SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains.
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
09 Mar 2022
09 Mar 2022
Historique:
entrez:
20
6
2022
pubmed:
21
6
2022
medline:
21
6
2022
Statut:
ppublish
Résumé
Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with eight C57BL/6 and five C57BL/10 closely related inbred substrains. Whole-genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 indels, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs), and 2,826 differentially expressed genes (DE genes) among these 14 strains; 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs, and frameshifting indels that were associated with DE genes. Our results can be used for both forward and reverse genetic approaches and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.
Identifiants
pubmed: 35720252
doi: 10.1016/j.xgen.2022.100102
pmc: PMC9205302
mid: NIHMS1787765
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM119128
Pays : United States
Organisme : NIMH NIH HHS
ID : T32 MH020065
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA051234
Pays : United States
Organisme : NIDA NIH HHS
ID : P50 DA037844
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH113715
Pays : United States
Organisme : NIMH NIH HHS
ID : T32 MH018399
Pays : United States
Déclaration de conflit d'intérêts
DECLARATION OF INTERESTS The authors declare no competing interests.
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