measuring the kinetics of mrna transcription in single living cells the transcriptional activity of rna polymerase ii pol ii is a dynamic process and therefore measuring the kinetics of the transcriptional process in vivo is of importance pol ii kinetics have been measured using biochemical or molecular methods in recent years with the development of new visualization methods it has become possible to follow transcription as it occurs in real time in single living cells herein we describe how to perform analysis of pol ii elongation kinetics on a specific gene in living cells using a cell line in which a specific gene locus dna its mrna product and the final protein product can be fluorescently labeled and visualized in vivo it is possible to detect the actual transcription of mrnas on the gene of interest the mrna is fluorescently tagged using the ms2 system for tagging mrnas in vivo where the 3utr of the mrna transcripts contain 24 ms2 stemloop repeats which provide highly specific binding sites for the yfpms2 coat protein that labels the mrna as it is transcribed to monitor the kinetics of transcription we use the fluorescence recovery after photobleaching frap method by photobleaching the yfpms2tagged nascent transcripts at the site of transcription and then following the recovery of this signal over time we obtain the synthesis rate of the newly made mrnas in other words yfpms2 fluorescence recovery reflects the generation of new ms2 stemloops in the nascent transcripts and their binding by fluorescent free yfpms2 molecules entering from the surrounding nucleoplasm the frap recovery curves are then analyzed using mathematical mechanistic models formalized by a series of differential equations in order to retrieve the kinetic time parameters of transcription