Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle

Abstract

Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.

Differential responses to maternal diabetes in embryo and visceral yolk sac

“…Strong correlations to somite stage that were uniquely detected only in the diabetic condition were enriched for transcripts encoding histones, which are also among the genes differentially expressed when diabetes-exposed and normal embryos are compared ( Supplementary File S5 ). The particular histone transcripts are known to be “replication-dependent” ( Suzuki et al, 2023 ) and are increased during S-phase of the cell cycle ( Fritz et al, 2023 ), annotation that was not revealed by IPA pathway analysis but confirmed independently by Reactome annotation in DAVID. Increased transcription of these histone genes may indicate that a greater fraction of cells in the diabetes-exposed embryo are in S-phase, or that cells remain in S-phase for a longer time, thus accumulating increased levels of replication-dependent histone transcripts.…”