The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle

SUMMARY Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. We interrogated the genome‐wide distribution pattern of mono‐ and trimethylated histone H3 lysine 4 (H3K4) using chromatin‐immunoprecipitation followed by deep‐sequencing (ChIP‐seq) during key phases of the Chlamydomonas cell cycle: early G1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G0 phase (ZT23) when they are quiescent. Tri‐methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non‐poly‐adenylated transcripts, such as small nuclear RNAs and replication‐dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono‐methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP‐seq data served also as a annotation tool for validation of hundreds of long non‐coding RNA genes. Significance Statement Genome‐wide changes in histone modifications are understudied in green algae. In the present study, we interrogated the Chlamydomonas genome for changes in H3K4 methylation patterns over the vegetative cell cycle.