1
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Kaelin CB, McGowan KA, Hutcherson AD, Delay JM, Li JH, Kiener S, Jagannathan V, Leeb T, Murphy WJ, Barsh GS. Ancestry dynamics and trait selection in a designer cat breed. Curr Biol 2024; 34:1506-1518.e7. [PMID: 38531359 DOI: 10.1016/j.cub.2024.02.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/10/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats. The mean proportion of leopard cat DNA in the Bengal breed is 3.48%, lower than predicted from breed history, and is broadly distributed, covering 93% of the Bengal genome. Overall, leopard cat introgressions do not show strong signatures of selection across the Bengal breed. However, two popular color traits in Bengal cats, charcoal and pheomelanin intensity, are explained by selection of leopard cat genes whose expression is reduced in a domestic cat background, consistent with genetic incompatibility resulting from hybridization. We characterize several selective sweeps in the Bengal genome that harbor candidate genes for pelage and color pattern and that are associated with domestic, rather than leopard, cat haplotypes. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies glitter, a trait desired by breeders that affects hair texture and light reflectivity.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - John M Delay
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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2
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Cannon A, McMillan O, Kelley WV, East KM, Cochran ME, Miskell EL, Moss IP, Garner-Duckworth S, Redden DT, Might M, Barsh GS, Korf BR. Medical and psychosocial outcomes of state-funded population genomic screening. Clin Genet 2023; 104:434-442. [PMID: 37340305 DOI: 10.1111/cge.14394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
As the uptake of population screening expands, assessment of medical and psychosocial outcomes is needed. Through the Alabama Genomic Health Initiative (AGHI), a state-funded genomic research program, individuals received screening for pathogenic or likely pathogenic variants in 59 actionable genes via genotyping. Of the 3874 eligible participants that received screening results, 858 (22%) responded to an outcomes survey. The most commonly reported motivation for seeking testing through AGHI was contribution to genetic research (64%). Participants with positive results reported a higher median number of planned actions (median = 5) due to AGHI results as compared to negative results (median = 3). Interviews were conducted with survey participants with positive screening results. As determined by certified genetic counselors, 50% of interviewees took appropriate medical action based on their result. There were no negative or harmful actions taken. These findings indicate population genomic screening of an unselected adult population is feasible, is not harmful, and may have positive outcomes on participants now and in the future; however, further research is needed in order to assess clinical utility.
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Affiliation(s)
- Ashley Cannon
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olivia McMillan
- School of Health Professions, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Meagan E Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Edrika L Miskell
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Irene P Moss
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew Might
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Bruce R Korf
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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3
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Lemke AA, Thompson ML, Gimpel EC, McNamara KC, Rich CA, Finnila CR, Cochran ME, Lawlor JMJ, East KM, Bowling KM, Latner DR, Hiatt SM, Amaral MD, Kelley WV, Greve V, Gray DE, Felker SA, Meddaugh H, Cannon A, Luedecke A, Jackson KE, Hendon LG, Janani HM, Johnston M, Merin LA, Deans SL, Tuura C, Hughes T, Williams H, Laborde K, Neu MB, Patrick-Esteve J, Hurst ACE, Kirmse BM, Savich R, Spedale SB, Knight SJ, Barsh GS, Korf BR, Cooper GM, Brothers KB. Parents' Perspectives on the Utility of Genomic Sequencing in the Neonatal Intensive Care Unit. J Pers Med 2023; 13:1026. [PMID: 37511639 PMCID: PMC10382030 DOI: 10.3390/jpm13071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents' experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. METHODS Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child's sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. RESULTS Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child's future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent-infant bonding, and reported variable impact on their feelings of guilt. CONCLUSION Parents reported that GS during the neonatal period was useful because it provided a "backbone" for their child's care. Parents did not consistently endorse negative impacts like interference with parent-infant bonding.
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Affiliation(s)
- Amy A Lemke
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Emily C Gimpel
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Katelyn C McNamara
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carla A Rich
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Meagan E Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kevin M Bowling
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephanie A Felker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Hannah Meddaugh
- Department of Genetics, Ochsner Health System, New Orleans, LA 70121, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amanda Luedecke
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kelly E Jackson
- Division of Genetics, Norton Children's Genetics Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Laura G Hendon
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Hillary M Janani
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Marla Johnston
- Department of Pediatrics, Children's Hospital New Orleans, New Orleans, LA 70118, USA
| | - Lee Ann Merin
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sarah L Deans
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carly Tuura
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Trent Hughes
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Heather Williams
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Kelly Laborde
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Matthew B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian M Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Renate Savich
- Pediatrics Neonatology Division, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Steven B Spedale
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Sara J Knight
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
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4
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Barsh GS, Butler G, Copenhaver GP, Crosson S, Søgaard-Andersen L, Stukenbrock EH. Endless microbes most beautiful and most wonderful. PLoS Genet 2023; 19:e1010695. [PMID: 37079624 PMCID: PMC10118096 DOI: 10.1371/journal.pgen.1010695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Affiliation(s)
- Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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5
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Puckett EE, Davis IS, Harper DC, Wakamatsu K, Battu G, Belant JL, Beyer DE, Carpenter C, Crupi AP, Davidson M, DePerno CS, Forman N, Fowler NL, Garshelis DL, Gould N, Gunther K, Haroldson M, Ito S, Kocka D, Lackey C, Leahy R, Lee-Roney C, Lewis T, Lutto A, McGowan K, Olfenbuttel C, Orlando M, Platt A, Pollard MD, Ramaker M, Reich H, Sajecki JL, Sell SK, Strules J, Thompson S, van Manen F, Whitman C, Williamson R, Winslow F, Kaelin CB, Marks MS, Barsh GS. Genetic architecture and evolution of color variation in American black bears. Curr Biol 2023; 33:86-97.e10. [PMID: 36528024 PMCID: PMC10039708 DOI: 10.1016/j.cub.2022.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.
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Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA.
