Analysis Tools
mortality/aging
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• homozygotes produced by crossing of heterozygous mice are severely underrepresented; matings of homozygous females x heterozygous males and heterozygous females x homozygous males yield similar results
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• matings of heterozygous females x homozygous males produce an increased number of dead or absorbed embryos between E6.5 and E12.5 relative to control matings (wild-type females x homozygous males), suggesting that homozygous embryos die around gastrulation
• however, homozygous blastocysts are present at expected Mendelian ratios, suggesting normal preimplantation development
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embryo
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• GO enrichment analysis of differentially expressed genes (DEGs) in E12.5 embryos suggests that homozygotes die of genomic instability and associated lethal inflammation
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cellular
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• GO enrichment analysis of DEGs in E12.5 embryos shows that processes such as cellular response to DNA damage stimulus and DNA repair are enriched in downregulated DEGs
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• GO enrichment analysis of DEGs in E12.5 embryos shows that DNA replication is enriched among downregulated DEGs
• upon replication stress/fork stalling induced by hydroxyurea (HU) treatment, mouse embryonic stem cells (mESCs) derived from E3.5 blastocysts show defects in stalled fork restart and CDC45-MCM-GINS (CMG) helicase retention on chromatin; these defects can be fully rescued by re-expression of Lnc956
• HU-treated mESCs show impaired TRIM28-HSP90B1 interaction as well as impaired recruitment of TRIM28 and HSP90B1 to stalled replication forks; re-expression of full-length Lnc956 fully rescues these defects whereas re-expression of a truncated Lnc956 (which fails to interact with TRIM28- HSP90B1) has no rescue effect
• however, untreated mESCs show no significant change in the % of BrdU+ (S phase) cells and exhibit normal TRIM28-HSP90B1 association and loading onto replication forks
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• Neutral Comet Assays using single cells from E8.5, E10.5, and E12.5 homozygous embryos show a further increase in the level of DNA double-strand breaks (DSBs) at all stages relative to heterozygous embryos
• Dot immunoblotting of E12.5 embryos indicates that homozygous embryonic cells contain a significantly higher level of cytosolic double-strand DNA (dsDNA) than heterozygous cells
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homeostasis/metabolism
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• GO enrichment analysis of DEGs in E12.5 embryos shows that processes such as cellular response to DNA damage stimulus and DNA repair are enriched in downregulated DEGs
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• GO enrichment analysis of DEGs in E12.5 embryos shows that DNA replication is enriched among downregulated DEGs
• upon replication stress/fork stalling induced by hydroxyurea (HU) treatment, mouse embryonic stem cells (mESCs) derived from E3.5 blastocysts show defects in stalled fork restart and CDC45-MCM-GINS (CMG) helicase retention on chromatin; these defects can be fully rescued by re-expression of Lnc956
• HU-treated mESCs show impaired TRIM28-HSP90B1 interaction as well as impaired recruitment of TRIM28 and HSP90B1 to stalled replication forks; re-expression of full-length Lnc956 fully rescues these defects whereas re-expression of a truncated Lnc956 (which fails to interact with TRIM28- HSP90B1) has no rescue effect
• however, untreated mESCs show no significant change in the % of BrdU+ (S phase) cells and exhibit normal TRIM28-HSP90B1 association and loading onto replication forks
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immune system
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• GO enrichment analysis of DEGs in E12.5 embryos shows that inflammation response represents one of the top processes enriched in upregulated DEGs
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• GO enrichment analysis of DEGs in E12.5 embryos shows that innate immune response represents one of the top processes enriched in upregulated DEGs
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