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  • 1
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    Human-specific loss of regulatory DNA and the evolution of human-specific traits (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-11
    Description: Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071156/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071156/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLean, Cory Y -- Reno, Philip L -- Pollen, Alex A -- Bassan, Abraham I -- Capellini, Terence D -- Guenther, Catherine -- Indjeian, Vahan B -- Lim, Xinhong -- Menke, Douglas B -- Schaar, Bruce T -- Wenger, Aaron M -- Bejerano, Gill -- Kingsley, David M -- 1 F32 HD062137-01/HD/NICHD NIH HHS/ -- P50 HG002568/HG/NHGRI NIH HHS/ -- P50 HG002568-10/HG/NHGRI NIH HHS/ -- R01 HD059862/HD/NICHD NIH HHS/ -- R01 HD059862-03/HD/NICHD NIH HHS/ -- R01 HG005058/HG/NHGRI NIH HHS/ -- R01 HG005058-03/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Mar 10;471(7337):216-9. doi: 10.1038/nature09774.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21390129" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Brain/anatomy & histology/metabolism ; Chromosomes, Mammalian/genetics ; Conserved Sequence/genetics ; DNA/*genetics ; DNA, Intergenic/genetics ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; Genes, Tumor Suppressor ; Genome, Human/*genetics ; *Human Characteristics ; Humans ; Male ; Mice ; Organ Specificity ; Pan troglodytes/genetics ; Penis/anatomy & histology/metabolism ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Deletion/*genetics ; Species Specificity ; Transgenes/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Radial glia require PDGFD-PDGFRbeta signalling in human but not mouse neocortex (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-11-14
    Description: Evolutionary expansion of the human neocortex underlies many of our unique mental abilities. This expansion has been attributed to the increased proliferative potential of radial glia (RG; neural stem cells) and their subventricular dispersion from the periventricular niche during neocortical development. Such adaptations may have evolved through gene expression changes in RG. However, whether or how RG gene expression varies between humans and other species is unknown. Here we show that the transcriptional profiles of human and mouse neocortical RG are broadly conserved during neurogenesis, yet diverge for specific signalling pathways. By analysing differential gene co-expression relationships between the species, we demonstrate that the growth factor PDGFD is specifically expressed by RG in human, but not mouse, corticogenesis. We also show that the expression domain of PDGFRbeta, the cognate receptor for PDGFD, is evolutionarily divergent, with high expression in the germinal region of dorsal human neocortex but not in the mouse. Pharmacological inhibition of PDGFD-PDGFRbeta signalling in slice culture prevents normal cell cycle progression of neocortical RG in human, but not mouse. Conversely, injection of recombinant PDGFD or ectopic expression of constitutively active PDGFRbeta in developing mouse neocortex increases the proportion of RG and their subventricular dispersion. These findings highlight the requirement of PDGFD-PDGFRbeta signalling for human neocortical development and suggest that local production of growth factors by RG supports the expanded germinal region and progenitor heterogeneity of species with large brains.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231536/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lui, Jan H -- Nowakowski, Tomasz J -- Pollen, Alex A -- Javaherian, Ashkan -- Kriegstein, Arnold R -- Oldham, Michael C -- R01 NS021223/NS/NINDS NIH HHS/ -- R01 NS072630/NS/NINDS NIH HHS/ -- R01 NS075998/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Nov 13;515(7526):264-8. doi: 10.1038/nature13973.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25391964" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Cycle ; Cell Proliferation ; Gene Expression Profiling ; Humans ; Lymphokines/genetics/*metabolism ; Mice ; Neocortex/cytology/growth & development/*metabolism ; Neuroglia/cytology/*metabolism ; Platelet-Derived Growth Factor/genetics/*metabolism ; Receptor, Platelet-Derived Growth Factor beta/*metabolism ; *Signal Transduction/genetics ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The genomic basis of adaptive evolution in threespine sticklebacks (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-04-07
    Description: Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322419/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322419/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Felicity C -- Grabherr, Manfred G -- Chan, Yingguang Frank -- Russell, Pamela -- Mauceli, Evan -- Johnson, Jeremy -- Swofford, Ross -- Pirun, Mono -- Zody, Michael C -- White, Simon -- Birney, Ewan -- Searle, Stephen -- Schmutz, Jeremy -- Grimwood, Jane -- Dickson, Mark C -- Myers, Richard M -- Miller, Craig T -- Summers, Brian R -- Knecht, Anne K -- Brady, Shannon D -- Zhang, Haili -- Pollen, Alex A -- Howes, Timothy -- Amemiya, Chris -- Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Jaffe, David B -- Nicol, Robert -- Wilkinson, Jane -- Lander, Eric S -- Di Palma, Federica -- Lindblad-Toh, Kerstin -- Kingsley, David M -- 095908/Wellcome Trust/United Kingdom -- P50 HG002568/HG/NHGRI NIH HHS/ -- P50 HG002568-09/HG/NHGRI NIH HHS/ -- P50 HG002568-09S1/HG/NHGRI NIH HHS/ -- P50-HG002568/HG/NHGRI NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22481358" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Alaska ; Animals ; Aquatic Organisms/genetics ; *Biological Evolution ; Chromosome Inversion/genetics ; Chromosomes/genetics ; Conserved Sequence/genetics ; Ecotype ; Female ; Fresh Water ; Genetic Variation/genetics ; Genome/*genetics ; Genomics ; Molecular Sequence Data ; Seawater ; Sequence Analysis, DNA ; Smegmamorpha/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-12-08
    Description: Systematic analyses of spatiotemporal gene expression trajectories during organogenesis have been challenging because diverse cell types at different stages of maturation and differentiation coexist in the emerging tissues. We identified discrete cell types as well as temporally and spatially restricted trajectories of radial glia maturation and neurogenesis in developing human telencephalon. These lineage-specific trajectories reveal the expression of neurogenic transcription factors in early radial glia and enriched activation of mammalian target of rapamycin signaling in outer radial glia. Across cortical areas, modest transcriptional differences among radial glia cascade into robust typological distinctions among maturing neurons. Together, our results support a mixed model of topographical, typological, and temporal hierarchies governing cell-type diversity in the developing human telencephalon, including distinct excitatory lineages emerging in rostral and caudal cerebral cortex.
    Keywords: Neuroscience
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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