J. K. Wickiser Lab

Posts Tagged ‘Genetic Control’

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The essential genome of a bacterium: wants versus needs.

Tuesday, October 11, 2011

Lucy Shaprio and colleagues have identifed the minimal set of genes required for caulobacter to thrive on rich media. This work will help others bioengineer the organism to function in a variety of roles involving the production of small molecule metabolites and the generation of biosensor systems.

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Gene regulatory network inference: data integration in dynamic models-a review.

Wednesday, September 7, 2011

This review documents advances in the construction of Gene Regulatory Networks.

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Posted in Network Science, Review Paper | No Comments »

Global pattern of pairwise relationship in genetic network.

Monday, August 29, 2011

Gene-gene interactions pose a difficult problem for biologists to study int he context of an entire system (rather than a reductionist approach). Here’s a Genetic Networks paper detailing the challenge and some advances.

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Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques.

Friday, August 26, 2011

This review details a paper on the role of micro RNAs within gene regulatory networks. It’s hard to believe that this entire field science is only about 10 years old.

“This paper is very worth reading as it provides a new and more precise vision on the complex interrelationship between regulatory networks of messenger RNAs (mRNAs) and micro RNAs (miRNAs). Using integrative genomics approaches in the mouse liver, the authors identified a new role for ~30% of all known mouse miRNAs, which appear as highly connected hubs finely tuned by positive as well as negative feedback loops and by changes in mRNA expression levels.

MiRNAs are small, non-coding RNA molecules, which regulate the expression of target genes by annealing to the 3’-untranslated region of their mRNA. MiRNAs have been implicated in various key biological processes such as metabolism and immunity, in cancer and cardiovascular diseases. Predictions estimate that more than one third of all human genes are regulated by miRNAs encoded by ~3% of the human genome. As miRNA sequences became available, the majority of research groups opted for a combination of computational and experimental approaches to first predict the target mRNA molecules in silico and to further validate the findings in in vivo settings. However, even the most powerful computational programs used in the field currently display very high false-positive and false-negative rates.

Recently, the combination of gene expression profiling and classical genetic approaches led to the identification of the molecular causes of some complex phenotypes. In this paper, Su et al. report the first demonstration of how an integrative genomics approach can be used to study the regulation of miRNA expression and the miRNA-dependent modulation of gene expression. When examining in detail the expression of 187 miRNAs in the liver of mice of known genotypes, the authors ran into a series of surprising and unexpected findings: (1) they found a link between DNA sequence variation and miRNA expression variation similar to that known for mRNA expression; (2) in contrast to the widely accepted concept that miRNAs downregulate gene expression they observed that a large proportion of miRNAs are positively correlated to the abundance of their target mRNAs, suggesting the existence of complex feedback loops; (3) the set of protein coding gene transcripts predicted to regulate the abundance of a given miRNA exceeds in number that of its downstream target mRNAs; the relevance of this novel miRNA/mRNA hierarchy was confirmed through simulation experiments indicating overestimation of the number of predicted miRNAs and underestimation of the number of predicted miRNA regulators; (4) finally, they observed that miRNAs were often correlated with mRNA transcripts encoding proteins associated in a given pathway, nearly a quarter of them being associated to cell cycle regulation in the liver.

This study, thus, presents a new perspective on the regulatory roles of miRNAs by investigating, for the first time, their predicted causal regulators in addition to their classical mRNA targets. In this context, miRNAs are viewed as sensing changes in the level of expression of complex networks of mRNAs, modulating specific subsets of them in a reciprocal and interconnected fashion. If expanded in other studies using next-generation sequencing technologies, integrative genomics approaches have the potential to elucidate the circuitries of novel RNA-dependent mechanisms that regulate complex phenotypes. For example, they could explain how competition between gene and pseudogene transcripts results in buffering miRNA activity, providing an experimental basis for the groundbreaking competitive endogenous RNA (ceRNA) theory {1}.

References:
{1} Poliseno et al. Nature 2010, 465:1033-8 [PMID:20577206].
Competing interests: None declared”

Cite this evaluation
Vinciguerra M, Auffray C: “This paper is very worth reading as it provides a new and more precise vision…” Evaluation of: [Su WL et al. Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol. 2011 May 24; 7:490; doi: 10.1038/msb.2011.23]. Faculty of 1000, 13 Jul 2011. F1000.com/11351957

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Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins.

Wednesday, August 24, 2011

Here are two reviews of a cool paper detailing synthetic RNA switches in the cell.

“I found this paper interesting because the authors describe an innovative step towards engineering a regulatory system that can change the expression of targeted genes.

More importantly, their system senses specific endogenous signals defined by users and responds by directing the cells to an alternative behavior. Indeed, they showed that endogenous signalling pathways can be rerouted to induce novel cellular phenotypes, including apoptosis. Their sensing device is an RNA aptamer that, upon binding to a specific protein, changes its structure and function to modulate the alternative spicing of the gene in which it has been inserted. Their work emphasizes the efficacy and versatility of RNA aptamers for engineering gene regulation systems and hence for gene therapy.
Competing interests: None declared”

Cite this evaluation
DesGroseillers L: “I found this paper interesting because the authors describe an innovative step towards engineering a…” Evaluation of: [Culler SJ et al. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010 Nov 26; 330(6008):1251-5; doi: 10.1126/science.1192128]. Faculty of 1000, 03 Feb 2011. F1000.com/7626956

“Molecular biologists usually alter cellular functions by overexpressing, mutating, or knocking down components of transcription factor and signal transduction networks. However, a method for reprogramming cellular behavior in response to any user-defined component of endogenous signaling networks would provide an important tool both for measuring the activities of these networks and using them to tailor cellular function. Culler et al. have managed to devise such a method by engineering what they call, “RNA-based sensing actuation devices”.