| | - Isis S Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Dawn C Harper
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerrold L Belant
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Dean E Beyer
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Colin Carpenter
- West Virginia Division of Natural Resources, Beckley, WV 25801, USA
| | - Anthony P Crupi
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Maria Davidson
- The Louisiana Department of Wildlife and Fisheries, Baton Rouge, LA 70898, USA
| | - Christopher S DePerno
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Nicholas Forman
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, USA
| | - Nicholas L Fowler
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - David L Garshelis
- Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA; IUCN SSC Bear Specialist Group
| | - Nicholas Gould
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Kerry Gunther
- National Park Service, Yellowstone National Park, WY 82190-0168, USA
| | - Mark Haroldson
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Japan
| | - David Kocka
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Carl Lackey
- Nevada Department of Wildlife, Reno, NV 89512, USA
| | - Ryan Leahy
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Caitlin Lee-Roney
- National Park Service, Yosemite National Park Wildlife Management, Yosemite, CA 95389, USA
| | - Tania Lewis
- National Park Service, Glacier Bay National Park, Gustavus, AK 99826, USA
| | - Ashley Lutto
- U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, Soldotna, AK 99669, USA
| | - Kelly McGowan
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Mike Orlando
- Florida Fish and Wildlife Conservation Commission, Tallahassee, FL 32399, USA
| | - Alexander Platt
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew D Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Megan Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jaime L Sajecki
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Stephanie K Sell
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Douglas, Juneau, AK 99824, USA
| | - Jennifer Strules
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695-7646, USA
| | - Seth Thompson
- Virginia Department of Wildlife Resources, Verona, VA 24482, USA
| | - Frank van Manen
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Craig Whitman
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, MT 59715, USA
| | - Ryan Williamson
- National Park Service, Great Smoky Mountains National Park, Gatlinburg, TN 37738, USA
| | | | - Christopher B Kaelin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pathology and Laboratory Medicine and of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
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6
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Nelson NG, Wu L, Maier MT, Lam D, Cheang R, Alba D, Huang A, Neumann DA, Hill T, Vagena E, Barsh GS, Medina MW, Krauss RM, Koliwad SK, Xu AW. A gene-diet interaction controlling relative intake of dietary carbohydrates and fats. Mol Metab 2022; 58:101442. [PMID: 35051651 PMCID: PMC9710720 DOI: 10.1016/j.molmet.2022.101442] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Preference for dietary fat vs. carbohydrate varies markedly across free-living individuals. It is recognized that food choice is under genetic and physiological regulation, and that the central melanocortin system is involved. However, how genetic and dietary factors interact to regulate relative macronutrient intake is not well understood. METHODS We investigated how the choice for food rich in carbohydrate vs. fat is influenced by dietary cholesterol availability and agouti-related protein (AGRP), the orexigenic component of the central melanocortin system. We assessed how macronutrient intake and different metabolic parameters correlate with plasma AGRP in a cohort of obese humans. We also examined how both dietary cholesterol levels and inhibiting de novo cholesterol synthesis affect carbohydrate and fat intake in mice, and how dietary cholesterol deficiency during the postnatal period impacts macronutrient intake patterns in adulthood. RESULTS In obese human subjects, plasma levels of AGRP correlated inversely with consumption of carbohydrates over fats. Moreover, AgRP-deficient mice preferred to consume more calories from carbohydrates than fats, more so when each diet lacked cholesterol. Intriguingly, inhibiting cholesterol biosynthesis (simvastatin) promoted carbohydrate intake at the expense of fat without altering total caloric consumption, an effect that was remarkably absent in AgRP-deficient mice. Finally, feeding lactating C57BL/6 dams and pups a cholesterol-free diet prior to weaning led the offspring to prefer fats over carbohydrates as adults, indicating that altered cholesterol metabolism early in life programs adaptive changes to macronutrient intake. CONCLUSIONS Together, our study illustrates a specific gene-diet interaction in modulating food choice.
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Affiliation(s)
- Nnamdi G. Nelson
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Lili Wu
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA,Department of Integrated Medicine, Guangxi Medical University Cancer
Hospital, Nanning, Guangxi 530021, China
| | - Matthew T. Maier
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Diana Lam
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Rachel Cheang
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Diana Alba
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA,Department of Medicine, University of California, San Francisco, San
Francisco, CA 94143, USA
| | - Alyssa Huang
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA,Department of Pediatrics, University of California, San Francisco, San
Francisco, CA 94143, USA
| | - Drexel A. Neumann
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Tess Hill
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Eirini Vagena
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA
| | - Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford,
CA 94305, USA
| | - Marisa W. Medina
- Department of Pediatrics, University of California, San Francisco, San
Francisco, CA 94143, USA
| | - Ronald M. Krauss
- Department of Medicine, University of California, San Francisco, San
Francisco, CA 94143, USA,Department of Pediatrics, University of California, San Francisco, San
Francisco, CA 94143, USA
| | - Suneil K. Koliwad
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA,Department of Medicine, University of California, San Francisco, San
Francisco, CA 94143, USA,Corresponding author. Diabetes Center, University of California, San
Francisco, San Francisco, CA 94143, USA.
| | - Allison W. Xu
- Diabetes Center, University of California, San Francisco, San Francisco,
CA 94143, USA,Department of Anatomy, University of California, San Francisco, San
Francisco, CA 94143, USA,Corresponding author. Diabetes Center, University of California, San
Francisco, San Francisco, CA 94143, USA.
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7
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Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol 2021; 4:1412. [PMID: 34921240 PMCID: PMC8683477 DOI: 10.1038/s42003-021-02935-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC's ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Zoller
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Bernard Wooding
- Quagga Project, Elandsberg Farms, Hermon, 7308, South Africa
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | - Dewey Maddox
- White Oak Conservation, 581705 White Oak Road, Yulee, FL, 32097, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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8
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Lorenzana GP, Figueiró HV, Kaelin CB, Barsh GS, Johnson J, Karlsson E, Morato RG, Sana DA, Cullen L, May JA, Moraes EA, Kantek DLZ, Silveira L, Murphy WJ, Ryder OA, Eizirik E. Whole-genome sequences shed light onto the demographic history and contemporary genetic erosion of free-ranging jaguar (Panthera onca) populations. J Genet Genomics 2021; 49:77-80. [PMID: 34767971 DOI: 10.1016/j.jgg.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Gustavo P Lorenzana
- Pontifical Catholic University of Rio Grande do Sul, PUCRS. School of Health and Life Sciences, Porto Alegre, RS, 90619, Brazil
| | - Henrique V Figueiró
- Pontifical Catholic University of Rio Grande do Sul, PUCRS. School of Health and Life Sciences, Porto Alegre, RS, 90619, Brazil
| | | | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute, Cambridge, MA, 02142, USA
| | - Elinor Karlsson
- Vertebrate Genome Biology, Broad Institute, Cambridge, MA, 02142, USA
| | | | - Dênis A Sana
- PPG Biologia Animal, Instituto de Biociências, UFRGS, Porto Alegre, RS, 90650, Brazil
| | - Laury Cullen
- Instituto de Pesquisas Ecológicas, Teodoro Sampaio, SP, 19280, Brazil
| | - Joares A May
- UniSul, Tubarão, SC, 88704, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, 12945, Brazil
| | | | | | - Leandro Silveira
- Instituto Onça-pintada - Jaguar Conservation Fund, Mineiros, GO, 75830, Brazil
| | | | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego, CA, 92027, USA
| | - Eduardo Eizirik
- Pontifical Catholic University of Rio Grande do Sul, PUCRS. School of Health and Life Sciences, Porto Alegre, RS, 90619, Brazil; Instituto Pró-Carnívoros, Atibaia, SP, 12945, Brazil.
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9
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Sagar V, Kaelin CB, Natesh M, Reddy PA, Mohapatra RK, Chhattani H, Thatte P, Vaidyanathan S, Biswas S, Bhatt S, Paul S, Jhala YV, Verma MM, Pandav B, Mondol S, Barsh GS, Swain D, Ramakrishnan U. High frequency of an otherwise rare phenotype in a small and isolated tiger population. Proc Natl Acad Sci U S A 2021; 118:e2025273118. [PMID: 34518374 PMCID: PMC8488692 DOI: 10.1073/pnas.2025273118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.
