Noncovalent Binding of Poly(ADP-Ribose) to Nuclear Matrix Proteins: Developmental Changes and Tissue Specificity

2000 ◽  
Vol 381 (11) ◽  
pp. 1047-1053 ◽  
Author(s):  
M. Malanga ◽  
B. Farina
Keyword(s):  
Nuclear Matrix ◽  
Noncovalent Interactions ◽  
Specific Protein ◽  
Noncovalent Interaction ◽  
Matrix Proteins ◽  
Nuclear Proteins ◽  
Rat Tissues ◽  
Nuclear Matrix Proteins

Abstract Poly(ADP-ribose) is a nuclear polynucleotide involved in the regulation of chromatin functions via covalent and/or noncovalent modification of nuclear proteins. Using a binding assay on protein blots, we searched for poly(ADP-ribose) binding proteins in nuclear matrices from testes of differently aged rats as well as from various adult rat tissues (brain, liver, spleen). We found that nuclear matrix proteins represent a significant subset of the nuclear proteins that can establish noncovalent interactions with poly(ADP-ribose). The profiles of poly(ADP-ribose) binding nuclear matrix proteins appeared to be tissue-specific and changed during postnatal development in the testis. The isolation and analysis of endogenous poly (ADP-ribose) from rat testes showed that the ADP-ribose polymers that bind nuclear matrix proteins in vitro are also present under physiologic conditions in vivo. These results further substantiate the possibility that poly(ADP-ribose) may affect chromatin functions through noncovalent interaction with specific protein targets, including nuclear matrix components.

scholarly journals Crosslinking of nuclear proteins to DNA by cis -diammminedichloroplatinum in intact cells Involvement of nuclear matrix proteins

FEBS Letters ◽  
1992 ◽  
Vol 307 (3) ◽  
pp. 383-385 ◽  
Author(s):  
Anna Ferraro ◽  
Paolo Grandi ◽  
Margherita Eufemi ◽  
Fabio Altieri ◽  
Carlo Turano
Keyword(s):  
Nuclear Matrix ◽  
Matrix Proteins ◽  
Nuclear Proteins ◽  
Intact Cells ◽  
Nuclear Matrix Proteins

In Vitro Heat Exposure Induces a Redistribution of Nuclear Matrix Proteins in Human K562 Erythroleukemia Cells

1994 ◽  
Vol 213 (1) ◽  
pp. 275-285 ◽  
Author(s):  
L.M. Neri ◽  
S. Santi ◽  
R.A. Marugg ◽  
B.M. Riederer ◽  
S. Capitani ◽  
...  
Keyword(s):  
Nuclear Matrix ◽  
Heat Exposure ◽  
Matrix Proteins ◽  
Nuclear Matrix Proteins ◽  
Erythroleukemia Cells

scholarly journals MspI8, the repetitive sequence specifically interacting with nuclear matrix of rat testis cells.

1994 ◽  
Vol 41 (4) ◽  
pp. 459-466 ◽  
Author(s):  
J Rzeszowska-Wolny ◽  
J Rogoliński
Keyword(s):  
Nuclear Matrix ◽  
Gel Electrophoresis ◽  
Matrix Protein ◽  
Repetitive Sequences ◽  
Matrix Proteins ◽  
Nuclear Matrix Proteins ◽  
Rat Testis ◽  
The Matrix ◽  
Matrix Bound

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 MspI 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 complexed 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.

CORTISOL-INDUCED PHOSPHORYLATION OF RAT LIVER NUCLEAR MATRIX PROTEINS IN IN VITRO SYSTEM

1981 ◽  
Vol 9 (2) ◽  
pp. 353P-353P
Author(s):  
Lj. Ševaljević ◽  
N. Brajanović ◽  
D. Trajković ◽  
K. Krtolica
Keyword(s):  
Rat Liver ◽  
Nuclear Matrix ◽  
Matrix Proteins ◽  
In Vitro System ◽  
Nuclear Matrix Proteins

Common nuclear matrix proteins in rat tissues

1997 ◽  
Vol 18 (11) ◽  
pp. 2109-2115 ◽  
Author(s):  
Thomas Korosec ◽  
Christopher Gerner ◽  
Georg Sauermann
Keyword(s):  
Nuclear Matrix ◽  
Matrix Proteins ◽  
Rat Tissues ◽  
Nuclear Matrix Proteins

Specific Labeling of Protein Domains with Antibody Fragments

1981 ◽  
Vol 39 ◽  
pp. 416-417
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler
Keyword(s):  
Image Processing ◽  
Specific Protein ◽  
Antibody Fragments ◽  
Supramolecular Organization ◽  
Two Dimensional ◽  
Ordered Structures ◽  
Virus Capsids ◽  
Processing Techniques

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.

scholarly journals Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

2016 ◽  
Vol 113 (21) ◽  
pp. E2899-E2905 ◽  
Author(s):  
Irina O. Vvedenskaya ◽  
Hanif Vahedian-Movahed ◽  
Yuanchao Zhang ◽  
Deanne M. Taylor ◽  
Richard H. Ebright ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Specific Protein ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Bubble ◽  
Recognition Element

During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein–DNA interactions with the downstream part of the nontemplate strand of the transcription bubble (“core recognition element,” CRE). Here, we investigated whether sequence-specific RNAP–CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP–CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP–CRE interactions on TSS selection in vitro and in vivo for a library of 47 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP–CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid native-elongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP–CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP–CRE interactions determine TSS selection. Our findings establish RNAP–CRE interactions are a functional determinant of TSS selection. We propose that RNAP–CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).

scholarly journals Microtubule Actin Cross-Linking Factor (Macf)

1999 ◽  
Vol 147 (6) ◽  
pp. 1275-1286 ◽  
Author(s):  
Conrad L. Leung ◽  
Dongming Sun ◽  
Min Zheng ◽  
David R. Knowles ◽  
Ronald K.H. Liem
Keyword(s):  
Calcium Binding ◽  
Coiled Coil ◽  
Specific Protein ◽  
Binding Domain ◽  
Full Length ◽  
Actin Binding ◽  
Cross Linking ◽  
Actin Binding Domain

We cloned and characterized a full-length cDNA of mouse actin cross-linking family 7 (mACF7) by sequential rapid amplification of cDNA ends–PCR. The completed mACF7 cDNA is 17 kb and codes for a 608-kD protein. The closest relative of mACF7 is the Drosophila protein Kakapo, which shares similar architecture with mACF7. mACF7 contains a putative actin-binding domain and a plakin-like domain that are highly homologous to dystonin (BPAG1-n) at its NH2 terminus. However, unlike dystonin, mACF7 does not contain a coiled–coil rod domain; instead, the rod domain of mACF7 is made up of 23 dystrophin-like spectrin repeats. At its COOH terminus, mACF7 contains two putative EF-hand calcium-binding motifs and a segment homologous to the growth arrest–specific protein, Gas2. In this paper, we demonstrate that the NH2-terminal actin-binding domain of mACF7 is functional both in vivo and in vitro. More importantly, we found that the COOH-terminal domain of mACF7 interacts with and stabilizes microtubules. In transfected cells full-length mACF7 can associate not only with actin but also with microtubules. Hence, we suggest a modified name: MACF (microtubule actin cross-linking factor). The properties of MACF are consistent with the observation that mutations in kakapo cause disorganization of microtubules in epidermal muscle attachment cells and some sensory neurons.

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