Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1

Abstract

Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 A crystal structure of the apo SRA domain of human UHRF1 and a 2.2 A structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

UHRF1‐mediated tumor suppressor gene inactivation in nonsmall cell lung cancer

“…19,21,23,24 UHRF1 (also known as ICBP90) has recently been shown to play an important role in methylation maintenance. 25 It has the ability to bind hemimethylated DNA through its SET-and RING-associated domain, 26,27 triggering the recruitment of DNMT1 25,28 and histone deacetylace-1. 29 UHRF1-knockout mouse embryonic stem cells exhibit significant loss of genomic methylation.…”

UHRF1 is a novel molecular marker for diagnosis and the prognosis of bladder cancer

“…Recently, it was revealed that UHRF1 plays a central role in transferring DNA methylation status from mother cells to daughter cells. Its SET and RING finger-associated (SRA) domain recognises hemimethylated DNA that appears in newly synthesised daughter DNA strands during duplication of DNA strands through the S phase (Arita et al, 2008;Avvakumov et al, 2008;Hashimoto et al, 2008). The UHRF1 recruits DNA methyltransferase 1 (DNMT1) to the site with proliferating cell nuclear antigen (PCNA) and methylates the newly synthesised strands (Sharif et al, 2007;Achour et al, 2008).…”

La première étape de la transmission d’un caractère épigénétique suivie par fluorescence

“…La technologie mise en oeuvre devrait également permettre d'envisager le développement de tests de criblage pour identifier des inhibiteurs du basculement de la cytosine méthylée. ‡ The first stage of transmission of an epigenetic character followed by fluorescence aux changements structuraux mineurs accompagnant le basculement des bases [10]. Cette forte augmentation ne se produit que pour les séquences hémi-méthylées et non pour les séquences non méthylées correspondantes.…”

“…Cette forte augmentation ne se produit que pour les séquences hémi-méthylées et non pour les séquences non méthylées correspondantes. En outre, cette forte augmentation de fluorescence est abolie quand le domaine SRA est remplacé par une protéine mutante incapable d'induire un basculement de base [10]. Par ailleurs, nous avons véri-fié que (1) les analogues thG et 3HCnt n'affectent pas ou peu la stabilité du double brin d'ADN dans lequel ils sont insérés, et (2) qu'aux positions où ces sondes sont sensibles au basculement de base induit par SRA, ce domaine conserve une affinité préférentielle pour les séquences hémi-méthylées par rapport aux séquences non méthylées.…”