Abstract
ABSTRACTGene trapping is a high-throughput approach that has been used to introduce insertional mutations into the genome of mouse embryonic stem (ES) cells. It is performed with generic gene trap vectors that simultaneously mutate and report the expression of the endogenous gene at the site of insertion and provide a DNA sequence tag for the rapid identification of the disrupted gene. Large-scale international efforts assembled a gene trap library of 566,554 ES cell lines with single gene trap integrations distributed throughout the genome. Here, we re-investigated this unique library and identified mutations in 2202 non-coding RNA (ncRNA) genes, in addition to mutations in 12,078 distinct protein-coding genes. Moreover, we found certain types of gene trap vectors preferentially integrating into genes expressing specific long non-coding RNA (lncRNA) biotypes. Together with all other gene-trapped ES cell lines, lncRNA gene-trapped ES cell lines are readily available for functional in vitro and in vivo studies.
Highlights
The comprehensive annotation of the mouse genome has identified over 21,000 protein-coding genes (PCGs), along with more than 15,000 non-coding RNA genes
In this study, we re-analyzed a library of 566,554 mutant mouse embryonic stem (ES) cell lines produced in multiple large-scale gene trap mutagenesis projects
The library of mutant ES cell lines was originally produced to study the function of PCGs, the present analysis revealed that the library contains 31,069 ES cell lines with mutations in 2202 unique ncRNA genes, in addition to the ES cell lines with mutations
Summary
The comprehensive annotation of the mouse genome has identified over 21,000 protein-coding genes (PCGs), along with more than 15,000 non-coding RNA (ncRNA) genes. To address their function, platforms for large-scale mutagenesis in embryonic stem (ES) cells have been implemented, with the ultimate goal to convert all mutant ES cell lines into mice for subsequent phenotyping. Using high-throughput gene trapping and targeting, the International Knockout Mouse (IKMC) and International Mouse Phenotyping (IMPC) consortia have created an unprecedented resource comprising mutant ES cell lines harboring mutations in ∼18,500 unique PCGs. Of these, over 5000 have been converted into mice and subjected to high-throughput phenotyping.
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