DOI: 10.1083/jcb.146.3.543. Three-Dimensional Visualization of Transcription Sites and Their Association with Splicing Factor

Three-Dimensional Visualization of Transcription Sites and Their Association with Splicing Factor–Rich Nuclear Speckles

10.1083/jcb.146.3.543

Crossref journal-article

Rockefeller University Press

The Journal of Cell Biology (291)

Abstract

Transcription sites are detected by labeling nascent transcripts with BrUTP in permeabilized 3T3 mouse fibroblasts followed by laser scanning confocal microscopy. Inhibition and enzyme digestion studies confirm that the labeled sites are from RNA transcripts and that RNA polymerase I (RP I) and II (RP II) are responsible for nucleolar and extranucleolar transcription, respectively. An average of 2,000 sites are detected per nucleus with over 90% in the extranucleolar compartment where they are arranged in clusters and three-dimensional networklike arrays. The number of transcription sites, their three-dimensional organization and arrangement into functional zones (Wei et al. 1998) is strikingly maintained after extraction for nuclear matrix. Significant levels of total RP II mediated transcription sites (45%) were associated with splicing factor–rich nuclear speckles even though the speckles occupied &lt;10% of the total extranucleolar space. Moreover, the vast majority of nuclear speckles (&gt;90%) had moderate to high levels of associated transcription activity. Transcription sites were found along the periphery as well as inside the speckles themselves. These spatial relations were confirmed in optical sections through individual speckles and after in vivo labeling of nascent transcripts. Our results demonstrate that nuclear speckles and their surrounding regions are major sites of RP II-mediated transcription in the cell nucleus, and support the view that both speckle- and nonspeckle-associated regions of the nucleus contain sites for the coordination of transcription and splicing processes.

Bibliography

Wei, X., Somanathan, S., Samarabandu, J., & Berezney, R. (1999). Three-Dimensional Visualization of Transcription Sites and Their Association with Splicing FactorâRich Nuclear Speckles. The Journal of Cell Biology, 146(3), 543â558.

Authors 4

Xiangyun Wei (first)
Suryanarayan Somanathan (additional)
Jagath Samarabandu (additional)
Ronald Berezney (additional)

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Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 12:45 p.m.)
Deposited	2 years, 1 month ago (July 28, 2023, 9:03 p.m.)
Indexed	1 week ago (Aug. 28, 2025, 8:51 a.m.)
Issued	26 years ago (Aug. 9, 1999)
Published	26 years ago (Aug. 9, 1999)
Published Online	26 years ago (Aug. 9, 1999)
Published Print	26 years ago (Aug. 9, 1999)

Funders 0

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BibTeX

@article{Wei_1999, title={Three-Dimensional Visualization of Transcription Sites and Their Association with Splicing Factor–Rich Nuclear Speckles}, volume={146}, ISSN={1540-8140}, url={http://dx.doi.org/10.1083/jcb.146.3.543}, DOI={10.1083/jcb.146.3.543}, number={3}, journal={The Journal of Cell Biology}, publisher={Rockefeller University Press}, author={Wei, Xiangyun and Somanathan, Suryanarayan and Samarabandu, Jagath and Berezney, Ronald}, year={1999}, month=aug, pages={543–558} }

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  "abstract": "<jats:p>Transcription sites are detected by labeling nascent transcripts with BrUTP in permeabilized 3T3 mouse fibroblasts followed by laser scanning confocal microscopy. Inhibition and enzyme digestion studies confirm that the labeled sites are from RNA transcripts and that RNA polymerase I (RP I) and II (RP II) are responsible for nucleolar and extranucleolar transcription, respectively. An average of 2,000 sites are detected per nucleus with over 90% in the extranucleolar compartment where they are arranged in clusters and three-dimensional networklike arrays. The number of transcription sites, their three-dimensional organization and arrangement into functional zones (Wei et al. 1998) is strikingly maintained after extraction for nuclear matrix. Significant levels of total RP II mediated transcription sites (45%) were associated with splicing factor\u2013rich nuclear speckles even though the speckles occupied &amp;lt;10% of the total extranucleolar space. Moreover, the vast majority of nuclear speckles (&amp;gt;90%) had moderate to high levels of associated transcription activity. Transcription sites were found along the periphery as well as inside the speckles themselves. These spatial relations were confirmed in optical sections through individual speckles and after in vivo labeling of nascent transcripts. Our results demonstrate that nuclear speckles and their surrounding regions are major sites of RP II-mediated transcription in the cell nucleus, and support the view that both speckle- and nonspeckle-associated regions of the nucleus contain sites for the coordination of transcription and splicing processes.</jats:p>",
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