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1

In-silico prediction and observations of nuclear matrix attachment

100%

Platts A. E., Quayle A. K., Krawetz S. A.

Cellular and Molecular Biology Letters

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2006

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tom 11

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nr 2

The nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.

2

Msp18, the repetitive sequence specifically interacting with nuclear matrix of rat testis cells

88%

Rzeszowska-Wolny J., Rogolinski J.

Acta Biochimica Polonica

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1994

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tom 41

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nr 4

The nuclear matrix bound DNA fraction of rat testis showed enrichment in repetitive sequences found in the 450 bp band after gel electrophoresis of the Mspl digested rat DNA. DNA fragments isolated from this band were cloned. DNA of the clone pMspI8 showed homology to some representatives of rat LINE sequence family, and complcxcd in vitro more efficiently with testes nuclear matrix proteins than with yeast ARS1 sequence containing the matrix association region (MAR) or DNA from an other clone, MspI19. Western blot analysis showed that MspI8 sequence interacts with testes matrix protein of about 120 kDa.

3

Detection of novel DNA-nuclear matrix interactions

88%

Ferraro A., Altieri F., Cervoni L., Eufemi M., Coppari S., Turano C.

Cellular and Molecular Biology Letters

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1997

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tom 02

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nr 2

4

The bovine tyrosine hydroxylase gene associates in vitro with the nuclear matrix by its first intron sequence

88%

Lenartowski R., Grzybowski T., Miscicka-Sliwka D., Wojciechowski W., Goc A.

Acta Biochimica Polonica

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2003

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tom 50

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nr 3

Recently we have shown that in vitro binding of the proximal part of the human tyrosine hydroxylase gene to the nuclear matrix is correlated with its transcriptional activity. The strongest binding potential was predicted by computing for the first intron sequence (Lenartowski & Goc, 2002, Neurosci Lett.; 330: 151-154). In this study a 16 kb fragment of the bovine genomic DNA containing the tyrosine hydroxylase gene was investigated for its affinity to the nuclear matrix. Only a 950 bp fragment encoding the distal part of the first intron, second exon and a few nucleotides of the second intron bound to the nuclear matrix. The binding was independent of the tissue-specific tyrosine hydroxylase gene activation. The fragment was subcloned and sequenced. Computer search pointed to one potential intronic matrix attachment region with two AP1-like sites embedded in the sequence. We conclude that even if the position of the matrix binding region is conserved among the tyrosine hydroxylase genes in mammals, its tissue specificity and/or function is not preserved or is achieved by different mechanisms.

5

Proximal part of human tyrosine hydroxylase gene binds nuclear matrix in tissue specific manner

75%

Lenartowski R., Goc A.

Cellular and Molecular Biology Letters

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2000

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tom 05

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nr 2

6

Functional aspects of nuclear matrix

75%

Wanka F.

Acta Biochimica Polonica

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1995

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tom 42

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nr 2

A model is proposed of the way in which the unwinding of the chromosomal DNA loops is controlled during DNA replication. It is based on the observation of a permanent binding of replication origins to the nuclear matrix and of a transient attachment of replicating DNA regions to sites in the immediate neighbourhood. DNA unwinding is controlled while the replicating loops are reeled through the replication binding sites. Also a mechanism is proposed to explain how the once-per-cycle replication of individual replicons can be controlled. DNA synthesis is initiated at single-stranded loops exposed by tandemly repeated DNA sequences at the replication origins. The single-stranded loops turn into fully double-stranded DNA during replication, becoming inaccessible for a second initiation during the same cell cycle. The configuration competent for initiation is restored by specific protein-DNA rearrangements coupled to mitotic condensation of the matrix into chromosomal scaffolds and its reversal.

7

Proteins with sulfhydryl groups in nuclei and nuclear matrix of normal and tumour cells

75%

Kilianska Z., Szymczyk P., Grzesik P.

Acta Biochimica Polonica

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1994

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tom 41

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nr 2

8

Molecular cloning and sequencing of the cDNA encoding plant nuclear matrix endonuclease

75%

Markiwicz E., Rzepecki R., Szopa J.

Acta Biochimica Polonica

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1994

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tom 41

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nr 2

9

Interactions of rat repetitive sequence MspI8 with nuclear matrix proteins during spermatogenesis

75%

Rogolinski J., Widlak P., Rzeszowska-Wolny J.

Acta Biochimica Polonica

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1996

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tom 43

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nr 2

Using the Southwestern blot analysis we have studied the interactions between rat repetitive sequence MspI8 and the nuclear matrix proteins of rat testis cells. Starting from 2 weeks the young to adult animals showed differences in type of testis nuclear matrix proteins recognizing the MspI8 sequence. The same sets of nuclear matrix proteins were detected in some fractions enriched in spermatocytes and spermatides and obtained after fractionation of testis cells of aduit animals by the velocity sedimentation technique.

