Coding variants in mouse and rat model organisms: mousepost and ratpost.
Journal
Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
Titre abrégé: Mamm Genome
Pays: United States
ID NLM: 9100916
Informations de publication
Date de publication:
03 2022
03 2022
Historique:
received:
07
05
2021
accepted:
21
07
2021
pubmed:
28
7
2021
medline:
26
4
2022
entrez:
27
7
2021
Statut:
ppublish
Résumé
Mice and rats are the most commonly used vertebrate model organisms in biomedical research. The availability of a reference genome in both animals combined with the deep sequencing of several doze of popular inbred lines also provides rich sequence variation data in these species. In some cases, such sequence variants can be linked directly to a distinctive phenotype. In previous work, we created the mouse and rat online searchable databases ("Mousepost" and "Ratpost") where small variant information for protein coding transcripts in mouse and rat inbred strains can be easily retrieved at the amino acid level. These tools are directly useful in forward genetics strategies or as a repository of existing sequence variations. Here, we perform a comparison between the "Mousepost" and "Ratpost" databases and we couple these two tools to a database of human sequence variants ClinVar. We investigated the level of redundancy and complementarity of known variants in protein coding transcripts and found that the large majority of variants is species-specific. However, a small set of positions is conserved in an inbred line between both species. We conclude that both databases are highly complementary, but this may change with further sequencing efforts in both species.
Identifiants
pubmed: 34313794
doi: 10.1007/s00335-021-09898-w
pii: 10.1007/s00335-021-09898-w
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
81-87Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Atanur SS et al (2013) Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 154(3):691–703
doi: 10.1016/j.cell.2013.06.040
Beck JA et al (2000) Genealogies of mouse inbred strains. Nat Genet 24(1):23
doi: 10.1038/71641
Bergman I et al (2000) Comparison of in vitro antibody-targeted cytotoxicity using mouse, rat and human effectors. Cancer Immunol Immunother 49(4–5):259–266
doi: 10.1007/s002620000120
Choi Y et al (2012) Predicting the functional effect of amino acid substitutions and indels. PloS ONE 7(10):e46688
doi: 10.1371/journal.pone.0046688
Cock PJA et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11):1422–1423
doi: 10.1093/bioinformatics/btp163
Ellenbroek B, Youn J (2016) Rodent models in neuroscience research: is it a rat race? Dis Model Mech 9(10):1079–1087
doi: 10.1242/dmm.026120
Mouse Genome Sequencing Consortium et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562
Gibbs RA et al (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493–521
doi: 10.1038/nature02426
Hermsen R et al (2015) Genomic landscape of rat strain and substrain variation. BMC Genomics 16:357
doi: 10.1186/s12864-015-1594-1
Ibarra-Soria X et al (2017) Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated. eLife 6:e21476
doi: 10.7554/eLife.21476
Keane TM et al (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477(7364):289–294
doi: 10.1038/nature10413
Landrum MJ et al (2018) ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res 46(D1):D1062–D1067
doi: 10.1093/nar/gkx1153
Lu BS et al (2007) Generation of rat mutants using a coat color-tagged Sleeping Beauty transposon system. Mamm Genome 18(5):338–346
doi: 10.1007/s00335-007-9025-5
Modlinska K, Pisula W (2020) The Norway rat, from an obnoxious pest to a laboratory pet. eLife 9:e50651
doi: 10.7554/eLife.50651
Morse H (1981) The laboratory mouse—a historical perspective. In: Foster HL, Small JD, Fox JG (eds) The mouse in biomedical research. Academic Press, New York, pp 1–16
Mouse Genome Sequencing, C et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–62
doi: 10.1038/nature01262
Philipeaux J (1856) Note sur l’exstirpation des capsules surrenales chez les rats albinos (Mus rattus). Compt Rend Hebd Seances Acad Sci 43:904–906
Poltorak A et al (1998) Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science (New York, NY) 282(5396):2085–8
doi: 10.1126/science.282.5396.2085
Sharp PE, Villano JS (2013) The laboratory rat, 2nd edn. The laboratory animal pocket reference series. CRC Press, Boca Raton, Vol xxi, p 377
Smith JR et al (2020) The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res 48(D1):D731–D742
pubmed: 31713623
Timmermans S, Libert C (2021) Ratpost: a searchable database of protein-inactivating sequence variations in 40 sequenced rat-inbred strains. Mamm Genome 32(1):1–11
doi: 10.1007/s00335-020-09853-1
Timmermans S, Van Montagu M, Libert C (2017) Complete overview of protein-inactivating sequence variations in 36 sequenced mouse inbred strains. Proc Natl Acad Sci USA 114(34):9158–9163
doi: 10.1073/pnas.1706168114
Viney M, Lazarou L, Abolins S (2015) The laboratory mouse and wild immunology. Parasite Immunol 37(5):267–273
doi: 10.1111/pim.12150
Yates AD et al (2020) Ensembl 2020. Nucleic Acids Res 48(D1):D682–D688
pubmed: 31691826
Yeung F et al (2020) Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host Microbe 27(5):809
doi: 10.1016/j.chom.2020.02.015
Yokoyama T et al (1990) Conserved cysteine to serine mutation in tyrosinase is responsible for the classical albino mutation in laboratory mice. Nucleic Acids Res 18(24):7293–7298
doi: 10.1093/nar/18.24.7293
Zhou YY et al (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10:1523
doi: 10.1038/s41467-019-09234-6