DNA-protein complexes of the nuclear matrix: Visualization and partial characterization of the protein component

Chernokhvostov, Victor V.; Stel'mashchuk, V. Ya.; Razin, Sergey V.; Georgiev, G.P.

doi:10.1016/0006-291x(89)91978-5

Cited by 7 publications

(5 citation statements)

References 25 publications

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“…TBP distribution in the genome is site specific, and they are enriched in several reiterated sequences as well as in attachment sites to the nuclear skeleton (Werner and Rest, 1987;Neuer-Nitsche et al, 1988;Werner and Neuer-Nitsche, 1989;Pfü tz et al, 1992;Sjakste, 1997). The composition and features of the TBP in chicken erythroid cells have been characterized in detail (Razin et al, 1981(Razin et al, , 1988Chernokhvostov et al, 1989). Using this model, it was shown that their distribution in unique genes reflects the type of cell differentiation; for example, they are found in the globin genes of erythroid cells but not in nonerythroid cells (Razin et al, 1988).…”

Section: Introductionmentioning

confidence: 98%

Transcription- and Apoptosis-Dependent Long-Range Distribution of Tight DNA–Protein Complexes in the Chicken α-Globin Gene

Bielskienė

Bagdoniene

Juodka

et al. 2008

DNA and Cell Biology

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The proteins tightly bound to DNA (TBP) are a group of proteins that remain attached to DNA with covalent or noncovalent bonds after its deproteinization, and have been hypothesized to be involved in regulation of gene expression. To investigate this question further, oligonucleotide DNA arrays were used to determine the distribution of tightly bound proteins along a 100-kb DNA fragment surrounding the chicken alpha-globin gene domain in DNA from chicken erythrocytes, liver, and AEV-transformed HD3 (erythroblast) cells in different physiological conditions. DNA was fractionated into TBP-free (F) and TBP-enriched (R) fractions by separation on nitrocellulose, and these fractions were used as probes for hybridization with the microarray. In erythrocytes, the site 60 kb from the 5' end of the sequence and containing a LINE family CR1 repeat was TBP enriched, but in HD3 cells this sequence was devoid of TBPs. Thus cessation of transcription of the domain is followed by an F-R transition of this site. In apoptotic HD3 cells, TBPs remained attached to DNA only at a site situated 16 kb from the 5' end of the sequence. These data confirm and extend previous conclusions about the specificity of the DNA sequences that preferably form tight complexes with proteins and about the differentiation-specific distribution of the TBPs in different cell lineages. Binding of TBPs appears to be independent of primary DNA sequence.

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Section: Introductionmentioning

confidence: 98%

Transcription- and Apoptosis-Dependent Long-Range Distribution of Tight DNA–Protein Complexes in the Chicken α-Globin Gene

Bielskienė

Bagdoniene

Juodka

et al. 2008

DNA and Cell Biology

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“…Later the additional minor TBPs of 62, 52 and 40 kDa were described and it was reported that these proteins assemble in globules 12.8 nm in diameter (Loeffler et al, 1996). Similar globular structures were described for TBPs localized in interaction sites with the nuclear matrix, besides DNA and proteins (7 or 8 polypeptides) the globules contained RNA molecules (Chernokhvostov and Georgiev, 1990;Chernokhvostov et al, 1986Chernokhvostov et al, , 1989.…”

Section: Polypeptide Composition Of Tbps Its Tissue and Species Specmentioning

confidence: 90%

“…It was shown that eukaryotic DNA is interrupted every 50 kbp by a nick masked by RNA-protein complex (Gal et al, 2000;Székvölgyi et al, 2007;Varga et al, 1999). The composition of these linkers resembles DNA-TBPs complexes (Chernokhvostov and Georgiev, 1990;Chernokhvostov et al, 1986Chernokhvostov et al, , 1989.…”

Section: Chemical Bonds Between Tbps and Dnamentioning

confidence: 95%

“…The TBPs distribution in the chicken α-globin gene domain was studied already in the pioneering projects (Chernokhvostov et al, 1989;Razin et al, 1981Razin et al, , 1988. It was shown that TBPs binding to globin genes depends on cell differentiation, it is characteristic exclusively for erythroid cells (Razin et al, 1988).…”

