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PreprintCited by 27Chromosomal and Genetic VariationsDevelopmental Biology and Gene RegulationZebrafish Biomedical Research Applications

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Gag proteins encoded by endogenous retroviruses are required for zebrafish development

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Chang, Ni-Chen, Wells, Jonathan N., Wang, Andrew Y., Schofield, Phillip, Huang, Yi-Chia, Truong, Vinh H., Simoes-Costa, Marcos, Feschotte, Cédric·2024·Proceedings of the National Academy of Sciences
DOI 10.1101/2024.03.25.586437PMC PMC12067270

Preprint — published as 10.1073/pnas.2411446122 · Paper page

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Abstract

Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an “addiction” model to explain how active TEs can be integrated into conserved developmental processes.

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Research works printed but not linked: 85

  1. 10.1186/s13059-018-1577-z · DOI · Paper page
  2. 10.1146/ANNUREV-GENET-040620-022145 · DOI · Paper page
  3. 2019, Nat Rev Genet, 20, 760, 10.1038/s41576-019-0165-8 · DOI
  4. 2011, Proc Natl Acad Sci U S A, 108 Suppl 2, 10863
  5. 10.1146/annurev.ge.23.120189.001343 · DOI
  6. 10.1038/284601a0 · DOI
  7. 10.1038/284604a0 · DOI
  8. 10.1038/nrg.2016.139 · DOI
  9. 10.1101/gad.327312.119 · DOI
  10. 2023, Mob DNA, 14, 9, 10.1186/s13100-023-00297-3 · DOI
  11. 10.1146/annurev.genet.38.072902.093115 · DOI
  12. 10.1038/ng.3945 · DOI
  13. 10.1016/j.cell.2018.05.043 · DOI
  14. K. Kruse , et al., bioRxiv (2019).
  15. 10.1016/j.cell.2021.07.022 · DOI
  16. 10.1073/pnas.2221613120 · DOI
  17. 10.1038/s41588-023-01324-y · DOI
  18. P. G. M’Angale , et al., bioRxiv (2023).
  19. 2024, Genome Biol Evol, 16, evae010, 10.1093/gbe/evae010 · DOI
  20. 10.1098/rstb.2019.0345 · DOI
  21. 10.1093/molbev/mst045 · DOI
  22. 10.1101/gr.275655.121 · DOI
  23. 10.1016/S0925-4773(99)00104-5 · DOI
  24. 10.1002/1097-0177(2000)9999:9999<::AID-DVDY1097>3.0.CO;2-1 · DOI
  25. 10.1002/(SICI)1526-968X(200001)26:1<86::AID-GENE11>3.0.CO;2-Q · DOI
  26. 10.1126/science.aad2197 · DOI
  27. 10.1093/molbev/msaa272 · DOI
  28. 10.1128/JVI.75.9.4367-4375.2001 · DOI
  29. 10.1186/s12977-014-0087-7 · DOI
  30. 10.1093/molbev/msx281 · DOI · Paper page
  31. 10.1242/dev.122.1.271 · DOI
  32. 10.1242/dev.00314 · DOI
  33. 10.1016/bs.ctdb.2019.08.001 · DOI
  34. 10.1146/annurev.genet.37.110801.143752 · DOI
  35. 10.1016/j.ydbio.2007.06.008 · DOI
  36. 10.1002/dvdy.21295 · DOI
  37. 10.1186/1471-213X-7-130 · DOI
  38. 10.1016/j.mod.2013.12.001 · DOI
  39. 10.1371/journal.pbio.0050158 · DOI
  40. 10.1242/dev.02742 · DOI
  41. 10.1126/sciadv.abn1441 · DOI
  42. 10.1371/journal.pone.0092039 · DOI
  43. 10.1371/journal.pbio.1000002 · DOI
  44. 2007, J Mol Evol, 65, 215, 10.1007/s00239-007-9001-4 · DOI
  45. 10.1101/gr.2438005 · DOI
  46. 10.1038/ng.3844 · DOI
  47. 2022, Proc Natl Acad Sci U S A, 119, e2121978119, 10.1073/pnas.2121978119 · DOI · Paper page