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Affiliation(s)
- Vinay Sagar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Christopher B Kaelin
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Meghana Natesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Biology Department, Indian Institute of Science Education and Research, Tirupati 411008, India
| | - P Anuradha Reddy
- Laboratory for Conservation of Endangered Species, Center for Cellular & Molecular Biology, Hyderabad 500048, India
| | | | - Himanshu Chhattani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Prachi Thatte
- World Wide Fund for Nature - India, New Delhi 110003 India
| | - Srinivas Vaidyanathan
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu 605101 India
| | | | | | - Shashi Paul
- Odisha Forest Department, Bhubaneswar 751023, India
| | - Yadavendradev V Jhala
- Wildlife Institute of India, Dehradun 248001, India
- National Tiger Conservation Authority, Wildlife Institute of India Tiger Cell, Wildlife Institute of India, Dehradun 248001, India
| | | | | | | | - Gregory S Barsh
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Debabrata Swain
- Former Member Secretary, National Tiger Conservation Authority, New Delhi 110003, India
- Former Principal Chief Conservator of Forest and Head of Forest Force, Indian Forest Service, Bhubaneswar 751023, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- DBT - Wellcome Trust India Alliance, Hyderabad 500034, India
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10
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Kaelin CB, McGowan KA, Barsh GS. Author Correction: Developmental genetics of color pattern establishment in cats. Nat Commun 2021; 12:5584. [PMID: 34531402 PMCID: PMC8446057 DOI: 10.1038/s41467-021-25886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Abstract
Intricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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12
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East KM, Kelley WV, Cannon A, Cochran ME, Moss IP, May T, Nakano-Okuno M, Sodeke SO, Edberg JC, Cimino JJ, Fouad M, Curry WA, Hurst ACE, Bowling KM, Thompson ML, Bebin EM, Johnson RD, Cooper GM, Might M, Barsh GS, Korf BR. A state-based approach to genomics for rare disease and population screening. Genet Med 2021; 23:777-781. [PMID: 33244164 PMCID: PMC8311654 DOI: 10.1038/s41436-020-01034-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/31/2023] Open
Abstract
PURPOSE The Alabama Genomic Health Initiative (AGHI) is a state-funded effort to provide genomic testing. AGHI engages two distinct cohorts across the state of Alabama. One cohort includes children and adults with undiagnosed rare disease; a second includes an unselected adult population. Here we describe findings from the first 176 rare disease and 5369 population cohort AGHI participants. METHODS AGHI participants enroll in one of two arms of a research protocol that provides access to genomic testing results and biobank participation. Rare disease cohort participants receive genome sequencing to identify primary and secondary findings. Population cohort participants receive genotyping to identify pathogenic and likely pathogenic variants for actionable conditions. RESULTS Within the rare disease cohort, genome sequencing identified likely pathogenic or pathogenic variation in 20% of affected individuals. Within the population cohort, 1.5% of individuals received a positive genotyping result. The rate of genotyping results corroborated by reported personal or family history varied by gene. CONCLUSIONS AGHI demonstrates the ability to provide useful health information in two contexts: rare undiagnosed disease and population screening. This utility should motivate continued exploration of ways in which emerging genomic technologies might benefit broad populations.
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Affiliation(s)
- Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | | | - Ashley Cannon
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Irene P Moss
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Thomas May
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA, USA
| | - Mariko Nakano-Okuno
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen O Sodeke
- Center for Biomedical Research, Tuskegee University, Tuskegee, AL, USA
| | - Jeffrey C Edberg
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James J Cimino
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mona Fouad
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William A Curry
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna C E Hurst
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - E Martina Bebin
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert D Johnson
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Matthew Might
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Bruce R Korf
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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13
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Voskobiynyk Y, Battu G, Felker SA, Cochran JN, Newton MP, Lambert LJ, Kesterson RA, Myers RM, Cooper GM, Roberson ED, Barsh GS. Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy. PLoS Genet 2021; 17:e1009195. [PMID: 33411788 PMCID: PMC7790302 DOI: 10.1371/journal.pgen.1009195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Dravet syndrome (DS) is a developmental and epileptic encephalopathy that results from mutations in the Nav1.1 sodium channel encoded by SCN1A. Most known DS-causing mutations are in coding regions of SCN1A, but we recently identified several disease-associated SCN1A mutations in intron 20 that are within or near to a cryptic and evolutionarily conserved "poison" exon, 20N, whose inclusion is predicted to lead to transcript degradation. However, it is not clear how these intron 20 variants alter SCN1A expression or DS pathophysiology in an organismal context, nor is it clear how exon 20N is regulated in a tissue-specific and developmental context. We address those questions here by generating an animal model of our index case, NM_006920.4(SCN1A):c.3969+2451G>C, using gene editing to create the orthologous mutation in laboratory mice. Scn1a heterozygous knock-in (+/KI) mice exhibited an ~50% reduction in brain Scn1a mRNA and Nav1.1 protein levels, together with characteristics observed in other DS mouse models, including premature mortality, seizures, and hyperactivity. In brain tissue from adult Scn1a +/+ animals, quantitative RT-PCR assays indicated that ~1% of Scn1a mRNA included exon 20N, while brain tissue from Scn1a +/KI mice exhibited an ~5-fold increase in the extent of exon 20N inclusion. We investigated the extent of exon 20N inclusion in brain during normal fetal development in RNA-seq data and discovered that levels of inclusion were ~70% at E14.5, declining progressively to ~10% postnatally. A similar pattern exists for the homologous sodium channel Nav1.6, encoded by Scn8a. For both genes, there is an inverse relationship between the level of functional transcript and the extent of poison exon inclusion. Taken together, our findings suggest that poison exon usage by Scn1a and Scn8a is a strategy to regulate channel expression during normal brain development, and that mutations recapitulating a fetal-like pattern of splicing cause reduced channel expression and epileptic encephalopathy.
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Affiliation(s)
- Yuliya Voskobiynyk
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, and Evelyn F. McKnight Brain Institute, Departments, of Neurology and Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Stephanie A. Felker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Department of Biotechnology Science and Engineering, University of Alabama in Huntsville, Hunstville, AL, United States AL, United States of America
| | - J. Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Megan P. Newton
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Laura J. Lambert
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Robert A. Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Erik D. Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, and Evelyn F. McKnight Brain Institute, Departments, of Neurology and Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
- * E-mail: (GSB); (EDR)
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail: (GSB); (EDR)
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14
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Childerhose JE, Rich CA, East KM, Kelley WV, Simmons S, Finnila CR, Bowling KM, Amaral MD, Hiatt SM, Thompson M, Gray DE, Lawlor JMJ, Myers RM, Barsh GS, Bebin EM, Cooper GM, Brothers KB, Brothers KB. The Therapeutic Odyssey: Positioning Genomic Sequencing in the Search for a Child's Best Possible Life. AJOB Empir Bioeth 2021; 12:179-189. [PMID: 33843487 PMCID: PMC9922533 DOI: 10.1080/23294515.2021.1907475] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: The desire of parents to obtain a genetic diagnosis for their child with intellectual disability and associated symptoms has long been framed as a diagnostic odyssey, an arduous and sometimes perilous journey focused on the goal of identifying a cause for the child's condition.Methods: Semi-structured interviews (N = 60) were conducted with parents of children (N = 59, aged 2-24 years) with intellectual disability and/or developmental delay (IDD) who underwent genome sequencing at a single pediatric multispecialty clinic. Interviews were conducted after parents received their child's sequencing result (positive findings, negative findings, or variants of unknown significance). Thematic analysis was performed on all interviews.Results: Parents reported that obtaining a genetic diagnosis was one important step in their overall goal of helping their child live their best life possible life. They intended to use the result as a tool to help their child by seeking the correct school placement and obtaining benefits and therapeutic services.Conclusions: For the parents of children with IDD, the search for a genetic diagnosis is best conceptualized as a part of parents' ongoing efforts to leverage various diagnoses to obtain educational and therapeutic services for their children. Cleaving parents' search for a genetic diagnosis from these broader efforts obscures the value that some parents place on a sequencing result in finding and tailoring therapies and services beyond the clinic. Interviews with parents reveal, therefore, that genomic sequencing is best understood as one important stage of an ongoing therapeutic odyssey that largely takes place outside the clinic. Findings suggest the need to expand translational research efforts to contextualize a genetic diagnosis within parents' broader efforts to obtain educational and therapeutic services outside clinical contexts.
