.2.117 Muller, 1936, Bar duplication, Science, 83, 528, 10.1126/science.83.2161.528-a Marques-Bonet, 2009, A burst of segmental duplications in the genome of the African great ape ancestor, Nature, 457, 877, 10.1038/nature07744 Sudmant, 2013, Evolution and diversity of copy number variation in the great ape lineage, Genome Res, 23, 1373, 10.1101/gr.158543.113 Jiang, 2007, Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution, Nat Genet, 39, 1361, 10.1038/ng.2007.9 Ji, 2008, DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome, Genomics, 91, 249, 10.1016/j.ygeno.2007.10.014 Johnson, 2006, Recurrent duplication-driven transposition of DNA during hominoid evolution, Proc Natl Acad Sci U S A, 103, 17626, 10.1073/pnas.0605426103 Antonacci, 2010, A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk, Nat Genet, 42, 745, 10.1038/ng.643 Zody, 2008, Evolutionary toggling of the MAPT 17q21.31 inversion region, Nat Genet, 40, 1076, 10.1038/ng.193 Giannuzzi, 2013, Evolutionary dynamism of the primate LRRC37 gene family, Genome Res, 23, 46, 10.1101/gr.138842.112 Bekpen, 2012, Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region, Genome Res, 22, 1050, 10.1101/gr.134098.111 Popesco, 2006, Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains, Science, 313, 1304, 10.1126/science.1127980 Johnson, 2001, Positive selection of a gene family during the emergence of humans and African apes, Nature, 413, 514, 10.1038/35097067 Ciccarelli, 2005, Complex genomic rearrangements lead to novel primate gene function, Genome Res, 15, 343, 10.1101/gr.3266405 Dumas, 2012, DUF1220-domain copy number implicated in human brain-size pathology and evolution, Am J Hum Genet, 91, 444, 10.1016/j.ajhg.2012.07.016 Vandepoele, 2005, A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution, Mol Biol Evol, 22, 2265, 10.1093/molbev/msi222 Perry, 2008, Copy number variation and evolution in humans and chimpanzees, Genome Res, 18, 1698, 10.1101/gr.082016.108 Stahl, 2009, Human-specific genes may offer a unique window into human cell signaling, Sci Signal, 2, pe59, 10.1126/scisignal.289pe59 Zimmer, 2015, Phylogenetic analysis supports a link between DUF1220 domain number and primate brain expansion, Genome Biol Evol, 7, 2083, 10.1093/gbe/evv122 Davis, 2014, DUF1220 dosage is linearly associated with increasing severity of the three primary symptoms of autism, PLoS Genet, 10, e1004241, 10.1371/journal.pgen.1004241 Fortna, 2004, Lineage-specific gene duplication and loss in human and great ape evolution, PLoS Biol, 2, E207, 10.1371/journal.pbio.0020207 Sudmant, 2010, Diversity of human copy number variation and multicopy genes, Science, 330, 641, 10.1126/science.1197005 Coe, 2014, Refining analyses of copy number variation identifies specific genes associated with developmental delay, Nat Genet, 46, 1063, 10.1038/ng.3092 Cooper, 2011, A copy number variation morbidity map of developmental delay, Nat Genet, 43, 838, 10.1038/ng.909 Kaminsky, 2011, An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities, Genet Med, 13, 777, 10.1097/GIM.0b013e31822c79f9 Charrier, 2012, Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation, Cell, 149, 923, 10.1016/j.cell.2012.03.034 Dennis, 2012, Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication, Cell, 149, 912, 10.1016/j.cell.2012.03.033 Florio, 2015, Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion, Science, 347, 1465, 10.1126/science.aaa1975 Antonacci, 2014, Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability, Nat Genet, 46, 1293, 10.1038/ng.3120 Boyd, 2015, Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex, Curr Biol, 25, 772, 10.1016/j.cub.2015.01.041 Guerrier, 2009, The F-BAR domain of srGAP2 induces membrane protrusions required for neuronal migration and morphogenesis, Cell, 138, 990, 10.1016/j.cell.2009.06.047 Jobling, 2004 Sharp, 2008, A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures, Nat Genet, 40, 322, 10.1038/ng.93 Locke, 2003, Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization, Genome Res, 13, 347, 10.1101/gr.1003303 Sudmant, 2015, An integrated map of structural variation in 2504 human genomes, Nature, 526, 75, 10.1038/nature15394 Handsaker, 2015, Large multiallelic copy number variations in humans, Nat Genet, 47, 296, 10.1038/ng.3200 Campbell, 2011, Population-genetic properties of differentiated human copy-number polymorphisms, Am J Hum Genet, 88, 317, 10.1016/j.ajhg.2011.02.004 Redon, 2006, Global variation in copy number in the human genome, Nature, 444, 444, 10.1038/nature05329 Sudmant, 2015, Global diversity, population stratification, and selection of human copy-number variation, Science, 349, 10.1126/science.aab3761 Locke, 2006, Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome, Am J Hum Genet, 79, 275, 10.1086/505653 Perry, 2007, Diet and the evolution of human amylase gene copy number variation, Nat Genet, 39, 1256, 10.1038/ng2123 Groot, 1989, The human alpha-amylase multigene family consists of haplotypes with variable numbers of genes, Genomics, 5, 29, 10.1016/0888-7543(89)90083-9 Carpenter, 2015, Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes, Hum Mol Genet, 24, 3472, 10.1093/hmg/ddv098 Usher, 2015, Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity, Nat Genet, 47, 921, 10.1038/ng.3340 Stefansson, 2008, Large recurrent microdeletions associated with schizophrenia, Nature, 455, 232, 10.1038/nature07229 Fledel-Alon, 2011, Variation in human recombination rates and its genetic determinants, PLoS ONE, 6, e20321, 10.1371/journal.pone.0020321 Boettger, 2012, Structural haplotypes and recent evolution of the human 17q21.31 region, Nat Genet, 44, 881, 10.1038/ng.2334 Steinberg, 2012, Structural diversity and African origin of the 17q21.31 inversion polymorphism, Nat Genet, 44, 872, 10.1038/ng.2335 Koolen, 2006, A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism, Nat Genet, 38, 999, 10.1038/ng1853 Sharp, 2006, Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome, Nat Genet, 38, 1038, 10.1038/ng1862 Itsara, 2012, Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing, Am J Hum Genet, 90, 599, 10.1016/j.ajhg.2012.02.013 Koolen, 2012, Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome, Nat Genet, 44, 639, 10.1038/ng.2262 Ikram, 2012, Common variants at 6q22 and 17q21 are associated with intracranial volume, Nat Genet, 44, 539, 10.1038/ng0612-732c Chaisson, 2015, Genetic variation and the de novo assembly of human genomes, Nat Rev Genet, 16, 627, 10.1038/nrg3933 Chaisson, 2015, Resolving the complexity of the human genome using single-molecule sequencing, Nature, 517, 608, 10.1038/nature13907 Gordon, 2016, Long-read sequence assembly of the gorilla genome, Science, 352, aae0344, 10.1126/science.aae0344 Huddleston, 2014, Reconstructing complex regions of genomes using long-read sequencing technology, Genome Res, 24, 688, 10.1101/gr.168450.113 Tai, 2016, Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR, Nat Neurosci, 19, 517, 10.1038/nn.4235