scholarly journals RNA Interference Can Target Pre-mRNA: Consequences for Gene Expression in a Caenorhabditis elegans Operon

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1245-1256
Author(s):  
Julia M Bosher ◽  
Pascale Dufourcq ◽  
Satis Sookhareea ◽  
Michel Labouesse
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Gene Function ◽  
Direct Evidence ◽  
Embryonic Lethality ◽  
Null Mutation ◽  
Null Mutant ◽  
Double Stranded Rna ◽  
Severe Loss

Abstract In nematodes, flies, trypanosomes, and planarians, introduction of double-stranded RNA results in sequence-specific inactivation of gene function, a process termed RNA interference (RNAi). We demonstrate that RNAi against the Caenorhabditis elegans gene lir-1, which is part of the lir-1/lin-26 operon, induced phenotypes very different from a newly isolated lir-1 null mutation. Specifically, lir-1(RNAi) induced embryonic lethality reminiscent of moderately strong lin-26 alleles, whereas the lir-1 null mutant was viable. We show that the lir-1(RNAi) phenotypes resulted from a severe loss of lin-26 gene expression. In addition, we found that RNAi directed against lir-1 or lin-26 introns induced similar phenotypes, so we conclude that lir-1(RNAi) targets the lir-1/lin-26 pre-mRNA. This provides direct evidence that RNA interference can prevent gene expression by targeting nuclear transcripts. Our results highlight that caution may be necessary when interpreting RNA interference without the benefit of mutant alleles.

scholarly journals Stimulation of later functions of the yeast meiotic protein kinase Ime2p by the IDS2 gene product.

1995 ◽  
Vol 15 (10) ◽  
pp. 5279-5287 ◽  
Author(s):  
R A Sia ◽  
A P Mitchell
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Functional Relationship ◽  
Null Mutation ◽  
Null Mutant ◽  
Meiotic Gene ◽  
Late Genes ◽  
Gal1 Promoter ◽  
New Gene ◽  
Stimulation Of

Ime2p is a protein kinase that is expressed only during meiosis in Saccharomyces cerevisiae. Ime2p stimulates early, middle, and late meiotic gene expression and down-regulates expression of IME1, which specifies an activator of early meiotic genes that acts independently of Ime2p. We have identified a new gene, IDS2 (for IME2-dependent signaling), which has a functional relationship to Ime2p. An ids2 null mutation delays down-regulation of IME1 and expression of middle and late meiotic genes. In an ime1 null mutant that express IME2 from the GAL1 promoter (ime1 delta PGAL1-IME2 mutant), early meiotic gene expression depends only upon Ime2p. In such strains, Ids2p is dispensable for expression of the early genes HOP1 and SPO13 but is essential for expression of the middle and late genes SPS1, SPS2, and SPS100. Ids2p is also essential for the autoregulatory pathway through which Ime2p activates its own expression via the IME2 upstream activation sequences (UAS). An PGAL1-IME2 derivative that produces a truncated Ime2p (lacking its C-terminal 174 residues) permits IME2 UAS activation in the absence of Ids2p. This observation suggests that Ids2p acts upstream of Ime2p or that Ids2p and Ime2p act in independent, convergent pathways to stimulate IME2 UAS activity. Accumulation of epitope-tagged Ids2p derivatives is greatest in growing cells and declines during meiosis. We propose that Ids2p acts indirectly to modify Ime2p activity, thus permitting Ime2p to carry out later meiotic functions.

scholarly journals New strains for tissue-specific RNAi studies in Caenorhabditis elegans

2018 ◽  
Author(s):  
Jason S. Watts ◽  
Henry F. Harrison ◽  
Shizue Omi ◽  
Quentin Guenthers ◽  
James Dalelio ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Caenorhabditis Elegans ◽  
Gene Function ◽  
Target Genes ◽  
Resistant Mutant ◽  
Knockout Mutant ◽  
Tissue Specific ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Insight Into

AbstractRNA interference is a powerful tool for dissecting gene function. In Caenorhabditis elegans, ingestion of double stranded RNA causes strong, systemic knockdown of target genes. Further insight into gene function can be revealed by tissue-specific RNAi techniques. Currently available tissue-specific C. elegans strains rely on rescue of RNAi function in a desired tissue or cell in an otherwise RNAi deficient genetic background. We attempted to assess the contribution of specific tissues to polyunsaturated fatty acid (PUFA) synthesis using currently available tissue-specific RNAi strains. We discovered that rde-1 (ne219), a commonly used RNAi-resistant mutant strain, retains considerable RNAi capacity against RNAi directed at PUFA synthesis genes. By measuring changes in the fatty acid products of the desaturase enzymes that synthesize PUFAs, we found that the before mentioned strain, rde-1 (ne219) and the reported germline only RNAi strain, rrf-1 (pk1417) are not appropriate genetic backgrounds for tissue-specific RNAi experiments. However, the knockout mutant rde-1 (ne300) was strongly resistant to dsRNA induced RNAi, and thus is more appropriate for construction of a robust tissue-specific RNAi strains. Using newly constructed strains in the rde-1(null) background, we found considerable desaturase activity in intestinal, epidermal, and germline tissues, but not in muscle. The RNAi-specific strains reported in this study will be useful tools for C. elegans researchers studying a variety of biological processes.

Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference

2005 ◽  
Vol 25 (5-6) ◽  
pp. 299-307 ◽  
Author(s):  
Angelo Fortunato ◽  
Andrew G. Fraser
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Gene Function ◽  
Genetic Interactions ◽  
Loss Of Function ◽  
Future Directions ◽  
C Elegans ◽  
Genomics Tools ◽  
Almost All ◽  
Nematode Worm

RNA-mediated interference (RNAi) has emerged recently as one of the most powerful functional genomics tools. RNAi has been particularly effective in the nematode worm C. elegans where RNAi has been used to analyse the loss-of-function phenotypes of almost all predicted genes. In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner.

Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain

2004 ◽  
Vol 18 (3) ◽  
pp. 331-339 ◽  
Author(s):  
Dan Zhou ◽  
Jin Xue ◽  
Orit Gavrialov ◽  
Gabriel G. Haddad
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
Global Gene Expression ◽  
Brain Regions ◽  
Inhibitory Effect ◽  
Null Mouse ◽  
Null Mutation ◽  
Null Mutant ◽  
Altered Expression ◽  
Null Mutant Mice

Na+/H+ exchanger 1 (NHE1) is well known to function as a major regulator of intracellular pH (pHi). It is activated by low pHi and exchanges extracellular Na+ for intracellular H+ to maintain cellular homeostasis. Despite the fact that we now have evidence suggesting other roles for NHE1, there has been no comprehensive study investigating its role as a signaling molecule. Toward this aim, we used in this study NHE1 null mutant mice and cDNA microarrays to investigate the effects of NHE1 on global gene expression in various regions of the brain, e.g., cortex, hippocampus, brain stem-diencephalon, and cerebellum. We found that a total of 35 to 79 genes were up- or downregulated in each brain region, with the majority being downregulated. The effect of NHE1 null mutation on gene expression is region specific, and only 11 genes were changed in all brain regions studied. Further analysis of the cis-regulatory regions of downregulated genes revealed that transcription suppressors, BCL6 and E4BP4, were probable candidates that mediated the inhibitory effect of NHE1 null mutation. One of the genes, MCT-13, was not only downregulated in the NHE1 null mutant brain but also in tissue cultures treated with an NHE1 inhibitor. We conclude that 1) a relatively small number of genes were altered in the NHE1 null mouse brain; 2) the effects of NHE1 null mutation on gene expression are region specific; and 3) several genes implicated in neurodegeneration have altered expression, potentially offering a molecular explanation for the phenotype of the NHE1 null mouse.

scholarly journals RNAi targeting Caenorhabditis elegans α-arrestins has little effect on lifespan

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1515
Author(s):  
Sangsoon Park ◽  
Yoonji Jung ◽  
Seon Woo A. An ◽  
Heehwa G. Son ◽  
Wooseon Hwang ◽  
...  
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Functional Role ◽  
Future Research ◽  
Biological Processes ◽  
Receptor Desensitization ◽  
Double Stranded Rna ◽  
C Elegans

Background: α-arrestins are a family of proteins that are implicated in multiple biological processes, including metabolism and receptor desensitization. Methods: Here, we sought to examine the roles of α-arrestins in the longevity of Caenorhabditis elegans through an RNA interference screen. Results: We found that feeding worms with bacteria expressing double-stranded RNA against each of 24 out of total 29 C. elegans α-arrestins had little effect on lifespan. Thus, individual C. elegans α-arrestins may have minor effects on longevity. Conclusions: This study will provide useful information for future research on the functional role of α-arrestins in aging and longevity.

