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. 1997 Sep;17(9):5656–5666. doi: 10.1128/mcb.17.9.5656

Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG-binding protein MeCP2.

J M Weitzel 1, H Buhrmester 1, W H Strätling 1
PMCID: PMC232414  PMID: 9271441

Abstract

Here, we describe the cloning and further characterization of chicken ARBP, an abundant nuclear protein with a high affinity for MAR/SARs. Surprisingly, ARBP was found to be homologous to the rat protein MeCP2, previously identified as a methyl-CpG-binding protein. A region spanning 125 amino acids in the N-terminal halves is 96.8% identical between chicken ARBP and rat MeCP2. A deletion mutation analysis using Southwestern and band shift assays identified this highly conserved region as the MAR DNA binding domain. Alignment of chicken ARBP with rat and human MeCP2 proteins revealed six trinucleotide amplifications generating up to 34-fold repetitions of a single amino acid. Because MeCP2 was previously localized to pericentromeric heterochromatin in mouse chromosomes, we analyzed the in vitro binding of ARBP to various repetitive sequences. In band shift experiments, ARBP binds to two chicken repetitive sequences as well as to mouse satellite DNA with high affinity similar to that of its binding to chicken lysozyme MAR fragments. In mouse satellite DNA, use of several footprinting techniques characterized two high-affinity binding sites, whose sequences are related to the ARBP binding site consensus in the chicken lysozyme MAR (5'-GGTGT-3'). Band shift experiments indicated that methylation increased in vitro binding of ARBP to mouse satellite DNA two- to fivefold. Our results suggest that ARBP/MeCP2 is a multifunctional protein with roles in loop domain organization of chromatin, the structure of pericentromeric heterochromatin, and DNA methylation.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Belgrader P., Dey R., Berezney R. Molecular cloning of matrin 3. A 125-kilodalton protein of the nuclear matrix contains an extensive acidic domain. J Biol Chem. 1991 May 25;266(15):9893–9899. [PubMed] [Google Scholar]
  3. Benyajati C., Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976 Nov;9(3):393–407. doi: 10.1016/0092-8674(76)90084-2. [DOI] [PubMed] [Google Scholar]
  4. Buhrmester H., von Kries J. P., Strätling W. H. Nuclear matrix protein ARBP recognizes a novel DNA sequence motif with high affinity. Biochemistry. 1995 Mar 28;34(12):4108–4117. doi: 10.1021/bi00012a029. [DOI] [PubMed] [Google Scholar]
  5. Chirgwin J. M., Przybyla A. E., MacDonald R. J., Rutter W. J. Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry. 1979 Nov 27;18(24):5294–5299. doi: 10.1021/bi00591a005. [DOI] [PubMed] [Google Scholar]
  6. Cho Y., Gorina S., Jeffrey P. D., Pavletich N. P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science. 1994 Jul 15;265(5170):346–355. doi: 10.1126/science.8023157. [DOI] [PubMed] [Google Scholar]
  7. Cross S. H., Charlton J. A., Nan X., Bird A. P. Purification of CpG islands using a methylated DNA binding column. Nat Genet. 1994 Mar;6(3):236–244. doi: 10.1038/ng0394-236. [DOI] [PubMed] [Google Scholar]
  8. Dickinson L. A., Joh T., Kohwi Y., Kohwi-Shigematsu T. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell. 1992 Aug 21;70(4):631–645. doi: 10.1016/0092-8674(92)90432-c. [DOI] [PubMed] [Google Scholar]
  9. Dickinson L. A., Kohwi-Shigematsu T. Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol. 1995 Jan;15(1):456–465. doi: 10.1128/mcb.15.1.456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Forrester W. C., van Genderen C., Jenuwein T., Grosschedl R. Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science. 1994 Aug 26;265(5176):1221–1225. doi: 10.1126/science.8066460. [DOI] [PubMed] [Google Scholar]
  11. Frohman M. A., Dush M. K., Martin G. R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8998–9002. doi: 10.1073/pnas.85.23.8998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  13. Hakes D. J., Berezney R. Molecular cloning of matrin F/G: A DNA binding protein of the nuclear matrix that contains putative zinc finger motifs. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6186–6190. doi: 10.1073/pnas.88.14.6186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hengen P. N. Cycle sequencing through GC-rich regions. Trends Biochem Sci. 1996 Jan;21(1):33–34. [PubMed] [Google Scholar]