  48. 10.1093/nar/gkaa443 · DOI · Paper page
  49. 2018, Science, 360, eaar3131, 10.1126/science.aar3131 · DOI · Paper page
  50. 10.1242/dev.01943 · DOI
  51. 10.1002/dvdy.21577 · DOI
  52. 2024, Sci Adv, 10, eadk9394, 10.1126/sciadv.adk9394 · DOI
  53. 2021, Mol Biol Evol, 38, 3267, 10.1093/molbev/msab101 · DOI
  54. 10.1016/j.cell.2018.03.024 · DOI · Paper page
  55. 10.1126/science.abg6155 · DOI · Paper page
  56. 10.1086/282188 · DOI
  57. 10.1371/journal.pgen.1004351 · DOI
  58. 10.1186/s13100-015-0041-9 · DOI
  59. 10.1006/jmbi.1990.9999 · DOI · Paper page
  60. 10.1073/pnas.1921046117 · DOI · Paper page
  61. 2022, mBio, 13, e0018722, 10.1128/mbio.00187-22 · DOI
  62. 10.1093/molbev/mst010 · DOI · Paper page
  63. 10.1038/nmeth.4285 · DOI · Paper page
  64. 10.1093/molbev/msaa015 · DOI · Paper page
  65. 10.1093/sysbio/syw037 · DOI · Paper page
  66. 2021, Bioinformatics, 37, 4572, 10.1093/bioinformatics/btab705 · DOI
  67. 10.1093/bioinformatics/btq033 · DOI · Paper page
  68. 10.1093/bioinformatics/btp352 · DOI · Paper page
  69. 10.1038/S41592-022-01488-1 · DOI · Paper page
  70. 10.1016/j.celrep.2019.07.079 · DOI
  71. 10.1128/JVI.01502-15 · DOI · Paper page
  72. 10.1038/s41593-019-0569-y · DOI
  73. 10.1093/NAR/GKAB1061 · DOI · Paper page
  74. 10.1371/journal.ppat.1005981 · DOI
  75. 10.1093/protein/11.9.739 · DOI
  76. 10.1093/bioinformatics/btu170 · DOI · Paper page
  77. 10.1093/bioinformatics/bts635 · DOI · Paper page
  78. 10.1186/s13059-014-0550-8 · DOI · Paper page
  79. 10.1038/nprot.2007.514 · DOI
  80. 10.1038/nmeth.2019 · DOI · Paper page
  81. 10.1016/j.cub.2004.08.024 · DOI
  82. 2022, Dev Cell, 57, 2257, 10.1016/j.devcel.2022.09.006 · DOI
  83. 10.1016/S1534-5807(03)00088-1 · DOI
  84. 10.1016/j.devcel.2015.06.024 · DOI
  85. 2011, PLoS Computational Biology, 7, e1002195, 10.1371/journal.pcbi.1002195 · DOI · Paper page

Metadata

Authors
Chang, N.-C., Wells, J. N., Wang, A. Y., Schofield, P., Huang, Y.-C., Truong, V. H., Simoes-Costa, M., & Feschotte, C.
Affiliations
  • Cornell University (US)
  • Boston Children's Hospital (US)
Corresponding author
  • Chang, Ni-Chen
  • Wells, Jonathan N.
  • Feschotte, Cédric
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
openRxiv
Published
2024-03-25
Volume
122
Issue
18
Pages
e2411446122-e2411446122
ISSN
0027-8424 (ISSN-L)
DOI
10.1101/2024.03.25.586437
PMC
PMC12067270
OpenAlex
W4409872540
Cited by
27
References
1
Citations by year
2026: 12 · 2025: 14 · 2024: 1
FWCI
14.05
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed Central (submittedVersion, cc-by)
Funders
  • Human Frontier Science Program (LT000017/2019-L)
  • National Institutes of Health
  • National Institute of General Medical Sciences (R35GM122550)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
Keywords
endogenous retroviruses, Gag protein, transposable elements, mesoderm formation, neural crest development, cell migration, cell membrane association, zebrafish embryonic development, addiction models

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