qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells
We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of livi...
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| Format: | Article |
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Nature Publishing Group
2018
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| Online Access: | http://hdl.handle.net/1721.1/118788 https://orcid.org/0000-0003-1867-4380 https://orcid.org/0000-0001-9336-0686 https://orcid.org/0000-0002-2269-3253 https://orcid.org/0000-0001-8493-4721 https://orcid.org/0000-0001-9746-6007 https://orcid.org/0000-0003-0362-0072 https://orcid.org/0000-0002-2406-8160 https://orcid.org/0000-0002-8764-1809 |
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| author | Andrews, James Owen Conway, W. Cho, Won-ki Narayanan, Arjun Spille, Jan Hendrik Jayanth, Namrata Inoue, Takuma Thaler, Jesse Cisse, Ibrahim I Mullen, Susan |
| author2 | Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences |
| author_facet | Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences Andrews, James Owen Conway, W. Cho, Won-ki Narayanan, Arjun Spille, Jan Hendrik Jayanth, Namrata Inoue, Takuma Thaler, Jesse Cisse, Ibrahim I Mullen, Susan |
| author_sort | Andrews, James Owen |
| collection | MIT |
| description | We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell. |
| first_indexed | 2024-09-23T13:10:44Z |
| format | Article |
| id | mit-1721.1/118788 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:10:44Z |
| publishDate | 2018 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1187882022-09-28T12:27:01Z qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells Andrews, James Owen Conway, W. Cho, Won-ki Narayanan, Arjun Spille, Jan Hendrik Jayanth, Namrata Inoue, Takuma Thaler, Jesse Cisse, Ibrahim I Mullen, Susan Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences Massachusetts Institute of Technology. Department of Physics Andrews, James Owen Conway, W. Cho, Won-ki Narayanan, Arjun Spille, Jan Hendrik Jayanth, Namrata Inoue, Takuma Thaler, Jesse Cisse, Ibrahim I Mullen, Susan We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell. National Institutes of Health (U.S.) National Cancer Institute (U.S.) (NIH Director’s New Innovator Award DP2-CA195769) Massachusetts Institute of Technology. Department of Physics 2018-10-25T20:08:03Z 2018-10-25T20:08:03Z 2018-05 2017-12 2018-10-11T16:36:05Z Article http://purl.org/eprint/type/JournalArticle 2045-2322 http://hdl.handle.net/1721.1/118788 Andrews, J. O., et al. “QSR: A Quantitative Super-Resolution Analysis Tool Reveals the Cell-Cycle Dependent Organization of RNA Polymerase I in Live Human Cells.” Scientific Reports, vol. 8, no. 1, Dec. 2018. © 2018 The Authors https://orcid.org/0000-0003-1867-4380 https://orcid.org/0000-0001-9336-0686 https://orcid.org/0000-0002-2269-3253 https://orcid.org/0000-0001-8493-4721 https://orcid.org/0000-0001-9746-6007 https://orcid.org/0000-0003-0362-0072 https://orcid.org/0000-0002-2406-8160 https://orcid.org/0000-0002-8764-1809 http://dx.doi.org/10.1038/s41598-018-25454-0 Scientific Reports Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Nature |
| spellingShingle | Andrews, James Owen Conway, W. Cho, Won-ki Narayanan, Arjun Spille, Jan Hendrik Jayanth, Namrata Inoue, Takuma Thaler, Jesse Cisse, Ibrahim I Mullen, Susan qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title | qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title_full | qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title_fullStr | qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title_full_unstemmed | qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title_short | qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells |
| title_sort | qsr a quantitative super resolution analysis tool reveals the cell cycle dependent organization of rna polymerase i in live human cells |
| url | http://hdl.handle.net/1721.1/118788 https://orcid.org/0000-0003-1867-4380 https://orcid.org/0000-0001-9336-0686 https://orcid.org/0000-0002-2269-3253 https://orcid.org/0000-0001-8493-4721 https://orcid.org/0000-0001-9746-6007 https://orcid.org/0000-0003-0362-0072 https://orcid.org/0000-0002-2406-8160 https://orcid.org/0000-0002-8764-1809 |
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