Mobile elements create structural variation: analysis of a complete human genome.

Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed approximately 126 kb of sequence from the HuRef genome. Overall, approximately 10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation.

[1]  M. Batzer,et al.  An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. , 2009, Genomics.

[2]  M. Batzer,et al.  Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons , 2008, PloS one.

[3]  M. Batzer,et al.  L1 recombination-associated deletions generate human genomic variation , 2008, Proceedings of the National Academy of Sciences.

[4]  Hugo Y. K. Lam,et al.  Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. , 2008, Genome research.

[5]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[6]  Fengtang Yang,et al.  Copy number variation and evolution in humans and chimpanzees. , 2008, Genome research.

[7]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[8]  H. Kazazian,et al.  Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites , 2008, Cell.

[9]  Joshua M. Korn,et al.  Integrated detection and population-genetic analysis of SNPs and copy number variation , 2008, Nature Genetics.

[10]  Joshua M. Korn,et al.  Mapping and sequencing of structural variation from eight human genomes , 2008, Nature.

[11]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[12]  P. Deininger,et al.  Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. , 2008, Genome research.

[13]  Zachary A. Szpiech,et al.  Genotype, haplotype and copy-number variation in worldwide human populations , 2008, Nature.

[14]  P. Stenson,et al.  Human Gene Mutation Database: towards a comprehensive central mutation database , 2007, Journal of Medical Genetics.

[15]  J. Lupski,et al.  A DNA Replication Mechanism for Generating Nonrecurrent Rearrangements Associated with Genomic Disorders , 2007, Cell.

[16]  Philip M. Kim,et al.  Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome , 2007, Science.

[17]  Michael M. Murphy,et al.  IgH class switching and translocations use a robust non-classical end-joining pathway , 2007, Nature.

[18]  M. Batzer,et al.  Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome , 2007, PLoS genetics.

[19]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[20]  Charles Lee,et al.  Copy number variations and clinical cytogenetic diagnosis of constitutional disorders , 2007, Nature Genetics.

[21]  S. Mccarroll,et al.  Copy-number variation and association studies of human disease , 2007, Nature Genetics.

[22]  H. Kazazian,et al.  Progress in understanding the biology of the human mutagen LINE‐1 , 2007, Human mutation.

[23]  M. Batzer,et al.  Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome , 2007, Nucleic acids research.

[24]  D. Altshuler,et al.  Completing the map of human genetic variation , 2007, Nature.

[25]  Webb Miller,et al.  Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome , 2007, Science.

[26]  Miriam K. Konkel,et al.  Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. , 2007, Gene.

[27]  M. Batzer,et al.  Mobile DNA elements in primate and human evolution. , 2007, American journal of physical anthropology.

[28]  Carolyn J. Brown,et al.  A comprehensive analysis of common copy-number variations in the human genome. , 2007, American journal of human genetics.

[29]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[30]  Matthew D. Dyer,et al.  Human genomic deletions mediated by recombination between Alu elements. , 2006, American journal of human genetics.

[31]  Richard Cordaux,et al.  Estimating the retrotransposition rate of human Alu elements. , 2006, Gene.

[32]  Ryan E. Mills,et al.  Recently mobilized transposons in the human and chimpanzee genomes. , 2006, American journal of human genetics.

[33]  Deepak Grover,et al.  dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans , 2006, Human mutation.

[34]  D. Cooper,et al.  LINE-1 Endonuclease-Dependent Retrotranspositional Events Causing Human Genetic Disease: Mutation Detection Bias and Multiple Mechanisms of Target Gene Disruption , 2006, Journal of biomedicine & biotechnology.

[35]  Jerilyn A. Walker,et al.  SVA elements: a hominid-specific retroposon family. , 2005, Journal of molecular biology.

[36]  J. V. Moran,et al.  Multiple Fates of L1 Retrotransposition Intermediates in Cultured Human Cells , 2005, Molecular and Cellular Biology.

