Gel images for each experiment are representative of two to three separate trials.
(a) Interaction between individual MeCP2 domains and DNA. Domains (NTD, MBD, ID, TRD, CTD-α, CTD-β, TRD-CTDα-CTDβ) were incubated with methylated 601-12 DNA at molar input ratios of 0 to 8, and the products are displayed on 1% agarose gels. The ID, TRD and CTD-α induce substantial retardation of the DNA. In contrast, the MBD shows only minor shifts and the NTD appears to have virtually no interaction with DNA.
(b) To examine methylation specificity, MBD and constructs that include its flanking domains were incubated with unmethylated (−) or methylated (+) DNA in the presence of two-fold excess of 208-1 DNA competitor at molar input ratios of 0 to 10. A distinct methylation-dependent enhancement of the gel shifts is seen in all constructs containing the MBD. Of particular interest is the large shift shown by the NTD-MBD construct, which suggests a synergism between these two domains. Full length MeCP2 produces pronounced gel shift at much lower input than the MBD containing contiguous domain fusions.
(c) The ID and TRD-CTD polypeptides produce strong shifts, but there is no methylation-dependent enhancement.
(d, e) as (a, b) but with 601-12 nucleosomal arrays (NAs) as substrate and 208-1 mononucleosomes as competitor. With the exception of CTD-β which induces a moderate but consistent mobility shift with chromatin but not with naked DNA, the patterns of electrophoretic shift with DNA and NAs are similar.
M denotes molecular weight marker lanes.