Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA
3f). In line with their 2CLC identity8,23, they express the transcription factor Dux and MERVL activation—as determined using the 2C reporter—that was dependent on Dux (Fig. 3e and Extended Data Fig. 4h). As USP7 can have multiple functions throughout the cell cycle24,25, we next ...
a The top significantly represented transcription factors targeting Trim33-deregulated genes in p19/Nras cells; data were analyzed using Enrichr70. b Cycloheximide chase assays in p19/Nras Trim33-WT and Trim33-KO cells; n = 3. Right panel shows the mean intensity (±SD) for three ...
6E). Notably, survival analysis indicated that tumors of patients having higher levels of transcription of replication stress signature genes experienced worse prognosis, extending the potential utility of this signature from a predictive biomarker to a predictive/prognostic biomarker (Fig. 6E). All ...
Type I IFN then induces the synthesis of interferon stimulated genes (ISGs) in infected and neighboring cells through activation of STAT1 and STAT2 transcription factors. Both SARS-CoV-2 nonstructural proteins (NSPs) and open reading frames (ORFs) have been shown to prevent the activation and ...
(Supplementary Fig.1d) and were enriched in RNA:DNA hybrids at both transcription start sites (TSS) and transcription termination sites (TTS; Fig.1e, f), which is consistent with earlier studies22. The enrichment of R-loops at the TTS of a subset of genes was confirmed by DRIP-qPCR (...
In unperturbed cells, MYC proteins bind to nearly all active promoters and control transcription by RNA polymerase II2,3. MYC proteins can also coordinate transcription with DNA replication4,5 and promote the repair of transcription-associated DNA damage6, but how they exert these mechanistically ...
Transcription direction is indicated. g Venn diagram showing R-loop (DRIPc; light blue), FANCD2 (purple) and SMARCA5 (yellow) genome-wide co-occurrence in control K562 cells. h Venn diagram showing R-loop (DRIPc; light blue), FANCD2 (purple) and YY1 (INO80; green) genome-wide co-...
–d), and the mRNA levels of these genes are negatively correlated toSPOPmRNA expression in prostate cancers (Supplementary Fig.1e-h). The patient specimen data stress that SPOP mutations may affect genome alterations via regulating DNA replication through mechanism(s) independent of transcription ...
Reverse transcription was done using the T100 thermal cycler (Bio-Rad). The qRT-PCR was performed with TaqMan gene expression assay probes (Thermo Fisher) according to the manufacturer’s instructions. The following probes (all from Thermo Fisher) were used: GAPDH (glyceraldehyde 3-phosphate ...