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Affiliation(s)
- Janet E. Childerhose
- Division of General Internal Medicine, The Ohio State University, Columbus, Ohio, USA.,Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
| | - Carla A. Rich
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
| | - Kelly M. East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Shirley Simmons
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Kevin M. Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - David E. Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - E. Martina Bebin
- The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Greg M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kyle B. Brothers
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA.,Correspondence to: Kyle B. Brothers, MD, PhD, University of Louisville School of Medicine, 231 E. Chestnut St., N-97, Louisville, KY 40202, Work Phone: 502-588-0797, Cell Phone: 502-762-8666, Fax: 502-629-5285,
| | - Kyle Bertram Brothers
- Division of Pediatric Clinical and Translational Research, University of Louisville, Louisville, Kentucky, USA
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15
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Larison B, Kaelin CB, Harrigan R, Henegar C, Rubenstein DI, Kamath P, Aschenborn O, Smith TB, Barsh GS. Population structure, inbreeding and stripe pattern abnormalities in plains zebras. Mol Ecol 2020; 30:379-390. [PMID: 33174253 DOI: 10.1111/mec.15728] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/14/2023]
Abstract
One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple subspecies. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent years but the extent to which their appearance is related to demography and/or genetics is unclear. Investigating population genetic health and genetic structure are essential for developing effective strategies for plains zebra conservation. We collected DNA from 140 plains zebra, including seven with abnormal stripe patterns, from nine locations across the range of plains zebra, and analyzed data from restriction site-associated and whole genome sequencing (RAD-seq, WGS) libraries to better understand the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes. We found that genetic structure did not coincide with described subspecific variation, but did distinguish geographic regions in which anthropogenic habitat fragmentation is associated with reduced gene flow and increased evidence of inbreeding, especially in certain parts of East Africa. Further, zebras with abnormal striping exhibited increased levels of inbreeding relative to normally striped individuals from the same populations. Our results point to a genetic cause of stripe pattern abnormalities, and dramatic evidence of the consequences of habitat fragmentation.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ryan Harrigan
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | | | - Daniel I Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Pauline Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Ortwin Aschenborn
- School of Veterinary Medicine, University of Namibia, Neudamm Windhoek, Namibia
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
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16
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Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
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17
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Kazamel M, Lopez MA, Bebin M, Bowling K, Korf BR, Barsh GS, Cooper GM, Hurst ACE, Ubogu EE. Fibulin-5 mutation featuring Charcot-Marie-Tooth disease, joint hyperlaxity, and scoliosis. Neurol Genet 2020; 6:e476. [PMID: 32802946 PMCID: PMC7413605 DOI: 10.1212/nxg.0000000000000476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/01/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Mohamed Kazamel
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Michael A Lopez
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Martina Bebin
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Kevin Bowling
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Bruce R Korf
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Gregory S Barsh
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Gregory M Cooper
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Anna C E Hurst
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
| | - Eroboghene E Ubogu
- Department of Neurology (M.K., M.B., E.E.U.), University of Alabama at Birmingham (UAB); Department of Pediatrics (M.A.L., M.B.), Children's of Alabama | UAB; HudsonAlpha Institute for Biotechnology (K.B., G.S.B., G.M.C.), Huntsville, AL; and Department of Genetics (B.R.K., A.C.E.H.), UAB
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18
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Affiliation(s)
- David J. Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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19
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Cogné B, Latypova X, Senaratne LDS, Martin L, Koboldt DC, Kellaris G, Fievet L, Le Meur G, Caldari D, Debray D, Nizon M, Frengen E, Bowne SJ, Cadena EL, Daiger SP, Bujakowska KM, Pierce EA, Gorin M, Katsanis N, Bézieau S, Petersen-Jones SM, Occelli LM, Lyons LA, Legeai-Mallet L, Sullivan LS, Davis EE, Isidor B, Buckley RM, Aberdein D, Alves PC, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RH, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y. Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy. Am J Hum Genet 2020; 106:893-904. [PMID: 32386558 DOI: 10.1016/j.ajhg.2020.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/02/2020] [Indexed: 11/26/2022] Open
Abstract
Kinesin-2 enables ciliary assembly and maintenance as an anterograde intraflagellar transport (IFT) motor. Molecular motor activity is driven by a heterotrimeric complex comprised of KIF3A and KIF3B or KIF3C plus one non-motor subunit, KIFAP3. Using exome sequencing, we identified heterozygous KIF3B variants in two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly; he harbors a de novo c.748G>C (p.Glu250Gln) variant affecting the kinesin motor domain encoded by KIF3B. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Affected individuals carry a heterozygous c.1568T>C (p.Leu523Pro) KIF3B variant segregating in an autosomal-dominant pattern. We observed a significant increase in primary cilia length in vitro in the context of either of the two mutations while variant KIF3B proteins retained stability indistinguishable from wild type. Furthermore, we tested the effects of KIF3B mutant mRNA expression in the developing zebrafish retina. In the presence of either missense variant, rhodopsin was sequestered to the photoreceptor rod inner segment layer with a concomitant increase in photoreceptor cilia length. Notably, impaired rhodopsin trafficking is also characteristic of recessive KIF3B models as exemplified by an early-onset, autosomal-recessive, progressive retinal degeneration in Bengal cats; we identified a c.1000G>A (p.Ala334Thr) KIF3B variant by genome-wide association study and whole-genome sequencing. Together, our genetic, cell-based, and in vivo modeling data delineate an autosomal-dominant syndromic retinal ciliopathy in humans and suggest that multiple KIF3B pathomechanisms can impair kinesin-driven ciliary transport in the photoreceptor.
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20
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Armstrong EE, Taylor RW, Miller DE, Kaelin CB, Barsh GS, Hadly EA, Petrov D. Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biol 2020; 18:3. [PMID: 31915011 PMCID: PMC6950864 DOI: 10.1186/s12915-019-0734-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.
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Affiliation(s)
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA
- End2EndGenomics, LLC, Davis, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Seattle Children's Hospital and The University of Washington, Seattle, WA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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21
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Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (GSB); (GPC)
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (GSB); (GPC)
| | - Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
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22
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Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | | | - Daniela C. Zarnescu
- Departments of Molecular and Cellular Biology, Neuroscience and Neurology, University of Arizona, Tucson, Arizona, United States of America
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23
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Johnson MR, Barsh GS, Mallarino R. Periodic patterns in Rodentia: Development and evolution. Exp Dermatol 2019; 28:509-513. [PMID: 30506729 PMCID: PMC6488409 DOI: 10.1111/exd.13852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/19/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022]
Abstract
Mammalian periodic pigment patterns, such as spots and stripes, have long interested mathematicians and biologists because they arise from non-random developmental processes that are programmed to be spatially constrained, and can therefore be used as a model to understand how organized morphological structures develop. Despite such interest, the developmental and molecular processes underlying their formation remain poorly understood. Here, we argue that Arvicanthines, a clade of African rodents that naturally evolved a remarkable array of coat patterns, represent a tractable model system in which to dissect the mechanistic basis of pigment pattern formation. Indeed, we review recent insights into the process of stripe formation that were obtained using an Arvicanthine species, the African striped mouse (Rhabdomys pumilio), and discuss how these rodents can be used to probe deeply into our understanding of the factors that specify and implement positional information in the skin. By combining naturally evolved pigment pattern variation in rodents with classic and novel experimental approaches, we can substantially advance our understanding of the processes by which spatial patterns of cell differentiation are established during embryogenesis, a fundamental question in developmental biology.
