PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription

Abstract

Histone post-translational modifications impact many aspects of chromatin and nuclear function. Histone H4 Lys 20 methylation (H4K20me) has been implicated in regulating diverse processes ranging from the DNA damage response, mitotic condensation, and DNA replication to gene regulation. PR-Set7/Set8/KMT5a is the sole enzyme that catalyzes monomethylation of H4K20 (H4K20me1). It is required for maintenance of all levels of H4K20me, and, importantly, loss of PR-Set7 is catastrophic for the earliest stages of mouse embryonic development. These findings have placed PR-Set7, H4K20me, and proteins that recognize this modification as central nodes of many important pathways. In this review, we discuss the mechanisms required for regulation of PR-Set7 and H4K20me1 levels and attempt to unravel the many functions attributed to these proteins.

Figure 1.

Overview of H4K20me. (A) Schematic diagram of the different methylation states of histone H4K20; from left to right: unmethylated (H4K20), monomethylated (H4K20me1), dimethylated (H4K20me2), and trimethylated (H4K20me3), with the various mammalian enzymes that perform these post-translational modification. (B) Properties of each of the enzymes that affect H4K20 methylation.

Figure 2.

PR-Set7 is highly regulated during, and is important for multiple aspects of, the cell cycle. PR-Set7 levels oscillate—as shown by YFP-PR-Set7 (green) expression in the outer circle—during the different stages of the cell cycle (mCherry-PCNA). PR-Set7 is post-translationally regulated by multiple different enzymes during the cell cycle, including CRL4-Cdt2, SCF-Skp2, APC-Cdh1, and Cyclin B1/Cdk1. The various functions of PR-Set7 and H4K20me1 are listed within the cell cycle circle.

Figure 3.

Role of PR-Set7 in genome integrity. PR-Set7 has multiple functions that are important for proper genome stability and DNA damage response. (Top left) PR-Set7 methylates H4K20me1, which is important for recruiting 53BP1 recruitment to sites of DNA damage. (Top right) PR-Set7 alters p53-dependent gene expression, potentially regulating checkpoint and repair processes. (Bottom left) H4K20me alters chromatin compaction and mitotic condensation, thereby affecting higher-order chromatin structure. Finally, PR-Set7 and H4K20me are required for proper DNA replication, possibly through regulation of fork stability.

Figure 4.

Genome-wide distribution and features of H4K20me1 from the ENCODE project. Bioinformatic analysis (MACS) was used to analyze H4K20me1 genome-wide distribution from ENCODE data sets from nine different human cell lines: H1 (human ES cells), K562 (erythrocytic leukemia), GM12878 (B-lymphoblastoid), HepG2 (hepatocellular carcinoma), NHEK (normal human epidermal keratinocytes), HSMM (primary human skeletal muscle myoblasts), NHLF (normal human lung fibroblasts), Huvec (primary human umbilical vein endothelial cells), and HMEC (primary human mammary epithelial cells). (A) H4K20me1 is enriched on intragenic features in H1 cells, representative of other cell lines. (B) H4K20me1 is enriched downstream from the TSS in H1 cells, representative of other cell lines. (C) H4K20me1 is found within the gene body and is correlated best with the highly expressed genes (Q100) and less so with the lower expressed genes in H1 cells, representative of other cell lines. (D) Comparison across all nine cell lines; Q100 genes show a similar distribution, with differences in the level of enrichment. (E) Venn diagram comparing gene ontology term analysis of genes within 3 kb of an H4K20me1 peaks. Conserved genes with H4K20me1 peaks across all three cell lines are housekeeping genes required in all cell types, whereas cell-specific genes enriched with H4K20me1 are genes that are only highly expressed in that specific lineage.