Intricate Effects of α-Amino and Lysine Modifications on Arginine Methylation of the N-Terminal Tail of Histone H4

Abstract

Chemical modifications on the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The “histone code” hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) on the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and over 450 histone PTMs discovered, and the PTMs on lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood. In this study, we investigated how naturally occurring N-terminal acetylation and PTMs on histone H4 lysine-5 (H4K5) affect arginine-3 methylation catalyzed by both type I and type II PRMTs at the biochemical level. Our studies found that acylations of H4K5 resulted in decreased arginine methylation by PRMT1, PRMT3, and PRMT8. In contrast, PRMT5 exhibits increased arginine methylation upon H4K5 acetylation, propionylation, and crotonylation, but not upon H4K5 methylation, butyrylation, or 2-hydroxyisobutyrylation. Methylation of H4K5 did not affect arginine methylation by PRMT1 or PRMT5. There was a small increase in arginine methylation by PRMT8. Strikingly, a marked increase in arginine methylation was observed for PRMT3. Finally, N-terminal acetylation reduced arginine methylation by PRMT3, but had little influence on PRMT1, 5, and 8 activity. These results together highlight the underlying mechanistic differences in substrate recognition among different PRMTs and pay the way for the elucidation of the complex interplays of histone modifications.

Mechanisms and Inhibitors of Histone Arginine Methylation

“…H4K5 ac promotes H4 arginine methylation by PRMT5 in vivo and in vitro , while H4K8 ac and H4K12 ac do not have as strong of an activating effect on PRMT5 activity. [65b,70b,75] Interestingly, including H4K20 me3 with H4K5 ac or H4K12 me3 with H4K16 ac are strongly activating PTM combinations for PRMT5 activity. [75] It is not clear though how H4R3 me2s may affect HAT activity on the H4 lysine residues.…”

“…The mutual exclusivity of H3K4 me3 and H3R2 me2a is conserved from yeast to humans. [51b,80] In contrast, while acetylated H4 is inhibitory to PRMT1 catalyzed methylation of H4R3 in mammalian cells, [65b,70] acetylated H4 (particularly H4K8 ac ) is a preferred substrate for the PRMT1 functional homologue in yeast, hnRNP arginine N-methyl methyltransferase 1 (HMT1), and the resulting H4R3 me2a mark is transcriptionally repressive in yeast. [81] These and other crosstalk events have been well reviewed by others.…”

Proteins and Proteoforms: New Separation Challenges

“…37 These proteins are involved in modifying each histone at 6–10 sites (Figure 2) in multiple ways. 38 Lysine and arginine modifications each accommodate four types of marks; the native form along with mono-, di-, or trimethylation. Acetylation, propionylation, an malonylation, in addition to ubiquitination are other ways lysine can be modified.…”

Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie

“…Hier werden Ansätze der chemischen Biologie zur Untersuchung der KAT-Aktivitätu nd -Funktion erläutert. [10] Ob diese Mechanismen nun alleinig oder gemeinsam wirken, so werden Veränderungen im Chromatin durch Acetylierung wiederum zu biologischen Abweichungen führen. bekannt, durch die die Histon-Acetylierung die mit Chromatin verknüpften Prozesse beeinflusst.…”

“…[9] Wirbeobachteten kürzlich, dass die Histon-H4K5-Acetylierung die symmetrische Methylierung von H4R3 aktiviert, doch die asymmetrische Methylierung unterdrückt. [10] Ob diese Mechanismen nun alleinig oder gemeinsam wirken, so werden Veränderungen im Chromatin durch Acetylierung wiederum zu biologischen Abweichungen führen. Neben Histonen treten acetylierte Proteine innerhalb und außerhalb des Zellkerns auf und kontrollieren eine Unzahl von zellulären Prozessen, wie Tr anskriptionsregulation, Signalübertragung und Stoffwechselvorgänge.…”