  15. Hochuli E., Döbeli H., Schacher A. New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. J Chromatogr. 1987 Dec 18;411:177–184. doi: 10.1016/s0021-9673(00)93969-4. [DOI] [PubMed] [Google Scholar]
  16. Hörz W., Altenburger W. Nucleotide sequence of mouse satellite DNA. Nucleic Acids Res. 1981 Feb 11;9(3):683–696. doi: 10.1093/nar/9.3.683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jenuwein T., Forrester W. C., Fernández-Herrero L. A., Laible G., Dull M., Grosschedl R. Extension of chromatin accessibility by nuclear matrix attachment regions. Nature. 1997 Jan 16;385(6613):269–272. doi: 10.1038/385269a0. [DOI] [PubMed] [Google Scholar]
  18. Kirillov A., Kistler B., Mostoslavsky R., Cedar H., Wirth T., Bergman Y. A role for nuclear NF-kappaB in B-cell-specific demethylation of the Igkappa locus. Nat Genet. 1996 Aug;13(4):435–441. doi: 10.1038/ng0895-435. [DOI] [PubMed] [Google Scholar]
  19. Kodama H., Saitoh H., Tone M., Kuhara S., Sakaki Y., Mizuno S. Nucleotide sequences and unusual electrophoretic behavior of the W chromosome-specific repeating DNA units of the domestic fowl, Gallus gallus domesticus. Chromosoma. 1987;96(1):18–25. doi: 10.1007/BF00285878. [DOI] [PubMed] [Google Scholar]
  20. Konig P., Giraldo R., Chapman L., Rhodes D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell. 1996 Apr 5;85(1):125–136. doi: 10.1016/s0092-8674(00)81088-0. [DOI] [PubMed] [Google Scholar]
  21. Kozak M. Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984 Jan 25;12(2):857–872. doi: 10.1093/nar/12.2.857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Laudet V., Hänni C., Coll J., Catzeflis F., Stéhelin D. Evolution of the nuclear receptor gene superfamily. EMBO J. 1992 Mar;11(3):1003–1013. doi: 10.1002/j.1460-2075.1992.tb05139.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lewis C. D., Laemmli U. K. Higher order metaphase chromosome structure: evidence for metalloprotein interactions. Cell. 1982 May;29(1):171–181. doi: 10.1016/0092-8674(82)90101-5. [DOI] [PubMed] [Google Scholar]
  24. Lewis J. D., Meehan R. R., Henzel W. J., Maurer-Fogy I., Jeppesen P., Klein F., Bird A. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell. 1992 Jun 12;69(6):905–914. doi: 10.1016/0092-8674(92)90610-o. [DOI] [PubMed] [Google Scholar]
  25. Lichtenstein M., Keini G., Cedar H., Bergman Y. B cell-specific demethylation: a novel role for the intronic kappa chain enhancer sequence. Cell. 1994 Mar 11;76(5):913–923. doi: 10.1016/0092-8674(94)90365-4. [DOI] [PubMed] [Google Scholar]
  26. Ludérus M. E., de Graaf A., Mattia E., den Blaauwen J. L., Grande M. A., de Jong L., van Driel R. Binding of matrix attachment regions to lamin B1. Cell. 1992 Sep 18;70(6):949–959. doi: 10.1016/0092-8674(92)90245-8. [DOI] [PubMed] [Google Scholar]
  27. Manuelidis L. Consensus sequence of mouse satellite DNA indicates it is derived from tandem 116 basepair repeats. FEBS Lett. 1981 Jun 29;129(1):25–28. doi: 10.1016/0014-5793(81)80746-6. [DOI] [PubMed] [Google Scholar]
  28. Meehan R. R., Lewis J. D., Bird A. P. Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA. Nucleic Acids Res. 1992 Oct 11;20(19):5085–5092. doi: 10.1093/nar/20.19.5085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nan X., Campoy F. J., Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell. 1997 Feb 21;88(4):471–481. doi: 10.1016/s0092-8674(00)81887-5. [DOI] [PubMed] [Google Scholar]
  30. Nan X., Meehan R. R., Bird A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res. 1993 Oct 25;21(21):4886–4892. doi: 10.1093/nar/21.21.4886. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nan X., Tate P., Li E., Bird A. DNA methylation specifies chromosomal localization of MeCP2. Mol Cell Biol. 1996 Jan;16(1):414–421. doi: 10.1128/mcb.16.1.414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Orlando V., Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell. 1993 Dec 17;75(6):1187–1198. doi: 10.1016/0092-8674(93)90328-n. [DOI] [PubMed] [Google Scholar]
