The composition dynamics of transposable elements in human blastocysts.
Journal
Journal of human genetics
ISSN: 1435-232X
Titre abrégé: J Hum Genet
Pays: England
ID NLM: 9808008
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
received:
20
01
2023
accepted:
03
06
2023
revised:
11
05
2023
medline:
26
9
2023
pubmed:
13
6
2023
entrez:
12
6
2023
Statut:
ppublish
Résumé
Transposable elements (TEs) are mobile DNA sequences that can replicate themselves and play significant roles in embryo development and chromosomal structure remodeling. In this study, we investigated the variation of TEs in blastocysts with different parental genetic backgrounds. We analyzed the proportions of 1137 TEs subfamilies from six classes at the DNA level using Bowtie2 and PopoolationTE2 in 196 blastocysts with abnormal parental chromosomal diseases. Our findings revealed that the parental karyotype was the dominant factor influencing TEs frequencies. Out of the 1116 subfamilies, different frequencies were observed in blastocysts with varying parental karyotypes. The development stage of blastocysts was the second most crucial factor influencing TEs proportions. A total of 614 subfamilies exhibited different proportions at distinct blastocyst stages. Notably, subfamily members belonging to the Alu family showed a high proportion at stage 6, while those from the LINE class exhibited a high proportion at stage 3 and a low proportion at stage 6. Moreover, the proportions of some TEs subfamilies also varied depending on blastocyst karyotype, inner cell mass status, and outer trophectoderm status. We found that 48 subfamilies displayed different proportions between balanced and unbalanced blastocysts. Additionally, 19 subfamilies demonstrated varying proportions among different inner cell mass scores, and 43 subfamilies exhibited different proportions among outer trophectoderm scores. This study suggests that the composition of TEs subfamilies may be influenced by various factors and undergoes dynamic modulation during embryo development.
Identifiants
pubmed: 37308564
doi: 10.1038/s10038-023-01169-7
pii: 10.1038/s10038-023-01169-7
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
681-688Subventions
Organisme : Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province)
ID : 2021A1515011183
Organisme : Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province)
ID : 2020B1212060018
Informations de copyright
© 2023. The Japan Society of Human Genetics.
Références
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.
doi: 10.1038/35057062
pubmed: 11237011
Finnegan DJ. Eukaryotic transposable elements and genome evolution. Trends Genet. 1989;5:103–7.
doi: 10.1016/0168-9525(89)90039-5
pubmed: 2543105
Seberg O, Petersen G. A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat Rev Genet. 2009;10:276.
doi: 10.1038/nrg2165-c3
pubmed: 19238178
Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA. 2001;98:8714–9.
doi: 10.1073/pnas.151269298
pubmed: 11447285
pmcid: 37501
Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009;10:691–703.
doi: 10.1038/nrg2640
pmcid: 2884099
Hsu PS, Yu SH, Tsai YT, Chang JY, Tsai LK, Ye CH, et al. More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation. J Biomed Sci. 2021;28:58.
doi: 10.1186/s12929-021-00754-2
pubmed: 34364371
pmcid: 8349491
RN Platt 2nd, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res. 2018;26:25–43.
doi: 10.1007/s10577-017-9570-z
Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 2008;9:397–405.
doi: 10.1038/nrg2337
pmcid: 2596197
Surm JM, Moran Y. Transposons Increase Transcriptional Complexity: The Good Parasite? Trends Genet. 2021;37:606–7.
doi: 10.1016/j.tig.2021.03.009
Wu J, Xu J, Liu B, Yao G, Wang P, Lin Z, et al. Chromatin analysis in human early development reveals epigenetic transition during ZGA. Nature. 2018;557:256–60.
doi: 10.1038/s41586-018-0080-8
pubmed: 29720659
Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, et al. Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell. 2018;173:248–59.
doi: 10.1016/j.cell.2018.02.028
pubmed: 29526463
Liu L, Leng L, Liu C, Lu C, Yuan Y, Wu L, et al. An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos. Nat Commun. 2019;10:364.
