Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules
Fig 3
(A) Mean number of nascent RNAs for six different yeast genes.
We use the nascent RNA distribution data for six constitutively expressed yeast genes: KAP104, TAF5, TAF6, TAF12, RPB2, RPB3 and plot the mean of the distributions as a function of the gene length. The mean of the distribution increases linearly with the gene length indicating that the transcription of all six genes is initiating at the same rate. The initiation rate of these genes extracted from the data is 0.145±0.025/min, where the rate of elongation is taken to be 0.8 kb/min [4]. (B) Fano factor for the nascent RNA distribution of six different yeast genes. Using the data for the nascent RNA distributions for the same six yeast genes described in (A) we compute the Fano factor and compare it to predictions from our model. The shaded region shows the possible values that the Fano factor can take depending on the ratio of kLOAD and kESC given the initiation rate determined from the mean in part (A). The boundary of the shaded region corresponds to the minimum amount of noise (as measured by the Fano factor) given the extracted rate of initiation in part (A), and it is obtained when the two rates are the same, i.e., kLOAD = kESC = 0.29±0.013/min. Interestingly enough the Fano factors characterizing the nascent RNA distribution for these six yeast genes seem to lie on this boundary. (The nascent RNA data for the six yeast genes used in our analysis is taken from ref. [25].)