We imaged transcription in living cells using a locus-specific reporter system, which allowed precise, single-cell kinetic measurements of promoter binding, initiation and elongation. Photobleaching of fluorescent RNA polymerase II revealed several kinetically distinct populations of the enzyme interacting with a specific gene. Photobleaching and photoactivation of fluorescent MS2 proteins used to label nascent messenger RNAs provided sensitive elongation measurements. A mechanistic kinetic model that fits our data was validated using specific inhibitors. Polymerases elongated at 4.3 kilobases min −1 , much faster than previously documented, and entered a paused state for unexpectedly long times. Transcription onset was inefficient, with only 1% of polymerase-gene interactions leading to completion of an mRNA. Our systems approach, quantifying both polymerase and mRNA kinetics on a defined DNA template in vivo with high temporal resolution, opens new avenues for studying regulation of transcriptional processes in vivo.Transcription by RNA polymerase II (Pol II) is at the core of gene expression and hence is the basis of all cellular activities. Little information exists about the kinetics of this process in live cells 1 , as understanding of gene expression regulation comes from studies using purified proteins. For instance, the subunits of the elongating Pol II are well known 2 and the crystal structure of this enzyme explains much of its behavior in vitro 3,4 . mRNA transcription can be deconstructed into a succession of steps: promoter assembly, clearanceCorrespondence should be addressed to R.H.S. (rhsinger@aecom.yu.edu). AUTHOR CONTRIBUTIONS All data were initially acquired by X.D. and Y.S.-T. Subsequent data were obtained by V.d.T. (Fig. 4a,b and Fig. 5a) and Y.B. (Fig. 9b). S.M.S. was responsible for the microscopy, built the wide-field microscope for live-cell imaging and wrote analysis software. X.D. performed the kinetic modeling. R.D.P. provided consultation on model formulation and testing, and training in the use of the ProcessDB software. R.H.S. supervised the project. COMPETING INTERESTS STATEMENTThe authors declare competing financial interests: details accompany the full-text HTML version of the paper at http:// www.nature.com/nsmb/. HHS Public AccessAuthor manuscript Nat Struct Mol Biol. Author manuscript; available in PMC 2016 July 12. Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript and escape 5 , followed by elongation and termination. The process of transcriptional initiation involves several structural changes in the polymerase as the nascent transcript elongates 6 . Early in initiation, the polymerase can produce abortive transcripts 7,8 . These abortive cycles have been observed with a single prokaryote polymerase (RNAP) releasing several transcripts without escaping the promoter 9,10 . The elongation step can be regulated by pausing for various times, as demonstrated using prokaryotic polymerases in vitro 11,12 .For eukaryotic cells, attempts have been mad...

We measured individual trajectories of fluorescently labeled telomeres in the nucleus of eukaryotic cells in the time range of 10 À2 -10 4 sec by combining a few acquisition methods. At short times the motion is subdiffusive with hr 2 i $ t and it changes to normal diffusion at longer times. The short times diffusion may be explained by the reptation model and the transient diffusion is consistent with a model of telomeres that are subject to a local binding mechanism with a wide but finite distribution of waiting times. These findings have important biological implications with respect to the genome organization in the nucleus. DOI: 10.1103/PhysRevLett.103.018102 PACS numbers: 87.16.Zg, 05.40.Jc, 87.15.Vv The nucleus of the eukaryotic cell contains tens of thousands of genes ($23 000 in human) organized as chromosomal DNA. This crowded environment contains packed genetic material, RNA transcripts, protein factors, and a variety of nuclear bodies. The genetic information (DNA) can be either replicated to form daughter cells, or transcribed to RNA molecules leading to protein translation. These processes depend on the ability of protein factors to locate and interact with specific DNA sequence within this packed nucleus [1], as well as on the organization and structure of chromatin in the nucleus [2]. Telomeres are the end caps of the linear eukaryotic chromosomes. They play an important role in maintaining chromosome organization and integrity throughout the cell cycle. The telomeres are protected by a number of