publication . Article . 2017

The evolution and population diversity of human-specific segmental duplications

Dennis, Megan Y; Harshman, Lana; Nelson, Bradley J; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; ...
Open Access English
  • Published: 17 Feb 2017 Journal: volume 1eissn: 2397-334X, Copyright policy
  • Publisher: eScholarship, University of California
Abstract
© 2017 Macmillan Publishers Limited, part of Springer Nature. Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families). We show that HSDs are non-randomly organized, associate preferential...
Subjects
free text keywords: Biotechnology, Genetics, Clinical Research, Human Genome, Article
Funded by
NIH| Improving the Human Reference Genome Resource
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U41HG007635-04S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NHMRC| Defining the role of Genetic Variants in Systemic Lupus Erythematosus: Copy Number Variants and Epigenetic Mechanisms
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1073726
  • Funding stream: Early Career Fellowships
,
NIH| Characterization of Human-Specific Duplicated Genes Implicated in Neurocognitive
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R00NS083627-05
  • Funding stream: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
,
NIH| Sequence and Assembly of Segmental Duplications
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002385-15
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| Sporadic Mutations and Autism Spectrum Disorders
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 4R01MH101221-04
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
79 references, page 1 of 6

O’Bleness, M, Searles, VB, Varki, A, Gagneux, P, Sikela, JM. Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet. 2012; 13: 853-866 [OpenAIRE] [PubMed] [DOI]

Gallego Romero, I. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015; 4: e07103 [OpenAIRE] [PubMed] [DOI]

Khan, Z. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. 2013; 342: 1100-1104 [OpenAIRE] [PubMed] [DOI]

McLean, CY. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 2011; 471: 216-219 [OpenAIRE] [PubMed] [DOI]

Prescott, SL. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell. 2015; 163: 68-83 [OpenAIRE] [PubMed] [DOI]

Vermunt, MW. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016; 19: 494-503 [OpenAIRE] [PubMed] [DOI]

Eichler, EE, Clark, RA, She, X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet. 2004; 5: 345-354 [PubMed] [DOI]

Ohno, S. Evolution by gene duplication. 1970

Boyd, JL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol. 2015; 25: 772-779 [OpenAIRE] [PubMed] [DOI]

Charrier, C. Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell. 2012; 149: 923-935 [OpenAIRE] [PubMed] [DOI]

Dennis, MY. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell. 2012; 149: 912-922 [OpenAIRE] [PubMed] [DOI]

Florio, M. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science. 2015; 347: 1465-1470 [PubMed] [DOI]

Marques-Bonet, T. A burst of segmental duplications in the genome of the African great ape ancestor. Nature. 2009; 457: 877-881 [OpenAIRE] [PubMed] [DOI]

Sudmant, PH. Evolution and diversity of copy number variation in the great ape lineage. Genome research. 2013; 23: 1373-1382 [OpenAIRE] [PubMed] [DOI]

Bailey, JA, Eichler, EE. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006; 7: 552-564 [PubMed] [DOI]

79 references, page 1 of 6
Abstract
© 2017 Macmillan Publishers Limited, part of Springer Nature. Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families). We show that HSDs are non-randomly organized, associate preferential...
Subjects
free text keywords: Biotechnology, Genetics, Clinical Research, Human Genome, Article
Funded by
NIH| Improving the Human Reference Genome Resource
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U41HG007635-04S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NHMRC| Defining the role of Genetic Variants in Systemic Lupus Erythematosus: Copy Number Variants and Epigenetic Mechanisms
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1073726
  • Funding stream: Early Career Fellowships
,
NIH| Characterization of Human-Specific Duplicated Genes Implicated in Neurocognitive
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R00NS083627-05
  • Funding stream: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
,
NIH| Sequence and Assembly of Segmental Duplications
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002385-15
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
NIH| Sporadic Mutations and Autism Spectrum Disorders
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 4R01MH101221-04
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
79 references, page 1 of 6

O’Bleness, M, Searles, VB, Varki, A, Gagneux, P, Sikela, JM. Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet. 2012; 13: 853-866 [OpenAIRE] [PubMed] [DOI]

Gallego Romero, I. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015; 4: e07103 [OpenAIRE] [PubMed] [DOI]

Khan, Z. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. 2013; 342: 1100-1104 [OpenAIRE] [PubMed] [DOI]

McLean, CY. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 2011; 471: 216-219 [OpenAIRE] [PubMed] [DOI]

Prescott, SL. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell. 2015; 163: 68-83 [OpenAIRE] [PubMed] [DOI]

Vermunt, MW. Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nat Neurosci. 2016; 19: 494-503 [OpenAIRE] [PubMed] [DOI]

Eichler, EE, Clark, RA, She, X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet. 2004; 5: 345-354 [PubMed] [DOI]

Ohno, S. Evolution by gene duplication. 1970

Boyd, JL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol. 2015; 25: 772-779 [OpenAIRE] [PubMed] [DOI]

Charrier, C. Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell. 2012; 149: 923-935 [OpenAIRE] [PubMed] [DOI]

Dennis, MY. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell. 2012; 149: 912-922 [OpenAIRE] [PubMed] [DOI]

Florio, M. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science. 2015; 347: 1465-1470 [PubMed] [DOI]

Marques-Bonet, T. A burst of segmental duplications in the genome of the African great ape ancestor. Nature. 2009; 457: 877-881 [OpenAIRE] [PubMed] [DOI]

Sudmant, PH. Evolution and diversity of copy number variation in the great ape lineage. Genome research. 2013; 23: 1373-1382 [OpenAIRE] [PubMed] [DOI]

Bailey, JA, Eichler, EE. Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006; 7: 552-564 [PubMed] [DOI]

79 references, page 1 of 6
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publication . Article . 2017

The evolution and population diversity of human-specific segmental duplications

Dennis, Megan Y; Harshman, Lana; Nelson, Bradley J; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; ...