Biochemical properties of attachment region binding protein ARBP

Kries, Jens Peter von; Rosorius, Olaf; Buhrmester, H; Strätling, Wolf H.

doi:10.1016/0014-5793(94)80497-4

Cited by 8 publications

(7 citation statements)

References 21 publications

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“…In our previous limited-digestion experiments, intermediate digestion products with MAR binding activity were not observed (with a single exception), suggesting that the flanks of the protein were readily cleaved off (48). Of further interest is the high degree of stability of the MAR binding domain to the denaturing conditions in Southwestern blotting experiments.…”

Section: Discussionmentioning

confidence: 90%

“…With correction for 22 non-ARBP amino acids in the bacterially expressed peptide 4, the 125-amino-acid MAR binding domain exhibits an apparent molecular mass of approximately 15.5 kDa. In previous studies (48), limited digestion of ARBP in isolated nuclei with various proteases generated two prominent limiting resistant peptides, which exhibited selective MAR binding activity: a 17-to 18-kDa peptide and a 14.5-to 15-kDa peptide. This shows that the size of the MAR binding domain determined here by in vitro studies compares well with the size of the DNA binding domain derived from experiments with intact nuclei.…”

Section: Discussionmentioning

confidence: 99%

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Chicken MAR-Binding Protein ARBP Is Homologous to Rat Methyl-CpG-Binding Protein MeCP2

Weitzel

Buhrmester

Strätling

1997

Molecular and Cellular Biology

107

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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 twoto 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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Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Chicken MAR-Binding Protein ARBP Is Homologous to Rat Methyl-CpG-Binding Protein MeCP2

Weitzel

Buhrmester

Strätling

1997

Molecular and Cellular Biology

107

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“…Furthermore, they may act as boundary elements for enhancers, restricting their long range effect to only the promoters that are located in the same chromatin domain (4). Although a number of interacting proteins have been identified [lamins (5), ARBP (6), hnRNP-U/SafA (7), SafB (8), SatB1 (9,10) and Bright (11)], the molecular mechanism by which these proteins affect transcription regulation is still unclear.…”

Section: Introductionmentioning

confidence: 99%

A bipartite sequence element associated with matrix/scaffold attachment regions

Drunen

Sewalt²,

Oosterling

et al. 1999

Nucleic Acids Research

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We have identified a MAR/SAR recognition signature (MRS) which is common to a large group of matrix and scaffold attachment regions. The MRS is composed of two degenerate sequences (AATAAYAA and AWWRTAANNWWGNNNC) within close proximity. Analysis of >300 kb of genomic sequence from a variety of eukaryotic organisms shows that the MRS faithfully predicts 80% of MARs and SARs. In each case where we find a MRS, the corresponding DNA region binds specifically to the nuclear scaffold. Although all MRSs are associated with a SAR, not all known SARs and MARs contain a MRS, suggesting that at least two classes exist, one containing a MRS, the other not. Evidence is presented that the two sequence elements of the bipartite MRS occupy a position on the nucleosome near the dyad axis, together creating a putative protein binding site. The identification of a MAR- and SAR-associated DNA element is an important step forward towards understanding the molecular mechanisms of these elements. It will allow: (i) analysis of the genomic location of SARs, e.g. in relationship to genes, based on sequence information alone, rather than on the basis of an elaborate biochemical assay; (ii) identification and analysis of proteins that specifically bind to the MRS.

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“…Quite a few matrix proteins are well known and some have been characterized extensively (lamins [Hozak et al, 1995; Barboro et al, 2002, 2003], NuMA [Barboro et al, 2002, 2003], proteins of RNP particles [Mattern et al, 1996, 1999; Nickerson, 2001], MAR‐binding proteins [von Kries et al, 1991, 1994a, b; Tsutsui et al, 1993; Weitzel et al, 1997; Lobov et al, 2000; Bode et al, 2003]. We could show recently that another major constituent of the nuclear matrix are prosomes [De Conto et al, 2000].…”

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confidence: 99%

RNA‐dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes

Ioudinkova

Razin

Borunova

et al. 2004

J of Cellular Biochemistry

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Previously, we have shown that in murine myoblasts prosomes are constituents of the nuclear matrix; a major part of the latter was found to be RNase sensitive. Here, we further define the RNA-dependent matrix in avian erythroblastosis virus (AEV) transformed erythroid cells in relation to its structure, presence of specific RNA, prosomes and/or proteasomes. These cells transcribe but do not express globin genes prior to induction. Electron micrographs show little difference in matrices treated with DNase alone or with both, DNase and RNase. In situ hybridization with alpha globin riboprobes shows that this matrix includes globin transcripts. Of particular interest is that, apparently, a nearly 35 kb long globin full domain transcript (FDT), including genes, intergenic regions and a large upstream domain is a part of the RNA-dependent nuclear matrix. The 23K-type of prosomes, previously shown to be co-localized with globin transcripts in the nuclear RNA processing centers, were found all over the nuclear matrix. Other types of prosomes show different distributions in the intact cell but similar distribution patterns on the matrix. Globin transcripts and at least 80% of prosomes disappear from matrices upon RNase treatment. Interestingly, the 19S proteasome modulator complex is insensitive to RNase treatment. Only 20S prosomes but not 26S proteasomes are thus part of the RNA-dependent nuclear matrix. We suggest that giant pre-mRNA and FDTs in processing, aligning prosomes and other RNA-binding proteins are involved in the organization of the dynamic nuclear matrix. It is proposed that the putative function of RNA within the nuclear matrix and, thus, the nuclear dynamic architecture, might explain the giant size and complex organization of primary transcripts and their introns.

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Biochemical properties of attachment region binding protein ARBP

Cited by 8 publications

References 21 publications

Chicken MAR-Binding Protein ARBP Is Homologous to Rat Methyl-CpG-Binding Protein MeCP2

Chicken MAR-Binding Protein ARBP Is Homologous to Rat Methyl-CpG-Binding Protein MeCP2

A bipartite sequence element associated with matrix/scaffold attachment regions

RNA‐dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes

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