Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [ChIP-seq]

The mechanisms by which epigenetic modifications are established in gene regulatory regions of active genes remain elusive. The data presented show that the establishment and recycling of a major epigenetic mark, the acetylated form of the replacement histone H2A.Z, is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed SPEARs (S Phase EArly RNAs), are induced in early S phase: their expression precedes that of the downstream genes on which they exert their regulatory action. SPEARs drive the modification and deposition of the acetylated form of histone H2A.Z by bringing together the replacement histone and the histone acetyl transferase TIP60. This widespread bimodal pathway constitutes a novel RNA-mediated mechanism for the establishment of epigenetic marks and cell-specific epigenetic profiles, thereby providing a unifying explanation for the accuracy and persistence of epigenetic marks on chromatin. Overall design: All samples were done using the cell line HL-60. 1 replicate each. RIP-Sequencing targetting acH2A.Z, H2A.Z and TIP60 with corresponding input. RNA-Sequencing on nuclear extract, nuclear-extracts synchronized at S-Phase and nascent nuclear-extracts synchronized at S-Phase. ChIP-Seq was performed targeting the acH2A.Z and H2A.Z histone marks with cells treated with DMSO, ACTD and DRB with appropriate controls.