Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules

Biosystems ◽  
2020 ◽  
Vol 197 ◽  
pp. 104206
Author(s):  
Hiromi Mutsuro-Aoki ◽  
Kokoro Hamachi ◽  
Ryodai Kurihara ◽  
Koji Tamura
2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Zhang ◽  
Tuan M. Nguyen ◽  
Xiao-Ou Zhang ◽  
Limei Wang ◽  
Tin Phan ◽  
...  

AbstractShort hairpin RNAs (shRNAs) are used to deplete circRNAs by targeting back-splicing junction (BSJ) sites. However, frequent discrepancies exist between shRNA-mediated circRNA knockdown and the corresponding biological effect, querying their robustness. By leveraging CRISPR/Cas13d tool and optimizing the strategy for designing single-guide RNAs against circRNA BSJ sites, we markedly enhance specificity of circRNA silencing. This specificity is validated in parallel screenings by shRNA and CRISPR/Cas13d libraries. Using a CRISPR/Cas13d screening library targeting > 2500 human hepatocellular carcinoma-related circRNAs, we subsequently identify a subset of sorafenib-resistant circRNAs. Thus, CRISPR/Cas13d represents an effective approach for high-throughput study of functional circRNAs.


Blood ◽  
2006 ◽  
Vol 108 (10) ◽  
pp. 3305-3312 ◽  
Author(s):  
T. Yamamoto ◽  
H. Miyoshi ◽  
N. Yamamoto ◽  
N. Yamamoto ◽  
J.-i. Inoue ◽  
...  

2008 ◽  
Vol 87 (11) ◽  
pp. 992-1003 ◽  
Author(s):  
P.N. Pushparaj ◽  
J.J. Aarthi ◽  
J. Manikandan ◽  
S.D. Kumar

RNA interference (RNAi), an accurate and potent gene-silencing method, was first experimentally documented in 1998 in Caenorhabditis elegans by Fire et al., who subsequently were awarded the 2006 Nobel Prize in Physiology/Medicine. Subsequent RNAi studies have demonstrated the clinical potential of synthetic small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) in dental diseases, eye diseases, cancer, metabolic diseases, neurodegenerative disorders, and other illnesses. siRNAs are generally from 21 to 25 base-pairs (bp) in length and have sequence-homology-driven gene-knockdown capability. RNAi offers researchers an effortless tool for investigating biological systems by selectively silencing genes. Key technical aspects—such as optimization of selectivity, stability, in vivo delivery, efficacy, and safety—need to be investigated before RNAi can become a successful therapeutic strategy. Nevertheless, this area shows a huge potential for the pharmaceutical industry around the globe. Interestingly, recent studies have shown that the small RNA molecules, either indigenously produced as microRNAs (miRNAs) or exogenously administered synthetic dsRNAs, could effectively activate a particular gene in a sequence-specific manner instead of silencing it. This novel, but still uncharacterized, phenomenon has been termed ‘RNA activation’ (RNAa). In this review, we analyze these research findings and discussed the in vivo applications of siRNAs, miRNAs, and shRNAs.


2008 ◽  
Vol 323 (1-2) ◽  
pp. 81-89 ◽  
Author(s):  
Z. X. Shan ◽  
Q. X. Lin ◽  
M. Yang ◽  
C. Y. Deng ◽  
S. J. Kuang ◽  
...  

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gonzalo Quiroga-Artigas ◽  
Alexandrea Duscher ◽  
Katelyn Lundquist ◽  
Justin Waletich ◽  
Christine E. Schnitzler

An amendment to this paper has been published and can be accessed via a link at the top of the paper.


2016 ◽  
Vol 16 (3) ◽  
pp. 735-739
Author(s):  
Federico González-Pozas ◽  
Rosa Montes ◽  
Lourdes López-Onieva ◽  
Tamara Romero ◽  
Joan Domingo-Reinés ◽  
...  

Urology ◽  
2009 ◽  
Vol 74 (4) ◽  
pp. S295-S296
Author(s):  
J. Zheng ◽  
J. Liu ◽  
L. Mao ◽  
W. Li ◽  
F. Sun ◽  
...  

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