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Affiliation(s)
- Matthew R. Johnson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
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24
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Affiliation(s)
- Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Sarah A. Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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25
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Copenhaver GP, Weir B, Rothstein M, Tang H, Williams SM, Barsh GS. Doubling down on forensic twin studies. PLoS Genet 2018; 14:e1007831. [PMID: 30571773 PMCID: PMC6301560 DOI: 10.1371/journal.pgen.1007831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Bruce Weir
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Mark Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Scott M. Williams
- Departments of Population and Quantitative Health Sciences, Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
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26
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Carvill GL, Engel KL, Ramamurthy A, Cochran JN, Roovers J, Stamberger H, Lim N, Schneider AL, Hollingsworth G, Holder DH, Regan BM, Lawlor J, Lagae L, Ceulemans B, Bebin EM, Nguyen J, Barsh GS, Weckhuysen S, Meisler M, Berkovic SF, De Jonghe P, Scheffer IE, Myers RM, Cooper GM, Mefford HC, Striano P, Zara F, Helbig I, Møller RS, von Spiczak S, Muhle H, Caglayan H, Sterbova K, Craiu D, Hoffman D, Lehesjoki AE, Selmer K, Depienne C, Lemke J, Marini C, Guerrini R, Neubauer B, Talvik T, Leguern E, de Jonghe P, Weckhuysen S. Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies. Am J Hum Genet 2018; 103:1022-1029. [PMID: 30526861 DOI: 10.1016/j.ajhg.2018.10.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of severe epilepsies characterized by refractory seizures and developmental impairment. Sequencing approaches have identified causal genetic variants in only about 50% of individuals with DEEs.1-3 This suggests that unknown genetic etiologies exist, potentially in the ∼98% of human genomes not covered by exome sequencing (ES). Here we describe seven likely pathogenic variants in regions outside of the annotated coding exons of the most frequently implicated epilepsy gene, SCN1A, encoding the alpha-1 sodium channel subunit. We provide evidence that five of these variants promote inclusion of a "poison" exon that leads to reduced amounts of full-length SCN1A protein. This mechanism is likely to be broadly relevant to human disease; transcriptome studies have revealed hundreds of poison exons,4,5 including some present within genes encoding other sodium channels and in genes involved in neurodevelopment more broadly.6 Future research on the mechanisms that govern neuronal-specific splicing behavior might allow researchers to co-opt this system for RNA therapeutics.
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Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
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Barsh GS, Bhalla N, Cole F, Copenhaver GP, Lacefield S, Libuda DE. 2018 PLOS Genetics Research Prize: Bundling, stabilizing, organizing-The orchestration of acentriolar spindle assembly by microtubule motor proteins. PLoS Genet 2018; 14:e1007649. [PMID: 30212501 PMCID: PMC6136686 DOI: 10.1371/journal.pgen.1007649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Needhi Bhalla
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Diana E. Libuda
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
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29
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Hiatt SM, Amaral MD, Bowling KM, Finnila CR, Thompson ML, Gray DE, Lawlor JMJ, Cochran JN, Bebin EM, Brothers KB, East KM, Kelley WV, Lamb NE, Levy SE, Lose EJ, Neu MB, Rich CA, Simmons S, Myers RM, Barsh GS, Cooper GM. Systematic reanalysis of genomic data improves quality of variant interpretation. Clin Genet 2018; 94:174-178. [PMID: 29652076 DOI: 10.1111/cge.13259] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/22/2018] [Accepted: 03/28/2018] [Indexed: 12/30/2022]
Abstract
As genomic sequencing expands, so does our knowledge of the link between genetic variation and disease. Deeper catalogs of variant frequencies improve identification of benign variants, while sequencing affected individuals reveals disease-associated variation. Accumulation of human genetic data thus makes reanalysis a means to maximize the benefits of clinical sequencing. We implemented pipelines to systematically reassess sequencing data from 494 individuals with developmental disability. Reanalysis yielded pathogenic or likely pathogenic (P/LP) variants that were not initially reported in 23 individuals, 6 described here, comprising a 16% increase in P/LP yield. We also downgraded 3 LP and 6 variants of uncertain significance (VUS) due to updated population frequency data. The likelihood of identifying a new P/LP variant increased over time, as ~22% of individuals who did not receive a P/LP variant at their original analysis subsequently did after 3 years. We show here that reanalysis and data sharing increase the diagnostic yield and accuracy of clinical sequencing.
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Affiliation(s)
- S M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - M D Amaral
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - K M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - C R Finnila
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - M L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - D E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - J M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - J N Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - E M Bebin
- University of Alabama at Birmingham, Birmingham, Alabama
| | | | - K M East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - W V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - N E Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - S E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - E J Lose
- University of Alabama at Birmingham, Birmingham, Alabama
| | - M B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - C A Rich
- University of Louisville, Louisville, Kentucky
| | - S Simmons
- University of Alabama at Birmingham, Birmingham, Alabama
| | - R M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - G S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - G M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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30
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Thompson ML, Finnila CR, Bowling KM, Brothers KB, Neu MB, Amaral MD, Hiatt SM, East KM, Gray DE, Lawlor JMJ, Kelley WV, Lose EJ, Rich CA, Simmons S, Levy SE, Myers RM, Barsh GS, Bebin EM, Cooper GM. Genomic sequencing identifies secondary findings in a cohort of parent study participants. Genet Med 2018; 20:1635-1643. [PMID: 29790872 PMCID: PMC6185813 DOI: 10.1038/gim.2018.53] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/06/2018] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Clinically relevant secondary variants were identified in parents enrolled with a child with developmental delay and intellectual disability. METHODS Exome/genome sequencing and analysis of 789 "unaffected" parents was performed. RESULTS Pathogenic/likely pathogenic variants were identified in 21 genes within 25 individuals (3.2%), with 11 (1.4%) participants harboring variation in a gene defined as clinically actionable by the American College of Medical Genetics and Genomics. These 25 individuals self-reported either relevant clinical diagnoses (5); relevant family history or symptoms (13); or no relevant family history, symptoms, or clinical diagnoses (7). A limited carrier screen was performed yielding 15 variants in 48 (6.1%) parents. Parents were also analyzed as mate pairs (n = 365) to identify cases in which both parents were carriers for the same recessive disease, yielding three such cases (0.8%), two of which had children with the relevant recessive disease. Four participants had two findings (one carrier and one noncarrier variant). In total, 71 of the 789 enrolled parents (9.0%) received secondary findings. CONCLUSION We provide an overview of the rates and types of clinically relevant secondary findings, which may be useful in the design and implementation of research and clinical sequencing efforts to identify such findings.
