Large replisome-dependent heterochromatic domains defining the transgenerational regulatory landscape

A missing piece in the puzzle to understanding transgenerational epigenetic inheritance (TEI) is a mechanism that allows epigenetic information to be stored and propagated, not only from one generation to the next, but across cell division. Histone modifications, along with small RNAs (sRNA) and DNA methylation, are known carriers of epigenetic information. Heterochromatin marks, such as trimethylation in lysine 9 and 27 of histone H3 (H3K9me3 and H3K27me3) are associated with gene repression, whilst euchromatic marks are associated with gene activation. Several components of the DNA replication machinery, such as the helicase subunit MCM-2, the leading strand polymerase Polε subunits POLE-3 and POLE-4 and the primase Polα subunit POLA-1 bind with histones, and that interaction is crucial for the maintenance of chromatin marks across the cell cycle, but their role in a transgenerational scale has not been explored in animals. In my thesis, I use replisome-mutant strains of the nematode Caenorhabditis elegans as a model to explore the role of replisome-histone interactions in TEI. These strains show epigenetic-related phenotypes such as deficient inheritance of RNA interference (RNAi) gene silencing and mortal germline that is reversible, suggesting an epigenetic basis. These mutants exhibited large disruptions to the heterochromatin landscape and changes in gene expression. Some of these changes form clusters of both gene and transposable element activation, resting on specific domains I named “corrie” domains. These domains sit on the border between a low and a high H3K9me3 region. They are depleted in H3K27me3. They contain a posed promoter on the low H3K9me3 region and the high H3K9me3 region is rich in piRNA loci and poor RNA PolII binding. Interestingly, these “corrie” domains tend to contain Helitron elements at the activation peak rich in periodic An/Tn sequences, which protect endogenous genes from sRNA silencing. This research highlights the importance of parental histone recycling in the maintenance of the regulatory status of large heterochromatic domains and demonstrates the role that replisome-histone interactions play in maintaining epigenetic memory on an in vivo scale.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2025

Author dc:creator

• Rueda Silva, Juan

Advisor dc:contributor.advisor

• Miska, Eric

• epigenetics
• chromatin
• c.elegans
• Replication
• Replisome
• Histone modifiations
• Inheritance

Licence

• https://www.repository.cam.ac.uk/bitstreams/bb74ec80-4e70-4bc5-b1f3-0ffb4b47e336/download
• https://creativecommons.org/licenses/by/4.0/

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.127929

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/399363