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Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes.

Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K - Nucleic Acids Res. (2011)

Bottom Line: We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present.MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA.In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology and Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523-1870, USA.

ABSTRACT
MeCP2 is a highly abundant chromatin architectural protein with key roles in post-natal brain development in humans. Mutations in MeCP2 are associated with Rett syndrome, the main cause of mental retardation in girls. Structural information on the intrinsically disordered MeCP2 protein is restricted to the methyl-CpG binding domain; however, at least four regions capable of DNA and chromatin binding are distributed over its entire length. Here we use small angle X-ray scattering (SAXS) and other solution-state approaches to investigate the interaction of MeCP2 and a truncated, disease-causing version of MeCP2 with nucleosomes. We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present. MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA. In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex. We present ab initio envelope reconstructions of nucleosomes and their complexes with MeCP2 from SAXS data. SAXS studies also revealed unexpected sequence-dependent conformational variability in the nucleosomes themselves.

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Domain structure of MeCP2. Dashed lines indicate the constructs used here, in addition to full length protein. NTD: N-terminal domain; MBD: methyl-CpG DNA binding domain, TRD: transcription repression domain, CTD: C-terminal domain. Red bars above indicate mapped DNA binding regions. The five most frequent mutations are indicated (percent occurrence given in brackets; nonsense mutations are indicated by asterisks).
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Figure 1: Domain structure of MeCP2. Dashed lines indicate the constructs used here, in addition to full length protein. NTD: N-terminal domain; MBD: methyl-CpG DNA binding domain, TRD: transcription repression domain, CTD: C-terminal domain. Red bars above indicate mapped DNA binding regions. The five most frequent mutations are indicated (percent occurrence given in brackets; nonsense mutations are indicated by asterisks).

Mentions: Methyl-CpG binding protein 2 (MeCP2) is a chromatin-associated protein that is highly abundant in neuronal cells, amounting to about one MeCP2 molecule for every two nucleosomes (1). Mutations in the coding region of MeCP2 lead to Rett syndrome (RTT), a neuro-developmental disease which is the main cause of mental retardation and autistic behaviour in girls [reviewed in ref. (2)]. The incidence of RTT is about 1 in every 10 000–15 000 female births (3). MeCP2 is also implicated in multiple other developmental disorders, suggesting that it occupies a central role in the post-natal development of the human brain (4). There are currently over 200 mutations found in the MeCP2 gene that cause RTT, most of which cluster around eight ‘hot spots’ distributed throughout the protein sequence (Figure 1). Four of the five most frequent RTT-causing mutations introduce stop codons into the transcription repression domain (TRD); the fifth most frequent mutation terminates at the end of the TRD (R294X; http://mecp2.chw.edu.au/mecp2/). A recent view suggests that MeCP2 dysfunction induces changes in the expression levels of thousands of genes, with a majority of genes being activated by MeCP2 (5). This suggests that MeCP2 under normal cellular conditions might not act as a gene specific transcriptional regulator as previously assumed (6,7), but instead might dampen transcriptional noise genome-wide in a DNA methylation-dependent manner (1).Figure 1.


Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes.

Yang C, van der Woerd MJ, Muthurajan UM, Hansen JC, Luger K - Nucleic Acids Res. (2011)

Domain structure of MeCP2. Dashed lines indicate the constructs used here, in addition to full length protein. NTD: N-terminal domain; MBD: methyl-CpG DNA binding domain, TRD: transcription repression domain, CTD: C-terminal domain. Red bars above indicate mapped DNA binding regions. The five most frequent mutations are indicated (percent occurrence given in brackets; nonsense mutations are indicated by asterisks).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105411&req=5

Figure 1: Domain structure of MeCP2. Dashed lines indicate the constructs used here, in addition to full length protein. NTD: N-terminal domain; MBD: methyl-CpG DNA binding domain, TRD: transcription repression domain, CTD: C-terminal domain. Red bars above indicate mapped DNA binding regions. The five most frequent mutations are indicated (percent occurrence given in brackets; nonsense mutations are indicated by asterisks).
Mentions: Methyl-CpG binding protein 2 (MeCP2) is a chromatin-associated protein that is highly abundant in neuronal cells, amounting to about one MeCP2 molecule for every two nucleosomes (1). Mutations in the coding region of MeCP2 lead to Rett syndrome (RTT), a neuro-developmental disease which is the main cause of mental retardation and autistic behaviour in girls [reviewed in ref. (2)]. The incidence of RTT is about 1 in every 10 000–15 000 female births (3). MeCP2 is also implicated in multiple other developmental disorders, suggesting that it occupies a central role in the post-natal development of the human brain (4). There are currently over 200 mutations found in the MeCP2 gene that cause RTT, most of which cluster around eight ‘hot spots’ distributed throughout the protein sequence (Figure 1). Four of the five most frequent RTT-causing mutations introduce stop codons into the transcription repression domain (TRD); the fifth most frequent mutation terminates at the end of the TRD (R294X; http://mecp2.chw.edu.au/mecp2/). A recent view suggests that MeCP2 dysfunction induces changes in the expression levels of thousands of genes, with a majority of genes being activated by MeCP2 (5). This suggests that MeCP2 under normal cellular conditions might not act as a gene specific transcriptional regulator as previously assumed (6,7), but instead might dampen transcriptional noise genome-wide in a DNA methylation-dependent manner (1).Figure 1.

Bottom Line: We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present.MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA.In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology and Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523-1870, USA.

ABSTRACT
MeCP2 is a highly abundant chromatin architectural protein with key roles in post-natal brain development in humans. Mutations in MeCP2 are associated with Rett syndrome, the main cause of mental retardation in girls. Structural information on the intrinsically disordered MeCP2 protein is restricted to the methyl-CpG binding domain; however, at least four regions capable of DNA and chromatin binding are distributed over its entire length. Here we use small angle X-ray scattering (SAXS) and other solution-state approaches to investigate the interaction of MeCP2 and a truncated, disease-causing version of MeCP2 with nucleosomes. We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present. MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA. In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex. We present ab initio envelope reconstructions of nucleosomes and their complexes with MeCP2 from SAXS data. SAXS studies also revealed unexpected sequence-dependent conformational variability in the nucleosomes themselves.

Show MeSH
Related in: MedlinePlus