Cargando…
The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy
While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10016678/ https://www.ncbi.nlm.nih.gov/pubmed/36867662 http://dx.doi.org/10.1371/journal.pgen.1010654 |
_version_ | 1784907453459070976 |
---|---|
author | Ball, Madeleine L. Koestler, Stefan A. Muresan, Leila Rehman, Sohaib Abdul O’Holleran, Kevin White, Robert |
author_facet | Ball, Madeleine L. Koestler, Stefan A. Muresan, Leila Rehman, Sohaib Abdul O’Holleran, Kevin White, Robert |
author_sort | Ball, Madeleine L. |
collection | PubMed |
description | While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription. |
format | Online Article Text |
id | pubmed-10016678 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-100166782023-03-16 The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy Ball, Madeleine L. Koestler, Stefan A. Muresan, Leila Rehman, Sohaib Abdul O’Holleran, Kevin White, Robert PLoS Genet Research Article While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription. Public Library of Science 2023-03-03 /pmc/articles/PMC10016678/ /pubmed/36867662 http://dx.doi.org/10.1371/journal.pgen.1010654 Text en © 2023 Ball et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Ball, Madeleine L. Koestler, Stefan A. Muresan, Leila Rehman, Sohaib Abdul O’Holleran, Kevin White, Robert The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title | The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title_full | The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title_fullStr | The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title_full_unstemmed | The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title_short | The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy |
title_sort | anatomy of transcriptionally active chromatin loops in drosophila primary spermatocytes using super-resolution microscopy |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10016678/ https://www.ncbi.nlm.nih.gov/pubmed/36867662 http://dx.doi.org/10.1371/journal.pgen.1010654 |
work_keys_str_mv | AT ballmadeleinel theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT koestlerstefana theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT muresanleila theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT rehmansohaibabdul theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT ohollerankevin theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT whiterobert theanatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT ballmadeleinel anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT koestlerstefana anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT muresanleila anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT rehmansohaibabdul anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT ohollerankevin anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy AT whiterobert anatomyoftranscriptionallyactivechromatinloopsindrosophilaprimaryspermatocytesusingsuperresolutionmicroscopy |