In each cell of an organism, the genome is read in a distinct manner which defines its identity. The organization of the genome into chromatin is crucial in this respect. Indeed, chromatin packages the genome in the nucleus of eukaryotic cells by wrapping DNA around histones. As the building blocks of chromatin, histones can thus modulate all DNA-based transactions in the nucleus. This capacity to modulate genome function takes advantage of their versatility. In most organisms, histones exist as distinct variants that can each harbor different modifications and interact with specific partners. Histone variants, together with their modifications and binding partners, produce a variety of chromatin states that mark the genome to distinguish active or repressed regions according to cell identity. Each cell thus harbors a distinct chromatin signature.
It is still unclear whether this signature can be transmitted to daughter cells after division. Throughout the cell cycle, chromatin states are constantly challenged by the disassembly, mobilization and turnover of histones at thousands of different sites involved in gene transcription or chromosome organization. Most striking is the challenge of DNA replication during S phase. Each time the genome is copied, chromatin is disassembled and doubled, and parental histones are displaced. Both old and new histones must be hence deposited in a coordinate manner to restore the existing chromatin landscape. In this context, different histone variants rely on the partnership with specific chaperones that handle their recycling or de novo deposition.
A major unresolved issue is how these different variants are deposited throughout the genome as DNA is replicated. This is particularly relevant for cancer cells, which divide and replicate indefinitely disregarding their original set of instructions.
Our objective was thus to characterize the de novo deposition of selected variants on replicating chromatin at genome-wide resolution. We focused on two highly conserved variants of the histone H3 family that are frequently mutated in pediatric brain tumors, namely H3.1 and H3.3. We combined novel sequencing assays with in-depth bioinformatics analyses to investigate their deposition patterns during S phase. Our findings reveal an unanticipated layer of chromatin organization in different functional states, that depends on the distinct deposition pathways of these variants.
