In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.
MBD1 is a mammalian protein that binds symmetrically methylated CpG sequences and regulates gene expression in association with DNA methylation. This protein possesses a conserved sequence, named methylCpG binding domain (MBD), among a family of methyl-CpG binding proteins that mediate the biological consequences of the methylation. In addition, MBD1 has at least five isoforms due to alternative splicing events, resulting in the presence of CXXC1, CXXC2, and CXXC3 in MBD1 isoforms v1 (MBD1v1) and MBD1v2, and CXXC1 and CXXC2 in MBD1v3 and -v4. In the present study, we have investigated the significance of MBD, CXXC, and the C-terminal transcriptional repression domain (TRD) in MBD1. A bacterially expressed MBD binds efficiently to densely methylated rather than to sparsely methylated DNAs. In both methylation-deficient Drosophila melanogaster SL2 cells and mammalian CHO-K1 cells, MBD1v1 represses transcription preferentially from both unmethylated and sparsely methylated promoters, while MBD1v3 inhibits densely methylated but not unmethylated promoter activities. The CXXC3 sequence in MBD1v1 is responsible for the ability to bind unmethylated promoter. Furthermore, we have constructed mutant-type MBD1s in which the functionally important residues Arg22, Arg30, Asp32, Tyr34, Arg44, Ser45, and Tyr52 are changed to alanine to investigate the correlation between the structure and function of the MBD in MBD1. Excepting those for Ser45 and Tyr52, none of the recombinant MBD mutants bound to the densely methylated or unmethylated DNAs, and green fluorescent protein-fused MBD1 mutants did not localize properly in the nucleus. All the MBD1v1 and -v3 mutants lost the activity of methylation-dependent gene repression. Based on these findings we have concluded that MBD1 acts as a transcriptional regulator depending on the density of methyl-CpG pairs through the cooperation of MBD, CXXC, and TRD sequences.
SummaryBackground:Although secondary renal involvement of non-Hodgkin lymphoma is frequently encountered, primary renal lymphoma is quite rare. We present a pediatric case of primary renal diffuse large B-cell lymphoma.Case Report:A 12-year-old girl presenting with gross hematuria was referred to our hospital. Abdominal ultrasonography and imaging revealed a mass lesion in the superior pole of the right kidney. Serum creatinine and blood urea nitrogen levels were within normal ranges. Preoperative assessment of the mass indicated unspecified renal tumor. Right nephrectomy was performed and pathological examination showed diffuse large B-cell lymphoma. Postoperative fluorodeoxyglucose-positron emission tomography/computed tomography showed a small high-uptake lesion in the thyroid gland and aspiration cytology of the thyroid tumor demonstrated involvement of lymphoma, so stage III tumor diagnosed. After one course of chemotherapy, the patient achieved complete remission. She remains alive without disease, 3 years after completing a total of six courses of chemotherapy.Conclusions:Primary renal lymphoma is a very rare entity and preoperative diagnosis may be difficult. However, this entity is often reported to show clinically aggressive characteristics and therefore should be considered among the differential diagnoses for unusual renal tumors in pediatric patients.
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