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      Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

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          Abstract

          Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches — including cell atlases and organoids — are enabling exploration of the candidate causal factors that underlie human-specific traits.

          Abstract

          In this Review, the authors discuss our latest understanding of evolutionary genetic changes that are specific to humans, which might endow uniquely human traits and capabilities. They describe how new cellular and molecular approaches are helping to decipher the functional implications of these human-specific changes.

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          Most cited references325

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          Is Open Access

          A global reference for human genetic variation

          The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
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            Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.

            Differentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming. Here, we demonstrate induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions. Unexpectedly, Nanog was dispensable. These cells, which we designated iPS (induced pluripotent stem) cells, exhibit the morphology and growth properties of ES cells and express ES cell marker genes. Subcutaneous transplantation of iPS cells into nude mice resulted in tumors containing a variety of tissues from all three germ layers. Following injection into blastocysts, iPS cells contributed to mouse embryonic development. These data demonstrate that pluripotent stem cells can be directly generated from fibroblast cultures by the addition of only a few defined factors.
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              Induction of pluripotent stem cells from adult human fibroblasts by defined factors.

              Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline transmission, from mouse somatic cells by transduction of four defined transcription factors. Here, we demonstrate the generation of iPS cells from adult human dermal fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc. Human iPS cells were similar to human embryonic stem (ES) cells in morphology, proliferation, surface antigens, gene expression, epigenetic status of pluripotent cell-specific genes, and telomerase activity. Furthermore, these cells could differentiate into cell types of the three germ layers in vitro and in teratomas. These findings demonstrate that iPS cells can be generated from adult human fibroblasts.
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                Author and article information

                Contributors
                alex.pollen@ucsf.edu
                craig.lowe@duke.edu
                jarrettgrayson.camp@unibas.ch
                Journal
                Nat Rev Genet
                Nat Rev Genet
                Nature Reviews. Genetics
                Nature Publishing Group UK (London )
                1471-0056
                1471-0064
                3 February 2023
                : 1-25
                Affiliations
                [1 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, , University of California, San Francisco, ; San Francisco, CA USA
                [2 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Neurology, , University of California, San Francisco, ; San Francisco, CA USA
                [3 ]GRID grid.417570.0, ISNI 0000 0004 0374 1269, Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, ; Basel, Switzerland
                [4 ]GRID grid.6612.3, ISNI 0000 0004 1937 0642, University of Basel, ; Basel, Switzerland
                [5 ]GRID grid.26009.3d, ISNI 0000 0004 1936 7961, Department of Molecular Genetics and Microbiology, , Duke University School of Medicine, ; Durham, NC USA
                Author information
                http://orcid.org/0000-0003-3263-8634
                http://orcid.org/0000-0002-6838-1976
                Article
                568
                10.1038/s41576-022-00568-4
                9897628
                36737647
                e81f5a95-3690-4601-8002-240eabc2f84d
                © Springer Nature Limited 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 8 December 2022
                Categories
                Review Article

                evolutionary genetics,development,neuroscience
                evolutionary genetics, development, neuroscience

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