Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation

Abstract

UHRF1 plays multiple roles in regulating DNMT1-mediated DNA methylation maintenance during DNA replication. The UHRF1 C-terminal RING finger functions as an ubiquitin E3 ligase to establish histone H3 ubiquitination at Lys18 and/or Lys23, which is subsequently recognized by DNMT1 to promote its localization onto replication foci. Here, we present the crystal structure of DNMT1 RFTS domain in complex with ubiquitin and highlight a unique ubiquitin binding mode for the RFTS domain. We provide evidence that UHRF1 N-terminal ubiquitin-like domain (UBL) also binds directly to DNMT1. Despite sharing a high degree of structural similarity, UHRF1 UBL and ubiquitin bind to DNMT1 in a very distinct fashion and exert different impacts on DNMT1 enzymatic activity. We further show that the UHRF1 UBL-mediated interaction between UHRF1 and DNMT1, and the binding of DNMT1 to ubiquitinated histone H3 that is catalyzed by UHRF1 RING domain are critical for the proper subnuclear localization of DNMT1 and maintenance of DNA methylation. Collectively, our study adds another layer of complexity to the regulatory mechanism of DNMT1 activation by UHRF1 and supports that individual domains of UHRF1 participate and act in concert to maintain DNA methylation patterns.

Defining UHRF1 Domains that Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties

“…UHRF1 has multiple domains with both chromatin reader and writer functions ( Figure 1A) (Citterio et al, 2004). The linked tandem Tudor domain (TTD) and PHD (Nady et al, 2011;Rajakumara et al, 2011;Rothbart et al, 2012), following the N-terminal ubiquitin-like domain (UBL) (Li et al, 2018), coordinately recognize a unique modification signature on the histone H3 tail (Arita et al, 2012;Cheng et al, 2013;Rothbart et al, 2013). Specifically, the PHD associates with the unmodified N terminus of H3 and is sensitive to methylation on arginine 2 (H3R2) (Cheng et al, 2013;Rajakumara et al, 2011;Veland et al, 2017), and this is enhanced by TTD recognition of di-or trimethylated lysine 9 on the same histone H3 tail (H3K9me2/me3) (Nady et al, 2011;Rothbart et al, 2012).…”

Chemical map–based prediction of nucleosome positioning using the Bioconductor package nuCpos

“…Furthermore, DNA methylation is correlated with nucleosome occupancy in humans [61]. Indeed, the nucleosome structure itself has been suggested as necessary for the maintenance of DNA methylation [62, 63]. In addition, many histone variants exist in mice, which might cause variability in the preferred sequence for nucleosome formation [64–66].…”

Chemical synthesis of the ubiquitinated form of histone H3 and its effect on DNA methyltransferase 1

“…In the cell division process, newly synthesized DNA is hemi‐methylated and is converted to its fully methylated form mainly by DNA methyltransferase 1 (Dnmt1) to maintain the methylation pattern . The ubiquitination of H3 at Lys18 or/and 23 was reported to regulate the maintenance DNA methylation by Dnmt1 …”

“…17 The ubiquitination of H3 at Lys18 or/and 23 was reported to regulate the maintenance DNA methylation by Dnmt1. 7,8,18,19 We reported that the ubiquitination of H3 stimulates Dnmt1 activity by the use of ubiquitinated H3 peptide analogs with an unnatural isopeptide mimetic structure. 18 In order to confirm the reliability of such analogs, we synthesized the ubiquitinated form of histone H3 with a native isopeptide structure, and examined its effect on Dnmt1.…”