Section: Dna Sequences Interacting With Tbpsmentioning

confidence: 99%

“…Operationally this protein fraction is defined as proteins remaining attached to DNA after its purification by conventional deproteinization methods (lysis in SDS with or without protease followed by extraction with phenol, chloroform, salting out). Investigation of the functional role of these proteins was a piece of cutting-edge research performed by several strong teams about twenty years ago (Bagdoniene et al, 1989;Chernokhvostov and Georgiev, 1990;Chernokhvostov et al, 1986Chernokhvostov et al, , 1989Juodka, 1984;Juodka et al, 1991Juodka et al, , 1995aJuodka et al, , 1995bNeuer-Nitsche et al, 1988;Pfütz et al, 1992;Razin et al, 1988;Werner and Neuer-Nitsche, 1989; reviewed in Drygin, 1998;Tsanev and Avramova, 1994). Despite promising results, these studies were abandoned mostly for subjective reasons.…”

Section: Introductionmentioning

confidence: 95%

See 2 more Smart Citations

Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes

Sjakste

Bielskienė

Bagdoniene

et al. 2012

Gene

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Nuclear skeleton, DNA domains and control of replication and transcription

Georgiev¹,

Vassetzky²,

Luchnik³

et al. 1991

EJB Reviews 1991

Self Cite

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Chromosomal DNA is organized in loops or domains of about 100 kb. Their ends seem to be attached to special protein skeletal structures. The DNA-attachment sites can be subdivided into permanent and transient types. The permanent or constitutive attachment sites, which are retained in all types of cells (including those inactive in replication and transcription), either coincide with or are located close to replication origins. This observation provides a simple way for isolation of DNA fragments containing replication origins. Such fragments from the chicken a-globin gene domain and other regions of the chicken genome contain DNA sequences which interact with nuclear proteins present in dividing cells, but absent from non-dividing cells. Several new consensus sequences interacting with nuclear proteins were detected. The 5' end region of the a-globin gene domain containing a replication origin was found to possess enhancer activity lacking tissue specificity. Hence, the domain organization of DNA is related to the organization of replication process. Other sets of data indicate that the integrity of DNA domains is important for maintaining transcription within the domain. According to these data, even a single nick at an distance of about 100 kbp seems to be sufficient for blocking transcription within the whole domain at the stage of RNA elongation. Thus, topological integrity of DNA may be an important factor involved in formation of active chromatin. Nuclear skeleton and D N A domainsThe first evidence for the existence of a nuclear skeleton was obtained in electron microscopic studies on nuclei from which chromatin had been removed by successive DNase I and high-salt treatment. In that case, thin fibrils composed mostly of proteins could be seen throughout the whole nucleus. They were designated as nucleonems. Some data indicated that the DNA in the nucleus was attached to nucleonems [l] (see Fig. 1). Several other authors also observed such a fibrillar nuclear network after removal of chromatin from nuclei [2, 31. Its protein content was rather complex according to the data of gel electrophoresis [4]. To designate the material remaining in the nucleus after chromatin removal, the term nuclear matrix was proposed [3]. The nuclear matrix contains, in addition to nucleonems, a residual nucleoli and the nuclear envelope [l, 31. The latter is represented by a nuclear membrane (if detergents are not used) and a nuclear lamina, a protein layer underlying the nuclear membrane [3].It was also demonstrated that the removal of histone made tightly packed chromosomal DNA to convert into large superhelical loops or domains attached to certain residual elements of the nuclei [5]. The DNA loops were clearly vi-Correspondence to G. P. Georgiev, Engelhardt Institute of Molecular Biology, USSR Academy of Sciences,Vavilova Street 32, Moscow Abbreviations. nmDNA, nuclear matrix DNA; oriDNA, DNA fraction enriched in replication origins; ARS, autonomously replicating sequences; TBD protein, protein tightly bound to DNA; CAT, chl...

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DNA-protein complexes of the nuclear matrix: Visualization and partial characterization of the protein component

Cited by 7 publications

References 25 publications

Transcription- and Apoptosis-Dependent Long-Range Distribution of Tight DNA–Protein Complexes in the Chicken α-Globin Gene

Transcription- and Apoptosis-Dependent Long-Range Distribution of Tight DNA–Protein Complexes in the Chicken α-Globin Gene

Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes

Nuclear skeleton, DNA domains and control of replication and transcription

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