Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications

https://doi.org/10.1016/j.bbagrm.2018.10.009Get rights and content
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Highlights

  • MLL1-CXXC is highly specific only for non-modified CpG.

  • TET3-CXXC has more relaxed specificity and may interact with modified CpG.

  • TET3-CXXC apparent specificity depends on register shifts.

  • We propose a structure-guided model for CXXC domains specificity.

Abstract

CXXC domains have traditionally been considered as CpG specific DNA binding domains that are repelled by cytosine modifications. This view has recently been challenged by the demonstration that CXXC domain of TET3 has relaxed sequence specificity and binds with the highest affinity to symmetric DNA duplex containing 5caCpG. Here, we present a comparative analysis of the MLL1-CXXC and TET3-CXXC sequence specificity and tolerance to cytosine modifications (5-methyl, 5-hydroxymethyl, 5-formyl, 5-carboxyl) in CpG and non-CpG context. For the first time, we take into consideration possible interference from cytosine bases elsewhere in the sequence. We show that despite similar overall structure, MLL1-CXXC has greater sequence and modification specificity than TET3-CXXC. MLL1-CXXC is specific only for CpG and does not tolerate any cytosine modifications. In contrast, TET3-CXXC does not require the CpG context of cytosine bases. Methyl-, formyl- and carboxyl-modifications are tolerated by TET3-CXXC, but only preceding G. Based on our and other data we propose a parsimonious model of MLL1-CXXC and TET3-CXXC DNA binding. This model explains why the binding of modified DNA duplexes by TET3-CXXC requires in some cases a register shift and is therefore context-dependent.

Abbreviations

MLL
mixed lineage leukemia
TET
ten-eleven translocation
MBD
methylated CpG binding domain
CGI
CpG island
C
cytosine
5mC
5-methylcytosine
5hmC
5-hydroxymethylcytosine
5fC
5-formylcytosine
5caC
5-carboxylcytosine
H3K4me1
H3K4 monomethylation
H3K4me3
H3K4 trimethylation
PC
pocket C
PG
pocket G
PG*
pocket G*
PC*
pocket C*
MLL1-CXXC
human MLL1 CXXC domain
TET3-CXXC
human TET3 CXXC domain
PBM
protein binding microarray
BER
base excision repair
EMSA
electrophoretic mobility shift assay

Keywords

CXXC domain
Mixed lineage leukemia (MLL)
K-specific methyltransferase (KMT2)
Ten-eleven-translocation (TET)
CpG island (CGI)
Cytosine modifications

Cited by (0)

1

Contributed equally.