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Affiliation(s)
| | | | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Matthew B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.,University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Edward J Lose
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carla A Rich
- Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Shirley Simmons
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - E Martina Bebin
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
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Affiliation(s)
- Hua Tang
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA.
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
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Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H, Visscher PM. Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models. Genetics 2017; 206:1113-1126. [PMID: 28381588 PMCID: PMC5499166 DOI: 10.1534/genetics.116.193383] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 03/28/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).
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Affiliation(s)
- Luke R Lloyd-Jones
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Matthew R Robinson
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Gerhard Moser
- Central Queensland University, Bellbowrie, Brisbane, Queensland 4070, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Sandra Beleza
- Department of Genetics, University of Leicester, LE1 7RH, United Kingdom
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
- Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
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Bowling KM, Thompson ML, Amaral MD, Finnila CR, Hiatt SM, Engel KL, Cochran JN, Brothers KB, East KM, Gray DE, Kelley WV, Lamb NE, Lose EJ, Rich CA, Simmons S, Whittle JS, Weaver BT, Nesmith AS, Myers RM, Barsh GS, Bebin EM, Cooper GM. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Med 2017; 9:43. [PMID: 28554332 PMCID: PMC5448144 DOI: 10.1186/s13073-017-0433-1] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 05/03/2017] [Indexed: 12/30/2022] Open
Abstract
Background Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-parent trios. Methods Whole-exome sequences (WES) were generated for 365 individuals (127 affected) and whole-genome sequences (WGS) were generated for 612 individuals (244 affected). Results Pathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11.3%). We found that a family history of neurological disease, especially the presence of an affected first-degree relative, reduces the pathogenic/likely pathogenic variant identification rate, reflecting both the disease relevance and ease of interpretation of de novo variants. We also found that improvements to genetic knowledge facilitated interpretation changes in many cases. Through systematic reanalyses, we have thus far reclassified 15 variants, with 11.3% of families who initially were found to harbor a VUS and 4.7% of families with a negative result eventually found to harbor a pathogenic or likely pathogenic variant. To further such progress, the data described here are being shared through ClinVar, GeneMatcher, and dbGaP. Conclusions Our data strongly support the value of large-scale sequencing, especially WGS within proband-parent trios, as both an effective first-choice diagnostic tool and means to advance clinical and research progress related to pediatric neurological disease. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0433-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Michelle L Thompson
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Michelle D Amaral
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Candice R Finnila
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Krysta L Engel
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Kelly M East
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Neil E Lamb
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Edward J Lose
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Jana S Whittle
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.,University of Alabama in Huntsville, Huntsville, AL, USA
| | - Benjamin T Weaver
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.,University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amy S Nesmith
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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Bogren LK, Grabek KR, Barsh GS, Martin SL. Comparative tissue transcriptomics highlights dynamic differences among tissues but conserved metabolic transcript prioritization in preparation for arousal from torpor. J Comp Physiol B 2017; 187:735-748. [PMID: 28332019 DOI: 10.1007/s00360-017-1073-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/02/2016] [Accepted: 02/26/2017] [Indexed: 12/01/2022]
Abstract
During the hibernation season, 13-lined ground squirrels spend days to weeks in torpor with body temperatures near freezing then spontaneously rewarm. The molecular drivers of the drastic physiological changes that orchestrate and permit torpor are not well understood. Although transcription effectively ceases at the low body temperatures of torpor, previous work has demonstrated that some transcripts are protected from bulk degradation in brown adipose tissue (BAT), consistent with the importance of their protein products for metabolic heat generation during arousal from torpor. We examined the transcriptome of skeletal muscle, heart, and liver to determine the patterns of differentially expressed genes in these tissues, and whether, like BAT, a subset of these were relatively increased during torpor. EDGE-tags were quantified from five distinct physiological states representing the seasonal and torpor-arousal cycles of 13-lined ground squirrels. Supervised clustering on relative transcript abundances with Random Forest separated the two states bracketing prolonged torpor, entrance into and aroused from torpor, in all three tissues. Independent analyses identified 3347, 6784, and 2433 differentially expressed transcripts among all sampling points in heart, skeletal muscle, and liver, respectively. There were few differentially expressed genes in common across all three tissues; these were enriched in mitochondrial and apoptotic pathway components. Divisive clustering of these data revealed unique cohorts of transcripts that increased across the torpor bout in each tissue with patterns reflecting various combinations of cycling within and between seasons as well as between torpor and arousal. Transcripts that increased across the torpor bout were likewise tissue specific. These data shed new light on the biochemical pathways that alter in concert with hibernation phenotype and provide a rich resource for further hypothesis-based studies.
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Affiliation(s)
- Lori K Bogren
- Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, USA.
| | | | | | - Sandra L Martin
- Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, USA
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Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Casey M. Bergman
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Christopher D. Brown
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nadia D. Singh
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
- * E-mail:
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology; Institute of Human Genetics; Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research; Department of Orofacial Sciences & Department of Anatomy; University of California San Francisco, San Francisco, California, United States of America
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Wendy A. Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Lin He
- Division of Cellular and Developmental Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Lisa Stubbs
- Institute for Genomic Biology, Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Wolf Reik
- Department of Epigenetics, The Babraham Institute, Cambridge, United Kingdom
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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Nix MA, Kaelin CB, Palomino R, Miller JL, Barsh GS, Millhauser GL. Electrostatic Similarity Analysis of Human β-Defensin Binding in the Melanocortin System. Biophys J 2016; 109:1946-58. [PMID: 26536271 DOI: 10.1016/j.bpj.2015.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
The β-defensins are a class of small cationic proteins that serve as components of numerous systems in vertebrate biology, including the immune and melanocortin systems. Human β-defensin 3 (HBD3), which is produced in the skin, has been found to bind to melanocortin receptors 1 and 4 through complementary electrostatics, a unique mechanism of ligand-receptor interaction. This finding indicates that electrostatics alone, and not specific amino acid contact points, could be sufficient for function in this ligand-receptor system, and further suggests that other small peptide ligands could interact with these receptors in a similar fashion. Here, we conducted molecular-similarity analyses and functional studies of additional members of the human β-defensin family, examining their potential as ligands of melanocortin-1 receptor, through selection based on their electrostatic similarity to HBD3. Using Poisson-Boltzmann electrostatic calculations and molecular-similarity analysis, we identified members of the human β-defensin family that are both similar and dissimilar to HBD3 in terms of electrostatic potential. Synthesis and functional testing of a subset of these β-defensins showed that peptides with an HBD3-like electrostatic character bound to melanocortin receptors with high affinity, whereas those that were anticorrelated to HBD3 showed no binding affinity. These findings expand on the central role of electrostatics in the control of this ligand-receptor system and further demonstrate the utility of employing molecular-similarity analysis. Additionally, we identified several new potential ligands of melanocortin-1 receptor, which may have implications for our understanding of the role defensins play in melanocortin physiology.
