Burst parameters for the different genes and conditions studied in the liver

Range Table - link
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. Supplemental Information Table S1PubMed 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.151 right column 2nd paragraph:"To further explore noise-response tradeoffs in liver gene expression parameter space, [investigators] performed [their] measurements on Pck1 [Phosphoenolpyruvate carboxykinase 1] and G6pc [Glucose-6-phosphatase, catalytic subunit (glucose 6-phosphatase alpha)], the key genes controlling hepatic glucose output, in fed, fasting, and refed mice. These conditions have been shown to lead to drastic changes in mRNA levels for these genes (Gebhardt, 1992 and Jungermann and Kietzmann, 1996). [They] find that Pck1 and G6pc are upregulated in fasting conditions through a coordinate increase in both transcript production (β=n⋅f⋅μ) and degradation rates (δ) compared to a high-fed state ( Figures 4C and 4D). High degradation rates enable a rapid decline in transcript numbers after a 1 hr period of refeeding (Figure 5). Interestingly, the increased transcript production is mainly a result of an increase in burst fraction (f, 10-fold increase for G6pc and 40-fold increase for Pck1 Table S1) and a more modest increase in transcription rate (μ, 1.4-fold for G6pc and 6-fold for Pck1 Figure 4D Table S1). The increase in transcript production rate predominantly via increased burst fraction is consistent with a strategy of minimizing burst-associated noise ( Figure 4A)." (M)=polymerase occupancy. (μ)=transcription rate. (PP)=periportal zone. (PC)=pericentral zone. Note-table is truncated on the right-most column
Entered by Uri M
ID 112174