scholarly journals Expression characteristics of triplet repeat-containing RNAs and triplet repeat-interacting proteins in human tissues.

2008 ◽  
Vol 55 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Anna J Jasinska ◽  
Piotr Kozlowski ◽  
Wlodzimierz J Krzyzosiak
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Tandem Repeats ◽  
Triplet Repeat ◽  
Interacting Proteins ◽  
Substantial Portion ◽  
Triplet Repeat Expansion ◽  
Different Types ◽  
Cug Repeats ◽  
Different Tissues

Numerous human transcripts contain tandem repeats of trinucleotide motifs, the function of which remains unknown. In this study we used the available gene expression EST data to characterize the abundance of a large group of these transcripts in different tissues and determine the mRNAs which had the highest contribution to the observed levels of transcripts containing different types of the CNG repeats. A more extensive characteristics was performed for transcripts containing the CUG repeats, and those encoding the repeat-binding proteins. The scarcity of double-stranded CUG repeats as well as various proportions of the single-stranded and double-stranded CUG repeat-binding proteins were revealed in the studied transcriptomes. The observed correlated levels of transcripts containing single-stranded CUG repeats and of proteins binding single-stranded CUG repeats may imply that in addition to transcripts which only provide binding sites for these proteins there may be a substantial portion of the transcripts whose metabolism is directly regulated by such proteins. Our results showing a highly variable composition of triplet repeat-containing transcripts and their interacting proteins in different tissues may contribute to a better understanding of the mechanism of RNA-mediated pathogenesis in triplet repeat expansion diseases.

scholarly journals Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Pipier ◽  
A. Devaux ◽  
T. Lavergne ◽  
A. Adrait ◽  
Y. Couté ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cyclic Peptide ◽  
Essential Feature ◽  
Interacting Proteins ◽  
Rna Pol Ii ◽  
Cell Extracts ◽  
Different Types ◽  
Pol Ii Pausing ◽  
Clastogenic Effect

AbstractG-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.

scholarly journals Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

2021 ◽  
Author(s):  
Angelique Pipier ◽  
Alexandre Devaux ◽  
Thomas Lavergne ◽  
Annie Adrait ◽  
Yohann Couté ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cyclic Peptide ◽  
Essential Feature ◽  
Interacting Proteins ◽  
Rna Pol Ii ◽  
Cell Extracts ◽  
Different Types ◽  
Pol Ii Pausing ◽  
Clastogenic Effect

G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.

Movement of Calcium Ions and their Role in the Activation of Platelets

1978 ◽  
Vol 40 (02) ◽  
pp. 212-218 ◽  
Author(s):  
P Massini ◽  
R Käser-Glanzmann ◽  
E F Lüscher
Keyword(s):  
Plasma Membrane ◽  
Platelet Activation ◽  
Calcium Ions ◽  
Binding Sites ◽  
Shape Change ◽  
Release Reaction ◽  
Dense Bodies ◽  
Activated Platelets ◽  
Different Types ◽  
Ca Ions

SummaryThe increase of the cytoplasmic Ca-concentration plays a central role in the initiation of platelet activation. Four kinds of movements of Ca-ions are presumed to occur during this process: a) Ca-ions liberated from membranes induce the rapid shape change, b) Vesicular organelles release Ca-ions into the cytoplasm which initiate the release reaction, c) The storage organelles called dense bodies, secrete their contents including Ca-ions to the outside during the release reaction, d) At the same time a rearrangement of the plasma membrane occurs, resulting in an increase in its permeability for Ca-ions as well as in an increase in the number of Ca-binding sites.Since most processes occurring during platelet activation are reversible, the platelet must be equipped with a mechanism which removes Ca-ions from the cytoplasm. A vesicular fraction obtained from homogenized platelets indeed accumulates Ca actively. This Ca- pump is stimulated by cyclic AMP and protein kinase; it may be involved in the recovery of platelets after activation.It becomes increasingly clear that the various manifestations of platelet activation are triggered by a rise in the cytoplasmic Ca2+-concentration. The evidence for this and possible mechanisms involved are discussed in some detail in the contributions by Detwiler et al. and by Gerrard and White to this symposium. In this article we shall discuss four different types of mobilization of Ca-ions which occur in the course of the activation of platelets. In addition, at least one transport step involved in the removal of Ca2+ must occur during relaxation of activated platelets.

scholarly journals Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

2015 ◽  
Vol 471 (3) ◽  
pp. 403-414 ◽  
Author(s):  
M. Florencia Rey-Burusco ◽  
Marina Ibáñez-Shimabukuro ◽  
Mads Gabrielsen ◽  
Gisela R. Franchini ◽  
Andrew J. Roe ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Ligand Binding ◽  
Tissue Distribution ◽  
Binding Sites ◽  
Binding Proteins ◽  
Retinol Binding Protein ◽  
Internal Cavity ◽  
Binding Characteristics ◽  
Necator Americanus ◽  
Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

Myotonic dystrophy type 1 (DM1): A triplet repeat expansion disorder

Gene ◽  
2013 ◽  
Vol 522 (2) ◽  
pp. 226-230 ◽  
Author(s):  
Ashok Kumar ◽  
Sarita Agarwal ◽  
Divya Agarwal ◽  
Shubha R. Phadke
Keyword(s):  
Myotonic Dystrophy ◽  
Repeat Expansion ◽  
Triplet Repeat ◽  
Myotonic Dystrophy Type 1 ◽  
Myotonic Dystrophy Type ◽  
Triplet Repeat Expansion

scholarly journals Differential ability of proximal and remote element pairs to cooperate in activating RNA polymerase II transcription.

1991 ◽  
Vol 11 (9) ◽  
pp. 4561-4571 ◽  
Author(s):  
W D Wang ◽  
J D Gralla
Keyword(s):  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Tandem Repeats ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Cooperative Interaction ◽  
Promoter Strength ◽  
Synthetic Promoters ◽  
Major Late Promoter ◽  
Test Gene

To investigate the synergism or cooperative interaction between transcription elements, we have designed and constructed a series of synthetic polymerase II promoters with different combinations of elements. These include three different CCAAT boxes, which correspond to the binding sites for CP1, CP2, and NFI, a GC box, a CACCC box, and an ATF/CREB-binding site. The synthetic promoters containing these elements in proximal positions were linked to a test gene (CAT). Tandem repeats of AP1- and AP2-binding sites, the simian virus 40 enhancer, and DNA-binding sites for GAL-estrogen receptor were cloned downstream of the test gene. The strength of these promoters was then tested in transient-expression assays in HeLa TK- cells. In the context of the adenovirus major late promoter TATA box, the promoters containing only certain combinations of elements are active in this assay. Some elements appear to cooperate nearly universally, but others exhibit strong selectivity. These results indicate strongly selective synergistic interactions between elements and suggest that levels of promoter strength may be determined by the extent of compatibility between factors bound to proximal and enhancer sites.

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