Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2021 Jul 9;433(14):167016.
doi: 10.1016/j.jmb.2021.167016. Epub 2021 May 2.

Towards a 'Spot On' Understanding of Transcription in the Nucleus

Simona Patange  1 , David A Ball  1 , Tatiana S Karpova  1 , Daniel R Larson  2
Affiliations
Review

Towards a 'Spot On' Understanding of Transcription in the Nucleus

Simona Patange et al. J Mol Biol. .

Abstract

Regulation of transcription by RNA Polymerase II (RNAPII) is a rapidly evolving area of research. Technological developments in microscopy have revealed insight into the dynamics, structure, and localization of transcription components within single cells. A frequent observation in many studies is the appearance of 'spots' in cell nuclei associated with the transcription process. In this review we highlight studies that characterize the temporal and spatial characteristics of these spots, examine possible pitfalls in interpreting these kind of imaging data, and outline directions where single-cell imaging may advance in ways to further our understanding of transcription regulation.

Keywords: fluorescence; microscopy; single-cell; splicing; transcription.

PubMed Disclaimer

Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Figure 1
Figure 1
(A) Transcription spots from the literature. From left to right: ‘Transcription Factories:’ HeLa cells incubated with Br-UTP to label newly synthesized RNA [5]; Live-cell imaging of YFP-RNAPII at a lacO array in U2OS cells [81]; tcPALM image of Dendra2-RNAPII in U2OS cells [12]; GFP-RPB1 knock-in human cell line [24] (B) Schematic of reference scenario discussed in this review.
Figure 2
Figure 2
(A) Schematic of HiLO microscopy combined with HaloTag expression to visualize single transcription factors. Cells expressing transcription factors fused to a HaloTag (Halo-TFs, gray circles) are excited under thin inclined illumination plane, causing a subset of the molecules to fluoresce (cyan circles). (B) A comparison of Halo-RPB1 expressed in the nucleus of a live cell visualized with different image processing methods. The montage represents a 600 frame timeseries imaged at 200ms intervals (~2 min duration total), with every 30 frames shown. The upper right image shows the 600 frames in a sum projection, a spatial projection of a temporal image image stack. Adjusting the sum projection towards high contrast (bottom right image) further alters the image. (C) As in (B) for Halo-MED1. (D) As in (B) for Halo-GR.
See this image and copyright information in PMC

References

    1. Cajal SR, “Un sencillo método de coloración selectiva del retículo protoplásmico y sus efectos en los diversos órganos nerviosos de vertebrados e invertebrados.,” Trab. Lab. Invest. Biol, vol. 2, no. 129–221, 1903.
    1. Dekker J, Rippe K, Dekker M, and Kleckner N, “Capturing chromosome conformation,” Science (80-. ), vol. 295, no. 5558, pp. 1306–1311, February. 2002, doi: 10.1126/science.1067799. - DOI - PubMed
    1. Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, and O’Shea CC, “ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells,” Science (80-. ), vol. 357, no. 6349, July. 2017, doi: 10.1126/science.aag0025. - DOI - PMC - PubMed
    1. Rodriguez J and Larson DR, “Transcription in Living Cells: Molecular Mechanisms of Bursting,” Annu. Rev. Biochem, vol. 89, no. 1, pp. 189–212, June. 2020, doi: 10.1146/annurev-biochem-011520-105250. - DOI - PubMed
    1. Jackson DA, Hassan AB, Errington RJ, and Cook PR, “Visualization of focal sites of transcription within human nuclei,” EMBO J, vol. 12, no. 3, pp. 1059–1065, 1993, doi: 10.1002/j.1460-2075.1993.tb05747.x. - DOI - PMC - PubMed

MeSH terms

Substances

LinkOut - more resources