Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs

cRNAs, a heterogeneous group of RNAs that copurify with chromatin, are abundant in heterochromatic transcripts that interact with the hnRNP proteins hrp36/hrp48. Histone H1 depletion alters heterochromatin organization and impairs assembly of hrp36/hrp48 onto heterochromatic cRNAs, facilitating R-loop formation.

Abstract

Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. Here, we address these questions in Drosophila. We find that cRNAs constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. We show that heterochromatic cRNAs interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. We also show that dH1 depletion alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin.

Reference:

Paula Bujosa, Oscar Reina, Adrià Caballé, Anna Casas-Lamesa, Mònica Torras-Llort, Juan Pérez-Roldán, Ana Silvina Nacht, Guillermo P. Vicent, Jordi Bernués, and Fernando Azorín. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Reports 2024;43(5):114137. doi: 10.1016/j.celrep.2024.114137