10

UV-photoproducts induced in kappa Ig MAR increase its affinity to nuclear matrices in vitro

75%

Widlak P., Rzeszowska-Wolny J.

Cellular and Molecular Biology Letters

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1997

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tom 02

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nr 2

11

Nuclear matrix localization of chicken HSP108

75%

Altieri F., Eufemi M., Maras B., Turano C.

Cellular and Molecular Biology Letters

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1997

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tom 02

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nr 4

A glycoprotein purified from the internal nuclear matrix of chicken liver nuclei has been identified, by partial sequencing and by Western blotting, as hsp108, which is a component of the hsp90 superfamily. This protein has been previously characterized as a protein which copurifies with the cytoplasmic progesterone receptor and as a transferrin-binding protein of the chicken oviduct cell membrane. We have found that hsp108 is present in the nuclear matrix even in the absence of a heat shock or of other noxious conditions. Some of the properties already described for its homologous proteins (endoplasmin, grp94, hsp100) might explain its function at the nuclear matrix level. Hsp108 isolated from the liver nuclear matrix has a carbohydrate composition significantly different from that of the protein of the oviduct cell membrane.

12

The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains?

75%

Razin S. V.

Cellular and Molecular Biology Letters

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2001

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tom 06

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nr 1

13

Organisation and composition of the plant nuclear matrix. Characterisation and subcellular distribution of a MAR-binding protein: AcMFP1

75%

Samaniego R., Diaz de la Espina S.M.

Cellular and Molecular Biology Letters

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2000

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tom 05

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nr 2

14

Modulation of some nuclear matrix enzymatic activities by free fatty acids

63%

Lubocka J., Szopa J., Kozubek A.

Acta Biochimica Polonica

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1995

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tom 42

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nr 2

It was shown that two of main enzymatic activities of plant nucleus and nuclear matrix, namely RNA-polymerasic and DNA-nucleolytic are susceptible to modulation with free fatty acids. The effects observed were dependent to both fatty acid length and degree of unsaturation. In nuclei a stimulation of nuclease activity was observed whereas in matrices short chain fatty acids inhibited the studied activity. The effect of fatty acids on RNA-poIymerase was also different in nuclei and matrices. In nuclei all fatty acids studied inhibited polymerasic activity whereas in matrices short chain fatty acids stimulated this activity by up to 80% and the long chain fatty acids inhibited by up over 70%. The overall alteration of studied activities in nuclei and matrices by unsaturated fatty acids was similar. Nucleolytic activity was stronger inhibited and polymerasic activity was stimulated when the effects of linoleic and linolenic acids were studied. The results suggest possible importance of lipid component in nuclear matrix biological function.

15

DNA-nuclear matrix interactions analyzed by cross-linking reactions in intact nuclei from avian liver

63%

Ferraro A., Eufemi M., Cervoni L., Altieri F., Turano C.

Acta Biochimica Polonica

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1995

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tom 42

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nr 2

To detect the interactions of DNA with the nuclear matrix proteins, DNA-protein cross-linkages were induced in intact nuclei from chicken liver by the use of ds-diammine dichloroplatinum. Methods have been devised for fast purification both of the proteins and of the DNA fragments involved in the cross-linked complexes. By Southern-Western blotting a number of matrix proteins isolated from the complexes have been shown to recognize specifically DNA sequences present in the cross-linked DNA fragments. This experimental approach not only allows to identify the nuclear matrix-DNA interactions existing in the nucleus before its disruption, but also provides a preparation of matrix proteins enriched in those species which are involved in such interactions and which can therefore be detected with high sensitivity.

16

Nuclear localization and binding affinity of STAT5b for the alpha2-macroglobulin gene promoter during rat liver development and the acute-phase response

63%

Mihailovic M., Dinic S., Bogojevic D., Ivanovic-Matic S., Uskokovic A., Arambasic J., Grigorov I., Grdovic N., Vidakovic M., Martinovic V., Petrovic M., Poznanovic G.

Acta Biochimica Polonica

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2007

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tom 54

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nr 2

Expression of the rat α2-macroglobulin (MG) gene undergoes dynamic changes throughout an individual's life and during the acute-phase (AP) response. Details of the participation of the STAT family of transcription factors in its control remain incompletely understood. Here we examined the involvement of STAT5b in MG gene expression during development and the AP response. Immuno-blot analysis revealed the highest nuclear level of STAT5b in the fetus and during postnatal development, whereas in the adult it decreased. Stimulation of MG expression during the AP response was accompanied by a decrease in STAT5b. Examination of STAT5b localization revealed that the relative concentrations of STAT5b were higher in the nuclear matrix than in the nuclear extract. Affinity chromatography with the extended promoter region of the MG gene (-825/+12), followed by immuno-blot analysis, revealed dynamic changes in STAT5b binding. The highest concentration of the promoter-binding form of STAT5b was observed in the fetus. As postnatal development progressed, the level of promoter-bound STAT5b decreased and in the adult liver it was the lowest. Stimulation of MG gene expression during the AP response in both the fetus and adult was accompanied by significantly decreased STAT5b binding to the MG promoter. The AP response was accompanied by lower levels of STAT5b serine and tyrosine phosphorylation in both fetus and adult. In the nuclear matrix derived from adult tissues, tyrosine phosphorylated species were completely absent. We conclude that developmental-stage differences in the mechanisms that determine STAT5b nuclear localization contribute to its activity in vivo.

