scholarly journals Role of Context in RNA Structure: Flanking Sequences Reconfigure CAG Motif Folding in Huntingtin Exon 1 Transcripts

Biochemistry ◽  
2013 ◽  
Vol 52 (46) ◽  
pp. 8219-8225 ◽  
Author(s):  
Steven Busan ◽  
Kevin M. Weeks
Keyword(s):  
Rna Structure ◽  
Exon 1 ◽  
Flanking Sequences

scholarly journals Thermodynamics of Homopeptide Aggregation

2020 ◽  
Author(s):  
Tam T. M. Phan ◽  
Jeremy D. Schmit
Keyword(s):  
Neurodegenerative Diseases ◽  
Disease Progression ◽  
Prion Diseases ◽  
Steric Repulsion ◽  
Polymer Micelles ◽  
Amyloid Aggregates ◽  
Exon 1 ◽  
Flanking Sequences ◽  
Precise Role

ABSTRACTAmyloid aggregates are found in many neurodegenerative diseases including Huntington’s, Alzheimer’s, and prion diseases. The precise role of the aggregates in disease progression has been difficult to elucidate due to the diversity of aggregated states they can adopt. Here we study the formation of fibrils and oligomers by exon 1 of huntingtin protein. We show that the oligomer states are consistent with polymer micelles that are limited in size by the stretching entropy of the polyglutamine region. The model shows how the sequences flanking the amyloid core modulate aggregation behavior. The N17 region promotes aggregation through weakly attractive interactions, while the C38 tail opposes aggregation via steric repulsion. We also show that the energetics of cross-β stacking by polyglutamine would produce fibrils with many alignment defects, but minor perturbations from the flanking sequences are sufficient to reduce the defects to the level observed in experiment. We conclude with a discussion of the implications of this model for other amyloid forming molecules.

Acquisition of an intracisternal A-particle element by a translocated c-myc gene in a murine plasma cell tumor

1985 ◽  
Vol 5 (12) ◽  
pp. 3625-3628
Author(s):  
R Greenberg ◽  
R Hawley ◽  
K B Marcu
Keyword(s):  
Plasma Cell ◽  
State Level ◽  
Cell Tumor ◽  
Gene Copy ◽  
Plasma Cell Tumor ◽  
Exon 1 ◽  
Myc Gene ◽  
Flanking Sequences ◽  
Intracisternal A Particle

The J558 plasma cell tumor contains two forms of a translocated c-myc gene which are distinguished by virtue of their 3' flanking sequences. The J558 alpha 4 and alpha 25 myc genes are broken by a 12;15 translocation which links c-myc exon 1 to C alpha switch sequences. Comparative restriction mapping and DNA sequence analyses demonstrated that an intracisternal A-particle (IAP) element inserted approximately 2 kilobases 3' of an alpha 4-type myc gene to generate the alpha 25 gene copy. The steady-state level of truncated myc RNAs in J558 was comparable to that in another plasma cell tumor line (MPC-11) which harbors a translocated c-myc locus without an IAP element. The significance of these observations for the putative role of IAP elements in the genesis or progression or both of plasma cell tumors is discussed.

scholarly journals Acquisition of an intracisternal A-particle element by a translocated c-myc gene in a murine plasma cell tumor.

1985 ◽  
Vol 5 (12) ◽  
pp. 3625-3628 ◽  
Author(s):  
R Greenberg ◽  
R Hawley ◽  
K B Marcu
Keyword(s):  
Plasma Cell ◽  
State Level ◽  
Cell Tumor ◽  
Gene Copy ◽  
Plasma Cell Tumor ◽  
Exon 1 ◽  
Myc Gene ◽  
Flanking Sequences ◽  
Intracisternal A Particle

The J558 plasma cell tumor contains two forms of a translocated c-myc gene which are distinguished by virtue of their 3' flanking sequences. The J558 alpha 4 and alpha 25 myc genes are broken by a 12;15 translocation which links c-myc exon 1 to C alpha switch sequences. Comparative restriction mapping and DNA sequence analyses demonstrated that an intracisternal A-particle (IAP) element inserted approximately 2 kilobases 3' of an alpha 4-type myc gene to generate the alpha 25 gene copy. The steady-state level of truncated myc RNAs in J558 was comparable to that in another plasma cell tumor line (MPC-11) which harbors a translocated c-myc locus without an IAP element. The significance of these observations for the putative role of IAP elements in the genesis or progression or both of plasma cell tumors is discussed.

scholarly journals The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

2021 ◽  
Vol 22 (5) ◽  
pp. 2409
Author(s):  
Anastasia A. Bizyaeva ◽  
Dmitry A. Bunin ◽  
Valeria L. Moiseenko ◽  
Alexandra S. Gambaryan ◽  
Sonja Balk ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Core Structure ◽  
Dna Aptamer ◽  
Tertiary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Flanking Sequences ◽  
Related Proteins

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.

scholarly journals Non-Cell Autonomous and Epigenetic Mechanisms of Huntington’s Disease

