Document Type
Article
Publication Date
5-10-2023
Original Citation
Ferraj A,
Audano P,
Balachandran P,
Czechanski A,
Flores J,
Radecki A,
Mosur V,
Gordon D,
Walawalkar I,
Eichler E,
Reinholdt L,
Beck C.
Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. Cell Genom. 2023;3(5):100291.
Keywords
JGM, JMG, SS1
JAX Source
Cell Genom. 2023;3(5):100291.
ISSN
2666-979X
PMID
37228752
DOI
https://doi.org/10.1016/j.xgen.2023.100291
Abstract
Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural vari- ants (SVs) (variants R 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic vari- ation. Here, we resolve genome-wide SVs in 20 genetically distinct inbred mice with long-read sequencing. We report 413,758 site-specific SVs affecting 13% (356 Mbp) of the mouse reference assembly, including 510 previously unannotated coding variants. We substantially improve the Mus musculus transposable element (TE) callset, and we find that TEs comprise 39% of SVs and account for 75% of altered bases. We further utilize this callset to investigate how TE heterogeneity affects mouse embryonic stem cells and find multiple TE classes that influence chromatin accessibility. Our work provides a comprehensive analysis of SVs found in diverse mouse genomes and illustrates the role of TEs in epigenetic differences.
Comments
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).