scholarly journals Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration

2014 ◽  
Vol 88 (15) ◽  
pp. 8565-8578 ◽  
Author(s):  
R. Meier ◽  
A. Franceschini ◽  
P. Horvath ◽  
M. Tetard ◽  
R. Mancini ◽  
...  
Keyword(s):  
Small Interfering Rna ◽  
Host Factor ◽  
Genome Wide ◽  
Novel Host ◽  
Interfering Rna

scholarly journals Genome-wide screens identify specific drivers of mutant hTERT promoters

2022 ◽  
Vol 119 (3) ◽  
pp. e2105171119
Author(s):  
Raghuvaran Shanmugam ◽  
Mert Burak Ozturk ◽  
Joo-Leng Low ◽  
Semih Can Akincilar ◽  
Joelle Yi Heng Chua ◽  
...  
Keyword(s):  
Small Interfering Rna ◽  
Regulatory Region ◽  
Telomerase Activity ◽  
Chromatin Interaction ◽  
Mediator Complex ◽  
Wild Type ◽  
Distal Regulatory Region ◽  
Genome Wide ◽  
Promoter Mutations ◽  
Interfering Rna

Cancer-specific hTERT promoter mutations reported in 19% of cancers result in enhanced telomerase activity. Understanding the distinctions between transcriptional regulation of wild-type (WT) and mutant (Mut) hTERT promoters may open up avenues for development of inhibitors which specially block hTERT expression in cancer cells. To comprehensively identify physiological regulators of WT- or Mut-hTERT promoters, we generated several isogenic reporter cells driven by endogenous hTERT loci. Genome-wide CRISPR-Cas9 and small interfering RNA screens using these isogenic reporter lines identified specific regulators of Mut-hTERT promoters. We validate and characterize one of these hits, namely, MED12, a kinase subunit of mediator complex. We demonstrate that MED12 specifically drives expression of hTERT from the Mut-hTERT promoter by mediating long-range chromatin interaction between the proximal Mut-hTERT promoter and T-INT1 distal regulatory region 260 kb upstream. Several hits identified in our screens could serve as potential therapeutic targets, inhibition of which may specifically block Mut-hTERT promoter driven telomerase reactivation in cancers.

A genome-wide survey of small interfering RNA and microRNA pathway genes in a galling insect

2013 ◽  
Vol 59 (3) ◽  
pp. 367-376 ◽  
Author(s):  
Jacob T. Shreve ◽  
Richard H. Shukle ◽  
Subhashree Subramanyam ◽  
Alisha J. Johnson ◽  
Brandon J. Schemerhorn ◽  
...  
Keyword(s):  
Small Interfering Rna ◽  
Genome Wide ◽  
A Genome ◽  
Microrna Pathway ◽  
Interfering Rna ◽  
Genome Wide Survey

scholarly journals Genomic Analysis of Anti-Hepatitis B Virus (HBV) Activity by Small Interfering RNA and Lamivudine in Stable HBV-Producing Cells

2005 ◽  
Vol 79 (22) ◽  
pp. 14392-14403 ◽  
Author(s):  
Yong Guo ◽  
Hongyan Guo ◽  
Liang Zhang ◽  
Hongying Xie ◽  
Xin Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Small Interfering Rna ◽  
Expression Profiles ◽  
Cell Interaction ◽  
Host Cells ◽  
Genome Wide ◽  
B Virus ◽  
Interfering Rna

ABSTRACT Hepatitis B virus (HBV) causes acute and chronic hepatitis and hepatocellular carcinoma. Small interfering RNA (siRNA) and lamivudine have been shown to have anti-HBV effects through different mechanisms. However, assessment of the genome-wide effects of siRNA and lamivudine on HBV-producing cell lines has not been reported, which may provide a clue to interrogate the HBV-cell interaction and to evaluate the siRNA's side effect as a potential drug. In the present study, we designed seven siRNAs based on the conserved HBV sequences and tested their effects on the expression of HBV genes following sorting of siRNA-positive cells. Among these seven siRNAs, siRNA-1 and siRNA-7 were found to effectively suppress HBV gene expression. We further addressed the global gene expression changes in stable HBV-producing cells induced by siRNA-1 and siRNA-7 by use of human genome-wide oligonucleotide microarrays. Data from the gene expression profiling indicated that siRNA-1 and siRNA-7 altered the expression of 54 and 499 genes, respectively, in HepG2.2.15 cells, which revealed that different siRNAs had various patterns of gene expression profiles and suggested a complicated influence of siRNAs on host cells. We further observed that 18 of these genes were suppressed by both siRNA-1 and siRNA-7. Interestingly, seven of these genes were originally activated by HBV, which suggested that these seven genes might be involved in the HBV-host cell interaction. Finally, we have compared the effects of siRNA and lamivudine on HBV and host cells, which revealed that siRNA is more effective at inhibiting HBV expression at the mRNA and protein level in vitro, and the gene expression profile of HepG2.2.15 cells treated by lamivudine is totally different from that seen with siRNA.

scholarly journals Genome-wide CRISPR screen identifies RACK1 as a critical host factor for flavivirus replication

2021 ◽  
Author(s):  
Byron Shue ◽  
Abhilash I. Chiramel ◽  
Berati Cerikan ◽  
Thu-Hien To ◽  
Sonja Frölich ◽  
...  
Keyword(s):  
Viral Replication ◽  
Host Factor ◽  
Host Protein ◽  
Ns1 Protein ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Cellular Factors ◽  
Novel Host ◽  
The Impact

Cellular factors have important roles in all facets of the flavivirus replication cycle. Deciphering viral-host protein interactions is essential for understanding the flavivirus lifecycle as well as development of effective antiviral strategies. To uncover novel host factors that are co-opted by multiple flaviviruses, a CRISPR/Cas9 genome wide knockout (KO) screen was employed to identify genes required for replication of Zika virus (ZIKV). Receptor for Activated Protein C Kinase 1 (RACK1) was identified as a novel host factor required for ZIKV replication, which was confirmed via complementary experiments. Depletion of RACK1 via siRNA demonstrated that RACK1 is important for replication of a wide range of mosquito- and tick-borne flaviviruses, including West Nile Virus (WNV), Dengue Virus (DENV), Powassan Virus (POWV) and Langat Virus (LGTV) as well as the coronavirus SARS-CoV-2, but not for YFV, EBOV, VSV or HSV. Notably, flavivirus replication was only abrogated when RACK1 expression was dampened prior to infection. Utilising a non-replicative flavivirus model, we show altered morphology of viral replication factories and reduced formation of vesicle packets (VPs) in cells lacking RACK1 expression. In addition, RACK1 interacted with NS1 protein from multiple flaviviruses; a key protein for replication complex formation. Overall, these findings reveal RACK1’s crucial role to the biogenesis of pan-flavivirus replication organelles. Importance Cellular factors are critical in all facets of viral lifecycles, where overlapping interactions between the virus and host can be exploited as possible avenues for the development of antiviral therapeutics. Using a genome-wide CRISPR knock-out screening approach to identify novel cellular factors important for flavivirus replication we identified RACK1 as a pro-viral host factor for both mosquito- and tick-borne flaviviruses in addition to SARS-CoV-2. Using an innovative flavivirus protein expression system, we demonstrate for the first time the impact of the loss of RACK1 on the formation of viral replication factories known as 'vesicle packets' (VPs). In addition, we show that RACK1 can interact with numerous flavivirus NS1 proteins as a potential mechanism by which VP formation can be induced by the former.

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