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Affiliation(s)
- Matthew A Nix
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California
| | - Rafael Palomino
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jillian L Miller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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Abstract
Live-cell imaging and genetic tools reveal a new way in which pigment cells communicate in zebrafish
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Affiliation(s)
- Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, United States.,Department of Genetics, Stanford University School of Medicine, Stanford, United States
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39
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Affiliation(s)
- Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail:
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Gregory P. Copenhaver
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Scott M. Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
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Copenhaver GP, Barsh GS. A Decad(e) of Reasons to Contribute to a PLOS Community-Run Journal. PLoS Genet 2015; 11:e1005557. [PMID: 26436996 PMCID: PMC4593542 DOI: 10.1371/journal.pgen.1005557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Will be part of a Tenth Anniversary Collection
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Affiliation(s)
- Gregory P Copenhaver
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory S Barsh
- Stanford University School of Medicine, Stanford, California, United States of America
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Dorshorst B, Henegar C, Liao X, Sällman Almén M, Rubin CJ, Ito S, Wakamatsu K, Stothard P, Van Doormaal B, Plastow G, Barsh GS, Andersson L. Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene. PLoS One 2015; 10:e0128969. [PMID: 26042826 PMCID: PMC4456281 DOI: 10.1371/journal.pone.0128969] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/01/2015] [Indexed: 12/31/2022] Open
Abstract
Coat color in Holstein dairy cattle is primarily controlled by the melanocortin 1 receptor (MC1R) gene, a central determinant of black (eumelanin) vs. red/brown pheomelanin synthesis across animal species. The major MC1R alleles in Holsteins are Dominant Black (MC1RD) and Recessive Red (MC1Re). A novel form of dominant red coat color was first observed in an animal born in 1980. The mutation underlying this phenotype was named Dominant Red and is epistatic to the constitutively activated MC1RD. Here we show that a missense mutation in the coatomer protein complex, subunit alpha (COPA), a gene with previously no known role in pigmentation synthesis, is completely associated with Dominant Red in Holstein dairy cattle. The mutation results in an arginine to cysteine substitution at an amino acid residue completely conserved across eukaryotes. Despite this high level of conservation we show that both heterozygotes and homozygotes are healthy and viable. Analysis of hair pigment composition shows that the Dominant Red phenotype is similar to the MC1R Recessive Red phenotype, although less effective at reducing eumelanin synthesis. RNA-seq data similarly show that Dominant Red animals achieve predominantly pheomelanin synthesis by downregulating genes normally required for eumelanin synthesis. COPA is a component of the coat protein I seven subunit complex that is involved with retrograde and cis-Golgi intracellular coated vesicle transport of both protein and RNA cargo. This suggests that Dominant Red may be caused by aberrant MC1R protein or mRNA trafficking within the highly compartmentalized melanocyte, mimicking the effect of the Recessive Red loss of function MC1R allele.
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Affiliation(s)
- Ben Dorshorst
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
| | - Corneliu Henegar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Xiaoping Liao
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Sällman Almén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi, Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi, Japan
| | - Paul Stothard
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | | | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Schneider A, Henegar C, Day K, Absher D, Napolitano C, Silveira L, David VA, O’Brien SJ, Menotti-Raymond M, Barsh GS, Eizirik E. Recurrent evolution of melanism in South American felids. PLoS Genet 2015; 11:e1004892. [PMID: 25695801 PMCID: PMC4335015 DOI: 10.1371/journal.pgen.1004892] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/13/2014] [Indexed: 12/04/2022] Open
Abstract
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations. Color polymorphism in closely related animal species provides an opportunity to study how the balance between natural selection and genetic drift shapes the evolution of appearance and form. The cat family, Felidae, is especially interesting; 13 of 37 extant species exhibit polymorphism for melanism, but evidence for any adaptive role is lacking, in part because the potential benefits of melanism to felid predators are not clear, and in part because the tools for genomic analysis of natural populations are limited. We identify the mutations responsible for melanism in three closely related South American wild felids, the pampas cat, the kodkod, and Geoffroy’s cat, then adapt a new approach for targeted genome sequencing to characterize molecular variation in the region surrounding each melanism mutation. We find that each mutation has developed independently, with strong evidence for natural selection in the black pampas cat, and reduced genetic variation in the entire population of kodkods. Our results demonstrate that some “black cats” are black not by chance, but by selection for a mutation that provides increased fitness.
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Affiliation(s)
- Alexsandra Schneider
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Corneliu Henegar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Constanza Napolitano
- Laboratorio de Ecología Molecular & Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Leandro Silveira
- Jaguar Conservation Fund, Instituto Onça-Pintada, Mineiros, Goiás, Brazil
| | - Victor A. David
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Informatics, St. Petersburg State University, St. Petersburg, Russia
| | - Marilyn Menotti-Raymond
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (GSB); (EE)
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- * E-mail: (GSB); (EE)
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Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. eLife 2015; 4. [PMID: 25626169 PMCID: PMC4383249 DOI: 10.7554/elife.04517] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022] Open
Abstract
During hibernation, animals cycle between torpor and arousal. These cycles involve
dramatic but poorly understood mechanisms of dynamic physiological regulation at the
level of gene expression. Each cycle, Brown Adipose Tissue (BAT) drives periodic
arousal from torpor by generating essential heat. We applied digital transcriptome
analysis to precisely timed samples to identify molecular pathways that underlie the
intense activity cycles of hibernator BAT. A cohort of transcripts increased during
torpor, paradoxical because transcription effectively ceases at these low
temperatures. We show that this increase occurs not by elevated transcription but
rather by enhanced stabilization associated with maintenance and/or extension of long
poly(A) tails. Mathematical modeling further supports a temperature-sensitive
mechanism to protect a subset of transcripts from ongoing bulk degradation instead of
increased transcription. This subset was enriched in a C-rich motif and genes
required for BAT activation, suggesting a model and mechanism to prioritize
translation of key proteins for thermogenesis. DOI:http://dx.doi.org/10.7554/eLife.04517.001 Many mammals hibernate to avoid food scarcity and harsh conditions during winter.
Hibernation involves entering a state called torpor, which drastically reduces the
amount of energy used by the body. During torpor, body temperature also decreases.
This is particularly exemplified in ground squirrels, whose body temperature can
hover at just above or even below the point of freezing. However, hibernating mammals
cannot remain in this state continuously over the months of hibernation but instead
cycle between bouts of torpor lasting for 1–3 weeks and brief periods of
‘arousal’ lasting between 12–24 hr, during which their body
rapidly warms up. The heat required to start warming up the hibernator is generated from a specialized
form of fat called brown adipose tissue. Normally, the bursts of metabolic activity
that are required to create this heat depend on certain proteins being produced.
