DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG.
DNA methylation is interpreted by a family of methyl-CpG binding domain (MBD) proteins that repress transcription through recruitment of corepressors that modify chromatin. To compare in vivo binding of MeCP2 and MBD2, we analyzed immunoprecipitated chromatin from primary human cells. Genomic sites occupied by the two MBD proteins were mutually exclusive. As MeCP2 was unable to colonize sites vacated by depletion of MBD2, we tested the hypothesis that methyl-CpG alone is insufficient to direct MeCP2 binding. In vitro selection for MeCP2 bound DNA-enriched fragments containing A/T bases ([A/T] > or = 4) adjacent to methyl-CpG. [A/T] > or = 4 was found to be essential for high-affinity binding at selected sites and at known MeCP2 target regions in the Bdnf and Dlx6 genes. MBD2 binding, however, did not require an A/T run. The unexpected restriction of MeCP2 to a defined subset of methyl-CpG sites will facilitate identification of genomic targets that are relevant to Rett Syndrome.
Klose
Robert J
RJ
Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom.
Sarraf
Shireen A
SA
Schmiedeberg
Lars
L
McDermott
Suzanne M
SM
Stancheva
Irina
I
Bird
Adrian P
AP
D000225:Adenine / Q000737:chemistry; D001483:Base Sequence; D019208:Brain-Derived Neurotrophic Factor / Q000235:genetics; D002460:Cell Line; D045744:Cell Line, Tumor; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism*; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D051783:Methyl-CpG-Binding Protein 2; D009154:Mutation; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D013941:Thymine / Q000737:chemistry
D019208:Brain-Derived Neurotrophic Factor; D002868:Chromosomal Proteins, Non-Histone; C491014:DLX6 protein, human; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; C489325:MBD2 protein, human; C497392:MECP2 protein, human; D051783:Methyl-CpG-Binding Protein 2; D012097:Repressor Proteins; D004247:DNA; D000225:Adenine; D013941:Thymine