protein factors that are collectively referred to as shelterin and can bind to either the nuclear envelope, nuclear matrix, or heterochromatin, depending on the cell species [3]. Therefore, studying the dynamics of telomeres can shed light on chromosome dynamics, the role of telomeres in genome organization, and the coordination of physical structures and biological processes in the nucleus [4].Chromosomes occupy specific nuclear volumes referred to as chromosome territories [5], and their motion is highly constrained. The diffusion of telomeres was previously studied on a limited time scale of either minutes [6] or 1-200 sec [7] and exhibited mainly normal constrained diffusion with a heterogeneous diffusion coefficient of 2-6 Â 10 À4 m 2 =s. This is significantly lower than the diffusion of small molecules such as dextran in the nucleus (10-100 m 2 =s), which reflects the dense nature of the nucleus. The dynamics of other nuclear bodies as well as messenger RNAs were also measured [8][9][10] and anomalous diffusion was found for specific DNA loci [11].In this study, we examined the diffusion properties of telomeres in the nucleus in a broad time range of almost 6 orders of magnitude (10 À2 -10 4 sec ). Such a broad time range was employed by combining two different imaging setups on the same microscope. We find that the diffusion is anomalous at short times of $10 À2 -10 3 sec . It changes to normal diffusion at longer time intervals and the diffusion constants are found to have a wide distribution...

Understanding gene expression requires the ability to follow the fate of individual molecules. Here we use a cellular system for monitoring messenger RNA (mRNA)expression to characterize the movement in real time of single mRNA-protein complexes (mRNPs) in the nucleus of living mammalian cells. This mobility was not directed but was governed by simple diffusion. Some mRNPs were partially corralled throughout the nonhomogenous nuclear environment, but no accumulation at subnuclear domains was observed. Following energy deprivation, energyindependent motion of mRNPs was observed in a highly ATP-dependent nuclear environment; movements were constrained to chromatin-poor domains and excluded by newly formed chromatin barriers. This observation resolves a controversy, showing that the energetic requirements of nuclear mRNP trafficking are consistent with a diffusional model. Recent technological developments have facilitated imaging of single RNA molecules in the cytoplasm of living cells (1). We have developed a cellular system in which the expression of a transgene array can be followed sequentially in single living cells, and we have previously analyzed the particular chromatin-related modifications occurring at this specific locus from a silenced state throughout its transcriptional activation (2). Here we use this system to address the mechanism by which individual mRNA transcripts move within the nucleoplasm after release from the transcription site.In this system, a genetic locus, its transcribed mRNAs, and the translated protein were rendered visible in cells after electroporation with the cyan fluorescent protein (CFP) or the red fluorescent protein (RFP)-lac repressor protein (marks the genomic locus), yellow fluorescent protein (YFP)-MS2 (labels the mRNA), and pTet-On (for transcriptional induction) (3). Transcriptional activation by doxycycline induced the unfolding of the integrated locus (4) and the recruitment of the YFP-MS2 protein to the locus as a result of the specific labeling of the nascent transcripts bearing the MS2 stem loops. Minutes after induction (15 to 30 min), the MS2 signal began accumulating in the nucleoplasm in a particulate pattern suggestive of mRNA-protein complexes (mRNPs). At later times (1 to 2 hours after induction), mRNPs were detected in the cytoplasm in conjunction with the Correspondence to: Robert H. Singer, rhsinger@aecom.yu.edu. The presence of the nascent RNAs at the site of transcription was verified using fluorescent in situ hybridization (FISH) on fixed cells with two different probes either to the MS2 repeats (located in the middle of the transcript) or to the β globin exon (3′ end). Both probes hybridized at the active locus, indicating that the complete pre-mRNA transcripts were retained at the transcription site before release ( fig. S2A to D). Colocalization of the mRNA signal (FISH) with the YFP signal demonstrated that the particles visualized in living cells were mRNPs (3). RNA quantification with single-molecule sensitivity was performed on deconvol...