2021 ◽  
Vol 22 (22) ◽  
pp. 12499
Author(s):  
Chaebin Kim ◽  
Ali Yousefian-Jazi ◽  
Seung-Hye Choi ◽  
Inyoung Chang ◽  
Junghee Lee ◽  
...  
Keyword(s):  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Trinucleotide Repeat ◽  
Neurodegenerative Disorder ◽  
Involuntary Movement ◽  
Therapeutic Approaches ◽  
Exon 1 ◽  
Human Chromosome 4 ◽  
The Brain

Huntington’s disease (HD) is a rare neurodegenerative disorder caused by an expansion of CAG trinucleotide repeat located in the exon 1 of Huntingtin (HTT) gene in human chromosome 4. The HTT protein is ubiquitously expressed in the brain. Specifically, mutant HTT (mHTT) protein-mediated toxicity leads to a dramatic degeneration of the striatum among many regions of the brain. HD symptoms exhibit a major involuntary movement followed by cognitive and psychiatric dysfunctions. In this review, we address the conventional role of wild type HTT (wtHTT) and how mHTT protein disrupts the function of medium spiny neurons (MSNs). We also discuss how mHTT modulates epigenetic modifications and transcriptional pathways in MSNs. In addition, we define how non-cell autonomous pathways lead to damage and death of MSNs under HD pathological conditions. Lastly, we overview therapeutic approaches for HD. Together, understanding of precise neuropathological mechanisms of HD may improve therapeutic approaches to treat the onset and progression of HD.

scholarly journals The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Yulia Sokurenko ◽  
Vera Ulyanova ◽  
Pavel Zelenikhin ◽  
Alexey Kolpakov ◽  
Dmitriy Blokhin ◽  
...  
Keyword(s):  
Metal Ions ◽  
Rna Structure ◽  
Metal Ion ◽  
Extracellular Enzymes ◽  
Bacillus Pumilus ◽  
Transition Metal Ions ◽  
The Body ◽  
Intestinal Microbiome ◽  
Phosphodiester Bond

Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of theBacillusgenus, likeBacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3′,5′-phosphodiester bond and generates 2′,3′-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2′,3′-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2′,3′-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases.

Identification of upstream regulatory regions in the heart-expressed homeobox gene Nkx2-5

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 839-849 ◽  
Author(s):  
J.M. Reecy ◽  
X. Li ◽  
M. Yamada ◽  
F.J. DeMayo ◽  
C.S. Newman ◽  
...  
Keyword(s):  
Homeobox Gene ◽  
Protein Isoforms ◽  
Proximal Promoter ◽  
Coding Region ◽  
Heart Tube ◽  
Regulatory Regions ◽  
Regulatory Domains ◽  
Exon 1 ◽  
Flanking Sequences ◽  
Upstream Exon

Nkx2-5 marks the earliest recognizable cardiac progenitor cells, and is activated in response to inductive signals involved in lineage specification. Nkx2-5 is also expressed in the developing foregut, thyroid, spleen, stomach and tongue. One approach to elucidate the signals involved in cardiogenesis was to examine the transcriptional regulation of early lineage markers such as Nkx2-5. We generated F0 transgenic mice, which carry Nkx2-5 flanking sequences linked to a lacZ reporter gene. We identified multiple regulatory regions located within the proximal 10.7 kb of the Nkx2-5 gene. In addition to a proximal promoter, we identified a second promoter and a novel upstream exon that could participate in the regulation of Nkx2-5 transcription. Although used rarely in normal development, this novel exon could be spliced into the Nkx2-5 coding region in several ways, thereby potentially creating novel Nkx2-5 protein isoforms, whose transcriptional activity is greatly diminished as compared to wild-type Nkx2-5. An enhancer that directs expression in pharynx, spleen, thyroid and stomach was identified within 3.5 kb of exon 1 between the coding exon 1 and the novel upstream exon 1a. Two or more enhancers upstream of exon 1a were capable of driving expression in the cardiac crescent, throughout the myocardium of the early heart tube, then in the outflow tract and right ventricle of the looped heart tube. A negative element was also located upstream of exon1a, which interacted in complex ways with enhancers to direct correct spatial expression. In addition, potential autoregulatory elements can be cooperatively stimulated by Nkx2-5 and GATA-4. Our results demonstrate that a complex suite of interacting regulatory domains regulate Nkx2-5 transcription. Dissection of these elements should reveal essential features of cardiac induction and positive and negative signaling within the cardiac field.

scholarly journals Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control

2020 ◽  
Vol 21 (14) ◽  
pp. 5161 ◽  
Author(s):  
Katarzyna Taylor ◽  
Krzysztof Sobczak
Keyword(s):  
Alternative Splicing ◽  
Rna Structure ◽  
The Other ◽  
Splicing Regulation ◽  
Rna Structures ◽  
Structural Arrangement ◽  
Biological Functionality ◽  
Cis And Trans ◽  
Structural Aspects

Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.

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