CRAMP1 drives linker histone expression to enable Polycomb repression

The essential role of the core histones (H2A, H2B, H3 and H4) in DNA packaging has been well-understood for decades, but the function of the linker histone (H1) remains enigmatic. H1 compacts nucleosome arrays in vitro, but the multiple H1 subtypes and variants encoded in mammalian genomes (11 in mice and humans) hamper genetic studies to determine H1 function in vivo. Challenging the prevailing view that linker histones are a general feature of heterochromatin, here I show a selective requirement for linker histones in the function of Polycomb Repressive complex 2 (PRC2) in human cancer cell lines. Through a CRISPR/Cas9 genetic screen in a fluorescent reporter cell line responsive to PRC2 perturbation, I identified an essential requirement for the poorly characterised gene CRAMP1 in PRC2-mediated repression. CRAMP1 localises to the promoters of all expressed H1 genes where it acts as a positive transcriptional regulator. Ablation of CRAMP1 provides a unique tool to simultaneously deplete all linker histones, which results in selective decompaction of H3K27me3-marked loci and derepression of PRC2 target genes without concomitant loss of PRC2 occupancy or enzymatic activity. Strikingly, in contrast to the broad genomic distribution previously ascribed to H1, I find that linker histones selectively localise to genomic loci marked by H3K27me3 across diverse human adult cell types and organisms. Extending these findings to developmental contexts, I show that in human embryonic stem cells (hESCs), linker histones do not co-localise with H3K27me3. Using neural differentiation, I demonstrate that the genomic distribution of both histone H1 and H3K27me3 changes during lineage specification, eventually resulting in co-localisation in mature neurones. I conclude that linker histones are not a general feature of repressed chromatin but rather are uniquely required for epigenetic repression by PRC2 in differentiated cells.

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

• Matthews, Rachael

Advisor dc:contributor.advisor

• Tchasovnikarova, Iva

• Biochemistry
• Epigenetics

Licence

• https://www.repository.cam.ac.uk/bitstreams/c443a86f-1991-4294-9927-cd5d49ebaa24/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.127959

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/399399