DNMT1 inhibition by pUG-fold quadruplex RNA

Abstract

Aberrant DNA methylation is one of the earliest hallmarks of cancer. DNMT1 is responsible for methylating newly replicated DNA, but the precise regulation of DNMT1 to ensure faithful DNA methylation remains poorly understood. A link between RNA and chromatin-associated proteins has recently emerged, and several studies have shown that DNMT1 can be regulated by a variety of RNAs. In this study we have confirmed that human DNMT1 indeed interacts with multiple RNAs, including its own nuclear mRNA. Unexpectedly, we found that DNMT1 exhibits a strong and specific affinity for GU-rich RNAs that form a pUG-fold, a non-canonical G-quadruplex. We find that pUG-fold-capable RNAs inhibit DNMT1 activity by inhibiting binding of hemimethylated DNA, and additionally provide evidence for multiple RNA binding modes with DNMT1. Together, our data indicates that a human chromatin-associated protein binds to and is regulated by pUG-fold RNA.

Structural basis for inactivation of PRC2 by G-quadruplex RNA

“…Besides PRC2, many chromatin-associated complexes have been found to interact with RNA molecules, including other histone modifiers ( 2 ), transcription factors ( 37, 46 ), RNA polymerase ( 47, 48 ), and DNA methyltransferase ( 49, 50 ). Like PRC2, they tend not to have canonical RNA-recognition motifs and bind RNA broadly, and obtaining molecular structures of the RNA-protein complexes has been very challenging.…”

MUT-7 exoribonuclease activity and localisation are mediated by an ancient domain

“…Following template RNA cleavage, the newly generated 3’ hydroxyl is modified by the nucleotidyltransferase MUT-2, which appends repeating dinucleotide UG-units 15 . In the presence of potassium ions, 11.5 UG/GU repeats can form a compact quadruplex (G4) structure named pUG fold 18,39 . We tested MUT-7’s ability to degrade (GU) 8 and (GU) 14 RNAs, with the (GU) 14 RNA being long enough to adopt a pUG fold in the presence of potassium but not lithium ions 18,39 , as shown by native PAGE (Fig.…”

“…In the presence of potassium ions, 11.5 UG/GU repeats can form a compact quadruplex (G4) structure named pUG fold 18,39 . We tested MUT-7’s ability to degrade (GU) 8 and (GU) 14 RNAs, with the (GU) 14 RNA being long enough to adopt a pUG fold in the presence of potassium but not lithium ions 18,39 , as shown by native PAGE (Fig. 5d).…”

HNEAP Regulates Necroptosis of Cardiomyocytes by Suppressing the m5C Methylation of Atf7 mRNA

“…Among them, DNMT1 is the main maintenance methylase, while DNMT3A and DNMT3B are responsible for de novo methylation. [34,35] However, DNMT1 is also involved in de novo methylation. [36] In general, decreased level of DNA methylation leads to genomic instability, whereas aberrant site-specific methylation of gene promoters leads to specific gene silencing.…”

“…[ 37 ] Many DNA‐binding chromatin‐modifying enzymes can also bind to RNA, and this binding is thought to play a role in the recruitment and regulation of enzyme activity. [ 35 ] However, the detailed mechanisms underlying RNA‐mediated regulation require further exploration. DNMT1 can directly associate with multiple RNAs, and different RNAs have distinct effects on the activity and localization of DNMT1.…”