3. RNA

2016 ◽  
Author(s):  
Aysha Divan ◽  
Janice A. Royds
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Rna Interference ◽  
Ribosomal Rna ◽  
Gene Function ◽  
Transfer Rna ◽  
Vast Number ◽  
Rna Molecules ◽  
Catalytic Rnas ◽  
Non Coding Rnas

The first RNA molecules to be discovered were those involved in protein synthesis, mRNA, transfer RNA (tRNA), and ribosomal RNA (rRNA). In recent years, a vast number of additional RNA molecules have been identified. ‘RNA’ explains that these are non-coding RNAs that are not involved in protein synthesis, but influence many normal cellular and disease processes by regulating gene expression. RNA interference (RNAi) as one of the main ways in which gene expression is regulated is described with applications to therapy. Classes of RNA, including long non-coding RNAs and catalytic RNAs, are explained along with RNA techniques used to study RNA molecule and gene function.

scholarly journals A gene-specific T2A-GAL4 library for Drosophila

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Pei-Tseng Lee ◽  
Jonathan Zirin ◽  
Oguz Kanca ◽  
Wen-Wen Lin ◽  
Karen L Schulze ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Function ◽  
High Sensitivity ◽  
Polyadenylation Signal ◽  
Loss Of Function ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Severe Loss ◽  
Lethal Mutations ◽  
Cdna Construct

We generated a library of ~1000 Drosophila stocks in which we inserted a construct in the intron of genes allowing expression of GAL4 under control of endogenous promoters while arresting transcription with a polyadenylation signal 3’ of the GAL4. This allows numerous applications. First, ~90% of insertions in essential genes cause a severe loss-of-function phenotype, an effective way to mutagenize genes. Interestingly, 12/14 chromosomes engineered through CRISPR do not carry second-site lethal mutations. Second, 26/36 (70%) of lethal insertions tested are rescued with a single UAS-cDNA construct. Third, loss-of-function phenotypes associated with many GAL4 insertions can be reverted by excision with UAS-flippase. Fourth, GAL4 driven UAS-GFP/RFP reports tissue and cell-type specificity of gene expression with high sensitivity. We report the expression of hundreds of genes not previously reported. Finally, inserted cassettes can be replaced with GFP or any DNA. These stocks comprise a powerful resource for assessing gene function.

scholarly journals RNA interference: advances and questions

2002 ◽  
Vol 357 (1417) ◽  
pp. 65-70 ◽  
Author(s):  
Elisabetta Ullu ◽  
Appolinaire Djikeng ◽  
Huafang Shi ◽  
Christian Tschudi
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Trypanosoma Brucei ◽  
Gene Function ◽  
Protozoan Parasite ◽  
Transcriptional Gene Silencing ◽  
Eukaryotic Lineage ◽  
Powerful Method ◽  
Double Stranded Rna ◽  
Post Transcriptional Gene Silencing

In animals and protozoa gene–specific double–stranded RNA triggers the degradation of homologous cellular RNAs, the phenomenon of RNA interference (RNAi). RNAi has been shown to represent a novel paradigm in eukaryotic biology and a powerful method for studying gene function. Here we discuss RNAi in terms of its mechanism, its relationship to other post–transcriptional gene silencing phenomena in plants and fungi, its connection to retroposon silencing and possibly to translation, and its biological role. Among the organisms where RNAi has been demonstrated the protozoan parasite Trypanosoma brucei represents the most ancient branch of the eukaryotic lineage. We provide a synopsis of what is currently known about RNAi in T. brucei and outline the recent advances that make RNAi the method of choice to disrupt gene function in these organisms.

Targeted suppression of E-cadherin gene expression in bovine preimplantation embryo by RNA interference technology using double-stranded RNA

2006 ◽  
Vol 73 (2) ◽  
pp. 153-163 ◽  
Author(s):  
Korakot Nganvongpanit ◽  
Heike Müller ◽  
Franca Rings ◽  
Markus Gilles ◽  
Danyel Jennen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Preimplantation Embryo ◽  
Double Stranded Rna ◽  
E Cadherin

scholarly journals Engineered symbionts activate honey bee immunity and limit pathogens

Science ◽  
2020 ◽  
Vol 367 (6477) ◽  
pp. 573-576 ◽  
Author(s):  
Sean P. Leonard ◽  
J. Elijah Powell ◽  
Jiri Perutka ◽  
Peng Geng ◽  
Luke C. Heckmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Immune Responses ◽  
Honey Bees ◽  
Host Gene Expression ◽  
Colony Losses ◽  
New Approach ◽  
Double Stranded Rna ◽  
Bee Health ◽  
Rnai Response

Honey bees are essential pollinators threatened by colony losses linked to the spread of parasites and pathogens. Here, we report a new approach for manipulating bee gene expression and protecting bee health. We engineered a symbiotic bee gut bacterium, Snodgrassella alvi, to induce eukaryotic RNA interference (RNAi) immune responses. We show that engineered S. alvi can stably recolonize bees and produce double-stranded RNA to activate RNAi and repress host gene expression, thereby altering bee physiology, behavior, and growth. We used this approach to improve bee survival after a viral challenge, and we show that engineered S. alvi can kill parasitic Varroa mites by triggering the mite RNAi response. This symbiont-mediated RNAi approach is a tool for studying bee functional genomics and potentially for safeguarding bee health.

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