  33. Paulson J. R., Laemmli U. K. The structure of histone-depleted metaphase chromosomes. Cell. 1977 Nov;12(3):817–828. doi: 10.1016/0092-8674(77)90280-x. [DOI] [PubMed] [Google Scholar]
  34. Poole E. S., Brown C. M., Tate W. P. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J. 1995 Jan 3;14(1):151–158. doi: 10.1002/j.1460-2075.1995.tb06985.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Saitoh Y., Mizuno S. Distribution of XhoI and EcoRI family repetitive DNA sequences into separate domains in the chicken W chromosome. Chromosoma. 1992 Jun;101(8):474–477. doi: 10.1007/BF00352469. [DOI] [PubMed] [Google Scholar]
  36. Saitoh Y., Saitoh H., Ohtomo K., Mizuno S. Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences. Chromosoma. 1991 Oct;101(1):32–40. doi: 10.1007/BF00360684. [DOI] [PubMed] [Google Scholar]
  37. Sap J., Muñoz A., Damm K., Goldberg Y., Ghysdael J., Leutz A., Beug H., Vennström B. The c-erb-A protein is a high-affinity receptor for thyroid hormone. Nature. 1986 Dec 18;324(6098):635–640. doi: 10.1038/324635a0. [DOI] [PubMed] [Google Scholar]
  38. Sen D., Gilbert W. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature. 1990 Mar 29;344(6265):410–414. doi: 10.1038/344410a0. [DOI] [PubMed] [Google Scholar]
  39. Stief A., Winter D. M., Strätling W. H., Sippel A. E. A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature. 1989 Sep 28;341(6240):343–345. doi: 10.1038/341343a0. [DOI] [PubMed] [Google Scholar]
  40. Strissel P. L., Espinosa R., 3rd, Rowley J. D., Swift H. Scaffold attachment regions in centromere-associated DNA. Chromosoma. 1996 Aug;105(2):122–133. doi: 10.1007/BF02509522. [DOI] [PubMed] [Google Scholar]
  41. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  42. Tate P., Skarnes W., Bird A. The methyl-CpG binding protein MeCP2 is essential for embryonic development in the mouse. Nat Genet. 1996 Feb;12(2):205–208. doi: 10.1038/ng0296-205. [DOI] [PubMed] [Google Scholar]
  43. Vettese-Dadey M., Walter P., Chen H., Juan L. J., Workman J. L. Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores. Mol Cell Biol. 1994 Feb;14(2):970–981. doi: 10.1128/mcb.14.2.970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Weitzel J., Strätling W. H. The case of chicken attachment region binding protein reinforces the importance of pre-screening of several libraries for cDNA cloning. Biochem J. 1997 Jan 1;321(Pt 1):261–262. doi: 10.1042/bj3210261u. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Woodford K., Weitzmann M. N., Usdin K. The use of K(+)-free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing. Nucleic Acids Res. 1995 Feb 11;23(3):539–539. doi: 10.1093/nar/23.3.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Zhang X. Y., Hörz W. Nucleosomes are positioned on mouse satellite DNA in multiple highly specific frames that are correlated with a diverged subrepeat of nine base-pairs. J Mol Biol. 1984 Jun 15;176(1):105–129. doi: 10.1016/0022-2836(84)90384-x. [DOI] [PubMed] [Google Scholar]
  47. Zhao K., Käs E., Gonzalez E., Laemmli U. K. SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 1993 Aug;12(8):3237–3247. doi: 10.1002/j.1460-2075.1993.tb05993.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. von Kries J. P., Buck F., Strätling W. H. Chicken MAR binding protein p120 is identical to human heterogeneous nuclear ribonucleoprotein (hnRNP) U. Nucleic Acids Res. 1994 Apr 11;22(7):1215–1220. doi: 10.1093/nar/22.7.1215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. von Kries J. P., Buhrmester H., Strätling W. H. A matrix/scaffold attachment region binding protein: identification, purification, and mode of binding. Cell. 1991 Jan 11;64(1):123–135. doi: 10.1016/0092-8674(91)90214-j. [DOI] [PubMed] [Google Scholar]
  50. von Kries J. P., Rosorius O., Buhrmester H., Strätling W. H. Biochemical properties of attachment region binding protein ARBP. FEBS Lett. 1994 Apr 4;342(2):185–188. doi: 10.1016/0014-5793(94)80497-4. [DOI] [PubMed] [Google Scholar]

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