[37]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[38]  Jeffrey S. Han,et al.  Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. , 2005, Genome research.

[39]  M. Batzer,et al.  Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages , 2005, Nucleic acids research.

[40]  S. Boissinot,et al.  The recent evolution of human L1 retrotransposons , 2005, Cytogenetic and Genome Research.

[41]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[42]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[43]  M. Batzer,et al.  Alu retrotransposition-mediated deletion. , 2005, Journal of molecular biology.

[44]  B. Mishra,et al.  Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Peter D Stenson,et al.  Meta‐Analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage , 2005, Human mutation.

[46]  Doree Sitkoff,et al.  models homology modeling : From sequence alignments to structural A comparative study of available software for high-accuracy , 2005 .

[47]  P. Simmonds,et al.  Allelic Variation of HERV-K(HML-2) Endogenous Retroviral Elements in Human Populations , 2004, Journal of Molecular Evolution.

[48]  C. Desmaze,et al.  Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. , 2004, Molecular cell.

[49]  Jinchuan Xing,et al.  Differential alu mobilization and polymorphism among the human and chimpanzee lineages. , 2004, Genome research.

[50]  Jef D. Boeke,et al.  Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes , 2004, Nature.

[51]  H. Kazazian.  Mobile Elements: Drivers of Genome Evolution , 2004, Science.

[52]  A. Kiltie,et al.  DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining. , 2004, Nucleic acids research.

[53]  E. Eichler,et al.  An Alu transposition model for the origin and expansion of human segmental duplications. , 2003, American journal of human genetics.

[54]  E. Eichler,et al.  Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. , 2003, Genome research.

[55]  M. Batzer,et al.  Comprehensive Analysis of Two Alu Yd Subfamilies , 2003, Journal of Molecular Evolution.

[56]  Jef D Boeke,et al.  Human L1 element target‐primed reverse transcription in vitro , 2002, The EMBO journal.

[57]  A. Pavlícek,et al.  Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. , 2002, Gene.

[58]  Giovanni Parmigiani,et al.  Human L1 Retrotransposition Is Associated with Genetic Instability In Vivo , 2002, Cell.

[59]  J. V. Moran,et al.  Genomic Deletions Created upon LINE-1 Retrotransposition , 2002, Cell.

[60]  J. V. Moran,et al.  DNA repair mediated by endonuclease-independent LINE-1 retrotransposition , 2002, Nature Genetics.

[61]  M. Batzer,et al.  Alu repeats and human genomic diversity , 2002, Nature Reviews Genetics.

[62]  P. Stankiewicz,et al.  Genome architecture, rearrangements and genomic disorders. , 2002, Trends in genetics : TIG.

[63]  E. Ostertag,et al.  Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. , 2001, Genome research.

[64]  E. Ostertag,et al.  Biology of mammalian L1 retrotransposons. , 2001, Annual review of genetics.

[65]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[66]  S T Sherry,et al.  Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. , 2000, Genome research.

[67]  M. Nachman,et al.  Estimate of the mutation rate per nucleotide in humans. , 2000, Genetics.

[68]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[69]  M. Batzer,et al.  Alu repeats and human disease. , 1999, Molecular genetics and metabolism.

[70]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[71]  I. Kanazawa,et al.  An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy , 1998, Nature.

[72]  J. V. Moran,et al.  The impact of L1 retrotransposons on the human genome , 1998, Nature Genetics.

[73]  M. Jasin,et al.  Homology-directed repair is a major double-strand break repair pathway in mammalian cells. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[74]  Jef D Boeke,et al.  Human L1 Retrotransposon Encodes a Conserved Endonuclease Required for Retrotransposition , 1996, Cell.

[75]  J. Haber,et al.  Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[76]  T. Eickbush,et al.  Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition , 1993, Cell.

[77]  S. Antonarakis,et al.  Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man , 1988, Nature.

[78]  G. Grimaldi,et al.  Defining the beginning and end of KpnI family segments. , 1984, The EMBO journal.