Repository logo

Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters

Published version

Repository DOI

Change log


Koestler, Stefan A 
Ball, Madeleine L 
Muresan, Leila 
Dinakaran, Vineet 
White, Robert 


jats:titleAbstract</jats:title>jats:pChromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of jats:italicDrosophila melanogaster</jats:italic> primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation.</jats:p>jats:pIn this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.</jats:p>jats:pThese results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation – with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene.</jats:p>


Acknowledgements: We thank Martin Lenz (Cambridge Advanced Imaging Centre) for expert microscopy support.

Funder: Isaac Newton Trust Research

Funder: Cambridge Biosciences Doctoral Training Partnership


Chromatin, Transcription loop, Nucleosome cluster, RNA polymerase II, Nucleosome, Histone modification, Super-resolution microscopy, Transcription, Epigenetic mark

Journal Title

Epigenetics &amp; Chromatin

Conference Name

Journal ISSN


Volume Title



Springer Science and Business Media LLC
Biotechnology and Biological Sciences Research Council (BB/S00758X/1)
Engineering and Physical Sciences Research Council (EP/R025398/1)