Genome-Wide Mapping of Major Histone Modifications Reveals Distinct Epigenetic Regulatory States in a Reef-Building Coral

Abstract

Reef-building corals exhibit extensive physiological and transcriptional plasticity, yet the chromatin-level regulation of coral gene expression remains poorly characterized. Here, we generated the first genome-wide maps of major histone modifications in a reef-building coral by performing chromatin immunoprecipitation sequencing (ChIP-seq) in adult Pocillopora damicornis maintained under ambient conditions. We profiled two active marks, H3K4me3 and H3K27ac, and two repressive marks, H3K27me3 and H3K9me3, and integrated these maps with RNA sequencing (RNA-seq) to relate chromatin state to transcriptional output. As in other eukaryotes, H3K4me3 and H3K27ac were enriched around transcriptional start sites and positively associated with gene expression, whereas H3K27me3 and H3K9me3 showed broader enrichment patterns and were negatively associated with transcription. Partitioning highly expressed genes by promoter chromatin state revealed that promoters with strong H3K4me3/H3K27ac signal carried YY1-family motifs and served core cellular functions, while a second group enriched for cell-surface receptors and proteolysis lacked these active promoter marks and motif repertoire, despite similar transcript abundance. Repressive marks also distinguished functional genomic states: H3K27me3 was enriched over lowly expressed receptor-like and developmental gene classes, whereas H3K9me3 was prominent at transposable element-like loci and broad non-genic regions. We further identified H3K27ac-enriched, H3K4me3-low candidate enhancer-like elements proximal to core promoters, many near genes with transcription factor-related functions. Together, these results define a baseline chromatin-state landscape in reef-building corals, offering a resource for validating targeted chromatin assays and a foundation for future studies of coral gene regulation across environmental, developmental, and symbiotic contexts.