Making a protein involves ‘translating’ its sequence from template
molecules called messenger RNA (mRNA), which are ‘transcribed’ from the
gene that encodes the protein. During the low body temperatures experienced during
torpor, both of these processes stop. So how is the hibernator able to quickly and
efficiently heat itself up during the arousal periods of hibernation? Grabek et al. investigated this by analyzing the relative levels of mRNA in the brown
adipose tissue of hibernating 13-lined ground squirrels. Using a special technique to
sample and sequence small fragments of mRNA taken from brown adipose tissue, Grabek
et al. compiled a profile of the mRNA molecules present at different points in the
torpor–arousal cycle and compared this with a similar profile taken from
squirrels that were not hibernating. From this analysis, Grabek et al. detected that a particular group of mRNA molecules
that are required for producing heat increase in abundance during torpor, even though
body temperature is low enough to stop gene transcription. This increased abundance
does not occur because more of the mRNA molecules are made; instead, the mRNA
molecules are modified to become more stable and long lasting. Once the animal warms
up during arousal, gene transcription is reactivated and more new mRNA molecules are
made. Grabek et al. suggest that the key mRNAs required for brown adipose tissue function
are selectively stabilized during torpor through a temperature-dependent protective
mechanism. These mRNAs are then preferentially translated into proteins during
arousal to rapidly and efficiently heat the hibernator. Most other mRNA molecules
degrade throughout torpor, and so their numbers decline as replacements are not
transcribed until body temperature briefly recovers during arousal. Whether this
protective mechanism is also used in other tissues during torpor remains a question
for future work. DOI:http://dx.doi.org/10.7554/eLife.04517.002
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Affiliation(s)
- Katharine R Grabek
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Cecilia Diniz Behn
- Department of Applied Math and Statistics, Colorado School of Mines, Golden, United States
| | - Gregory S Barsh
- Department of Research, HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Jay R Hesselberth
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
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Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araújo II, Anderson TM, Vilhjálmsson BJ, Nordborg M, Correia e Silva A, Shriver MD, Rocha J, Barsh GS, Tang H. Genetic architecture of skin and eye color in an African-European admixed population. PLoS Genet 2013; 9:e1003372. [PMID: 23555287 PMCID: PMC3605137 DOI: 10.1371/journal.pgen.1003372] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (∼44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ∼70% of the estimated heritability. Differences in skin and eye color are some of the most obvious traits that underlie human diversity, yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry. We have studied a unique population in Cape Verde, an archipelago located off the West African coast, in which extensive mixing between individuals of Portuguese and West African ancestry has given rise to a broad range of phenotypes and ancestral genome proportions. Our results help to explain how genes work together to control the full range of pigmentary phenotypic diversity, provide new insight into the evolution of these traits, and provide a model for understanding other types of quantitative variation in admixed populations.
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Affiliation(s)
- Sandra Beleza
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- * E-mail: (SB); (GSB)
| | - Nicholas A. Johnson
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Sophie I. Candille
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Marc A. Coram
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jailson Lopes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Universidade de Cabo Verde (Uni-CV), Praia, Santiago, Cabo Verde
| | - Joana Campos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Tovi M. Anderson
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | | | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jorge Rocha
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (SB); (GSB)
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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Silvius D, Pitstick R, Ahn M, Meishery D, Oehler A, Barsh GS, DeArmond SJ, Carlson GA, Gunn TM. Levels of the Mahogunin Ring Finger 1 E3 ubiquitin ligase do not influence prion disease. PLoS One 2013; 8:e55575. [PMID: 23383230 PMCID: PMC3559536 DOI: 10.1371/journal.pone.0055575] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/03/2013] [Indexed: 01/30/2023] Open
Abstract
Prion diseases are rare but invariably fatal neurodegenerative disorders. They are associated with spongiform encephalopathy, a histopathology characterized by the presence of large, membrane-bound vacuolar structures in the neuropil of the brain. While the primary cause is recognized as conversion of the normal form of prion protein (PrPC) to a conformationally distinct, pathogenic form (PrPSc), the cellular pathways and mechanisms that lead to spongiform change, neuronal dysfunction and death are not known. Mice lacking the Mahogunin Ring Finger 1 (MGRN1) E3 ubiquitin ligase develop spongiform encephalopathy by 9 months of age but do not become ill. In cell culture, PrP aberrantly present in the cytosol was reported to interact with and sequester MGRN1. This caused endo-lysosomal trafficking defects similar to those observed when Mgrn1 expression is knocked down, implicating disrupted MGRN1-dependent trafficking in the pathogenesis of prion disease. As these defects were rescued by over-expression of MGRN1, we investigated whether reduced or elevated Mgrn1 expression influences the onset, progression or pathology of disease in mice inoculated with PrPSc. No differences were observed, indicating that disruption of MGRN1-dependent pathways does not play a significant role in the pathogenesis of transmissible spongiform encephalopathy.
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Affiliation(s)
- Derek Silvius
- McLaughlin Research Institute, Great Falls, Montana, United States of America
| | - Rose Pitstick
- McLaughlin Research Institute, Great Falls, Montana, United States of America
| | - Misol Ahn
- Institute for Neurodegenerative Diseases and Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Delisha Meishery
- McLaughlin Research Institute, Great Falls, Montana, United States of America
| | - Abby Oehler
- Institute for Neurodegenerative Diseases and Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Gregory S. Barsh
- Departments of Genetics and Pediatrics, Stanford University, Stanford, California, United States of America
| | - Stephen J. DeArmond
- Institute for Neurodegenerative Diseases and Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - George A. Carlson
- McLaughlin Research Institute, Great Falls, Montana, United States of America
| | - Teresa M. Gunn
- McLaughlin Research Institute, Great Falls, Montana, United States of America
- * E-mail:
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Abstract
Color variation in companion animals has long been of interest to the breeding and scientific communities. Simple traits, like black versus brown or yellow versus black, have helped to explain principles of transmission genetics and continue to serve as models for studying gene action and interaction. We present a molecular genetic review of pigmentary variation in dogs and cats using a nomenclature and logical framework established by early leaders in the field. For most loci in which molecular variants have been identified (nine in dogs and seven in cats), homologous mutations exist in laboratory mice and/or humans. Exceptions include the K locus in dogs and the Tabby locus in cats, which give rise to alternating stripes or marks of different color, and which illustrate the continued potential of coat color genetics to provide insight into areas that transcend pigment cell biology.
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Affiliation(s)
- Christopher B. Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
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Kronforst MR, Barsh GS, Kopp A, Mallet J, Monteiro A, Mullen SP, Protas M, Rosenblum EB, Schneider CJ, Hoekstra HE. Unraveling the thread of nature's tapestry: the genetics of diversity and convergence in animal pigmentation. Pigment Cell Melanoma Res 2012; 25:411-33. [PMID: 22578174 DOI: 10.1111/j.1755-148x.2012.01014.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Animals display incredibly diverse color patterns yet little is known about the underlying genetic basis of these phenotypes. However, emerging results are reshaping our view of how the process of phenotypic evolution occurs. Here, we outline recent research from three particularly active areas of investigation: melanin pigmentation in Drosophila, wing patterning in butterflies, and pigment variation in lizards. For each system, we highlight (i) the function and evolution of color variation, (ii) various approaches that have been used to explore the genetic basis of pigment variation, and (iii) conclusions regarding the genetic basis of convergent evolution which have emerged from comparative analyses. Results from these studies indicate that natural variation in pigmentation is a particularly powerful tool to examine the molecular basis of evolution, especially with regard to convergent or parallel evolution. Comparison of these systems also reveals that the molecular basis of convergent evolution is heterogeneous, sometimes involving conserved mechanisms and sometimes not. In the near future, additional work in other emerging systems will substantially expand the scope of available comparisons.
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Kaelin CB, Xu X, Hong LZ, David VA, McGowan KA, Schmidt-Küntzel A, Roelke ME, Pino J, Pontius J, Cooper GM, Manuel H, Swanson WF, Marker L, Harper CK, van Dyk A, Yue B, Mullikin JC, Warren WC, Eizirik E, Kos L, O'Brien SJ, Barsh GS, Menotti-Raymond M. Specifying and sustaining pigmentation patterns in domestic and wild cats. Science 2012; 337:1536-41. [PMID: 22997338 DOI: 10.1126/science.1220893] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.
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Affiliation(s)
- Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Gregory P. Copenhaver
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Scott M. Williams
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
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