Basically, these devices comprise a three-exon mini-gene with two introns. The middle exon includes a translational stop codon that prevents translation of the open reading frame (ORF) encoded in the 3’-most exon. The critical component in this system is an RNA aptamer incorporated into the intronic sequences flanking the middle exon. The aptamer is first generated by in vitro selection to bind to a specific protein ligand. The authors show that association of the specific ligand with the inserted aptamer can act to alternatively splice the mini-gene such that the middle exon containing the stop codon is either included or excluded. The mechanism through which aptamer-ligand interaction influences splicing is unclear and the exact position of the aptamer within the intronic sequences required to trigger alternative splicing must be determined empirically for each aptamer. In principle, these devices could be employed to sense any endogenous protein and to respond by expressing any protein encoded in the 3’ exon ORF.

The authors provide several compelling demonstrations that their sensing devices work quite well. For example, inclusion of an aptamer that binds phage MS2 coat protein results in expression of the green florescent protein (GFP) signal encoded in the 3’ exon ORF in response to expression of the coat protein. Moreover, treatment of cells with exogenous factors that stimulate endogenous nuclear factor kappa B (NFkB)- or Wnt-signaling pathways also produce a robust GFP signal from mini-genes with aptamers binding NFkB p65 or beta-catenin, respectively. They also show that insertion of two aptamers can increase the response and that, at least in some cases, multiple ligands act to evoke a synergistic response. Lastly, they demonstrate that the system can be employed to regulate cell fate decisions. Thus, a mini-gene designed to ‘sense’ beta-catenin and produce the herpes simplex virus thymidine kinase from the 3’ ORF will trigger cell death in the presence of Wnt ligand and the pro-drug Ganciclovir.

This work underscores the versatility of RNA as both a biological sensor and regulator and suggests that the engineering of synthetic networks is within reach (also see related perspective by Liu and Arkin {1}).

References:
{1} Liu and Arkin, Science 2010, 330:1185-6 [PMID:21109657].
Competing interests: None declared”

Cite this evaluation
Eisenman R: “Molecular biologists usually alter cellular functions by overexpressing, mutating, or knocking down components of transcription…” Evaluation of: [Culler SJ et al. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010 Nov 26; 330(6008):1251-5; doi: 10.1126/science.1192128]. Faculty of 1000, 19 Jan 2011. F1000.com/7626956

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The Reactivity of the Cellular Transcriptome to Xenobiotic Compound Perturbation

Tuesday, August 23, 2011

This looks like it’ll be a very cool meeting at NYAS.

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Posted in Announcements & Admin | No Comments »

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

Friday, August 19, 2011

Here’s an evaluation of from the Faculty of 1000.

“Here is a method for determining, in a single experiment, rates of synthesis and decay of mRNAs, individually or genome-wide.

Modifying previously published procedures, the authors use 4-thiouridine (4-thio-U) for pulse-labeling newly synthesized RNA in mammalian cells. After RNA isolation, RNA containing 4-thio-U is selectively biotinylated. This newly synthesized RNA is separated from ‘old’ RNA, and all three fractions — total, new and old — can be analyzed, e.g. by microarrays. Rates of synthesis and decay are obtained from simple equations. The method can potentially replace separate determinations of synthesis and decay rates. Nuclear run-on experiments to determine rates of synthesis are tedious and based on assumptions. Actinomycin-D time courses for analysis of RNA decay run the risk of interfering with the process that is to be measured and cannot measure long half-lives reliably. Actinomycin-D can be avoided through the use of regulated promoters, but this almost invariably requires a separate construct to be made for every transcript to be examined. 4-thio-U labeling looks like an attractive alternative.

For a recent application of the procedure and its adaptation to Saccharomyces cerevisiae, please see ref. {1}.

References:
{1} Miller et al. Mol Syst Biol 2011, 7:458 [PMID:21206491].
Competing interests: None declared”

Citation:
Wahle E: “Here is a method for determining, in a single experiment, rates of synthesis and decay…” Evaluation of: [Dölken L et al. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA. 2008 Sep; 14(9):1959-72; doi: 10.1261/rna.1136108]. Faculty of 1000, 18 Apr 2011. F1000.com/9679960

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Posted in Current Data Papers, Network Science | No Comments »

Ghost of ancestor’s genes lingers: Antiobesity DNA is absent, but its benefits to mice remain

Tuesday, August 16, 2011

From Hannah Lachance (just before she headed right back up to UVM: An article in the April issue of Science News discusses the study of a gene that prevents mice from gaining weight even when on a high intake rich diet. Mice with this gene can eat as much as they want and they remain skinny even though they eat more and exercise less than the control group of mice which don’t have this gene and don’t have any ancestors that have this gene. The mice that are prone to obesity can have the DNA containing this gene injected successfully; they can eat as much as they want and they will not become obese. Researchers discovered that mice who don’t pass this gene on to their off-spring still have decedents up to 3 generations later that exhibit the effects of the gene. This is currently being explained by saying the gene passed on a “ghostly imprint” which is causing the effects to persist. Researchers aren’t exactly sure how this is occurring but they think it might in part be due to a change in the way that small pieces of RNA regulate protein production.

Science News article

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siRNA knockdown of mosquito sperm

Monday, August 15, 2011

Dylan Russell saw this story in the lay press:

http://io9.com/5828814/scientists-create-spermless-males-to-fight-the-spread-of-malaria

To produce the sterile male mosquitos, researchers targeted a sperm production gene using siRNA. The sterile males then mated with females and because females mate only once in their lifetime, shutdown the life cycle of the disease vector. Cool stuff and very promising research.

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Posted in Current Data Papers, Science in the Lay Press | No Comments »

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