doi: 10.1038/s41467-018-08244-0
pubmed: 30664750
pmcid: 6341076
Goke J, Lu X, Chan YS, Ng HH, Ly LH, Sachs F, et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell. 2015;16:135–41.
doi: 10.1016/j.stem.2015.01.005
pubmed: 25658370
Saksouk N, Simboeck E, Dejardin J. Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin. 2015;8:3.
doi: 10.1186/1756-8935-8-3
pmcid: 4363358
Burton A, Torres-Padilla ME. Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis. Nat Rev Mol Cell Biol. 2014;15:723–34.
doi: 10.1038/nrm3885
pubmed: 25303116
Martin C, Beaujean N, Brochard V, Audouard C, Zink D, Debey P. Genome restructuring in mouse embryos during reprogramming and early development. Dev Biol. 2006;292:317–32.
doi: 10.1016/j.ydbio.2006.01.009
pubmed: 16680825
Ge SX. Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development. BMC Genomics. 2017;18:200.
doi: 10.1186/s12864-017-3566-0
pubmed: 28231763
pmcid: 5324221
Yuan P, Zheng L, Ou S, Zhao H, Li R, Luo H, et al. Evaluation of chromosomal abnormalities from preimplantation genetic testing to the reproductive outcomes: a comparison between three different structural rearrangements based on next-generation sequencing. J Assist Reprod Genet. 2021;38:709–18.
doi: 10.1007/s10815-020-02053-5
pubmed: 33409753
pmcid: 7910334
Gardner DK and Schoolcraft WB In vitro culture of human blastocysts. In: Jansen R and Mortimer D, editors. Toward Reproductive Certainty: Fertility and Genetics Beyond 1999. London: Parthenon Publishing; 1999. p.378–88.
Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992;13:718–25.
doi: 10.1016/0888-7543(92)90147-K
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
doi: 10.1038/nmeth.1923
pubmed: 22388286
pmcid: 3322381
Kofler R, Gómez-Sánchez D, Schlötterer C. PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq. Mol Biol Evol. 2016;33:2759–64.
doi: 10.1093/molbev/msw137
pubmed: 27486221
pmcid: 5026257
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10:giab008.
doi: 10.1093/gigascience/giab008
pmcid: 7931819
Kazazian HHJ, Moran JV. Mobile DNA in Health and Disease. N Engl J Med. 2017;377:361–70.
doi: 10.1056/NEJMra1510092
pubmed: 28745987
pmcid: 5980640
Kazazian HHJ, Moran JV. The impact of L1 retrotransposons on the human genome. Nat Genet. 1998;19:19–24.
doi: 10.1038/ng0598-19
pubmed: 9590283
Richardson SR, Morell S, Faulkner GJ. L1 retrotransposons and somatic mosaicism in the brain. Annu Rev Genet. 2014;48:1–27.
doi: 10.1146/annurev-genet-120213-092412
pubmed: 25036377
Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci USA. 2003;100:5280–5.
doi: 10.1073/pnas.0831042100
pubmed: 12682288
pmcid: 154336
Kazazian HHJ, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 1988;332:164–6.
doi: 10.1038/332164a0
pubmed: 2831458
Jachowicz JW, Bing X, Pontabry J, Boskovic A, Rando OJ, Torres-Padilla ME. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Nat Genet. 2017;49:1502–10.
doi: 10.1038/ng.3945
pubmed: 28846101
Vitullo P, Sciamanna I, Baiocchi M, Sinibaldi-Vallebona P, Spadafora C. LINE-1 retrotransposon copies are amplified during murine early embryo development. Mol Reprod Dev. 2012;79:118–27.
doi: 10.1002/mrd.22003
Yandim C, Karakulah G. Expression dynamics of repetitive DNA in early human embryonic development. BMC Genomics. 2019;20:439.
doi: 10.1186/s12864-019-5803-1
pubmed: 31151386
pmcid: 6545021
Del Re B, Giorgi G. Long INterspersed element-1 mobility as a sensor of environmental stresses. Environ Mol Mutagen. 2020;61:465–93.
doi: 10.1002/em.22366
pubmed: 32144842