UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications

Abstract

Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying appropriate markers (on the tails of H3 and hemimethylated CpG sites) ready to be assembled into a nucleosome after replication.

Figure 1

UHRF1—a multi-domain protein. (A) Schematic representation of UHRF1 and its homolog UHRF2. (B) Five domain structures are currently available.

Figure 2

Structure of SRA-DNA complex. (A) The two loops—CpG recognition and base flipping—penetrate into the DNA helix from opposite directions. Adapted from ref. (B) The side chains of V451 of base flipping loop and R496 of CpG recognition loop are in direct van der Waals contact. Adapted from ref. (C) The 5mC flips out and is bound in a cage-like pocket.

Figure 3

Three new X-ray structures in which the thymine two bases 3′ to the 5mC are intrahelical (see Table 1). (A and B) Crystal packing force involving two DNA molecules stacking head-to-head. The SRA domain molecules involved in specific interactions are shown in blue, and the SRA domain in non-specific interactions in green. (C) Crystal packing force involving a single DNA molecule. (D) Structural comparison of DNA containing an extrahelical Ade (magenta) and intrahelical Thy (green). (E) Structure of E. coli β clamp-DNA shows a flipped-out nucleotide at the junction of double-strand (ds) and single-strand (ss) DNA.

Figure 4

Comparison of base flipping by the SRA domain and HhaI MTase. (Top) DNA structures bound by SRA (A) and HhaI (B) show a flipped nucleotide. The intercalating amino acids are shown in each case. (Bottom) Structures of SRA (A) and HhaI (B) show the two opposite-side DNA-approaching loops. Inserted are the major determinants of 5mC (A) and cytosine (B). (C) X-ray structure of MeCP2-DNA and (D) the NMR structure of MBD1-DNA shows MBD domain inserts a beta-hairpin through the DNA major groove. The methyl-binding domains of MBD1, and MeCP2, instead of using a base-flipping mechanism, recognize changes in hydration of the major groove of a fully methylated CpG rather than detecting methyl groups directly.

Figure 5

Methyllysine binding cage in tandom todor domain of (A) UHRF1 and (B) 53BP1.

Figure 6

Hypothetical model of UHRF1-mediated replication-coupled crosstalk between DNA methylation and histone modifications. Existence of both silencing mark readers recognizing DNA (via the SRA) and histone (via the Tudor and/or PHD) facilitates the idea of maintenance and conversion of epigenetic silencing marks on both DNA and histone modifications.