17

The association of 5' haptoglobin genes -flanking sequences with nuclear matrix proteins during the acute phase response

63%

Poznanovic G., Grujic V., Ivanovic-Matic S., Sevaljevic L.

Folia Histochemica et Cytobiologica

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1992

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tom 30

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nr 4

18

Sequences flanking rat hsp70.1 gene contain motifs specific for matrix attached regions and form complexes with nuclear matrix protein in vitro

63%

Widlak P., Rogolinski J., Lisowska K., Rzeszowska-Wolny J.

Cellular and Molecular Biology Letters

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1997

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tom 02

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nr 3

Eukaryotic chromatin is organized into looped domains formed by attachment of specific DNA sequences (termed MARs or SARs) to network of nuclear proteins (nuclear matrix). We have looked for matrix attachments within 4.9 kb DNA region encompassing rat hsp70.1 gene. Sequences that flank both 3'-end and 5'-end of the gene contain motifs characteristic for MAR/SARs identified in numerous other genes. These flanking sequences formed in vitro complexes with proteins of the nuclear matrix from different rat tissues. Using Southwestern analysis we showed that similar matrix proteins interacted with sequences flanking rat hsp70.1 gene and established MAR from mouse kappa immunoglobulin gene.

19

Poly[ADP-ribosyl]ation of proteins associated with nuclear matrix in rat testis

63%

Quesada P., d'Erme M., Atorino L., Faraone-Mennella M. R., Caiafa P., Farina B.

Acta Biochimica Polonica

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1995

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tom 42

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nr 2

We have previously demonstrated that a significant percentage of poly(ADPR) polymerase is present, as a tightly-bound form, at the third level of chromatin organisation defined by chromosomal loops and nuclear matrix. The present work is focused on the study of poly(ADP-ribosyl)ation of proteins present in these nuclear subfractions. It has been shown that, due to the action of poly(ADPR) polymerase, the ADP-ribose moiety of [14C]NAD is transferred to both loosely-bound and tightly-bound chromosomal proteins, which in consequence are modified by chain polymers of ADP-ribose of different lengths. Moreover, histone-like proteins seem to be ADP-ribosylated in chromosomal loops and nuclear matrix associated regions of DNA loops (MARS). A hypothesis can be put forward that the ADP-ribosylation system is functionally related to the nuclear processes, actively coordinated by the nuclear matrix.

20

Glycoproteins associated with nuclear matrix of higher Eucaryota

63%

Lipinska A., Krzeslak A., Sudak B.

Cellular and Molecular Biology Letters

|

1997

|

tom 02

|

nr 2

Ograniczanie wyników

In-silico prediction and observations of nuclear matrix attachment

Msp18, the repetitive sequence specifically interacting with nuclear matrix of rat testis cells

Detection of novel DNA-nuclear matrix interactions

The bovine tyrosine hydroxylase gene associates in vitro with the nuclear matrix by its first intron sequence

Proximal part of human tyrosine hydroxylase gene binds nuclear matrix in tissue specific manner

Functional aspects of nuclear matrix

Proteins with sulfhydryl groups in nuclei and nuclear matrix of normal and tumour cells

Molecular cloning and sequencing of the cDNA encoding plant nuclear matrix endonuclease

Interactions of rat repetitive sequence MspI8 with nuclear matrix proteins during spermatogenesis

UV-photoproducts induced in kappa Ig MAR increase its affinity to nuclear matrices in vitro

Nuclear matrix localization of chicken HSP108

The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains?

Organisation and composition of the plant nuclear matrix. Characterisation and subcellular distribution of a MAR-binding protein: AcMFP1

Modulation of some nuclear matrix enzymatic activities by free fatty acids

DNA-nuclear matrix interactions analyzed by cross-linking reactions in intact nuclei from avian liver

Nuclear localization and binding affinity of STAT5b for the alpha2-macroglobulin gene promoter during rat liver development and the acute-phase response

The association of 5' haptoglobin genes -flanking sequences with nuclear matrix proteins during the acute phase response

Sequences flanking rat hsp70.1 gene contain motifs specific for matrix attached regions and form complexes with nuclear matrix protein in vitro

Poly[ADP-ribosyl]ation of proteins associated with nuclear matrix in rat testis

Glycoproteins associated with nuclear matrix of higher Eucaryota