RNA polymerase II speed of transcription in liver

Value 34 bp/s Range: ±11 bp/s
Organism Mouse Mus musculus
Reference Bahar Halpern K. et al., Bursty gene expression in the intact mammalian liver. Mol Cell. 2015 Apr 2 58(1):147-56. doi: 10.1016/j.molcel.2015.01.027. p.150 left column top paragraphPubMed ID25728770
Method P.148 left column bottom paragraph:"To assess the intrinsic variability in the expression of liver genes, [investigators] imaged individual mRNA molecules in mouse liver frozen sections using smFISH [Single molecule fluorescence in situ hybridization](Itzkovitz et al., 2012 and Lyubimova et al., 2013) (Figures 1 and S1). [They] used simultaneous DAPI [4',6-diamidino-2-phenylindole, a fluorescent stain] nuclear staining and phalloidin membrane staining to assign mRNA dots to individual cells. [They] developed an in situ ploidy classification algorithm (Supplemental Experimental Procedures) that enabled stratifying [their] single-cell mRNA counts by both tissue zone and ploidy class (Figures S1D–S1F)."
Comments P.149 right column bottom paragraph to p.150 left column top paragraph:"Using intensity ratios of probe libraries targeting both ends of the gene, [investigators] demonstrated that >85% of nascent mRNAs at TSs [transcription sites] are attached to actively transcribing polymerase molecules (Figure S3). Thus, the number of nascent mRNA can be used as a proxy for polymerase occupancy (M). [They] next used polymerase occupancy to infer the transcription rate μ, the average rate of mRNA production from an active TS, using the equation μ=M⋅v/L, where L is the length of the gene and v = 34 ± 11 bp/s is the polymerase speed, which [they] calibrated using actinomycin D treatment (Experimental Procedures)."
Entered by Uri M
ID 112172