6 results on '"DeRisi JL"'
Search Results
2. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation.
- Author
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Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, and Fanidi A
- Subjects
- Apoptosis drug effects, Apoptosis genetics, Cell Cycle Checkpoints drug effects, Cell Cycle Checkpoints genetics, Cell Line, Tumor, DEAD-box RNA Helicases antagonists & inhibitors, DEAD-box RNA Helicases metabolism, Eukaryotic Initiation Factor-4A antagonists & inhibitors, Eukaryotic Initiation Factor-4A metabolism, Gene Expression Regulation, Neoplastic, Humans, Protein Biosynthesis drug effects, Protein Biosynthesis physiology, RNA, Messenger metabolism, Triterpenes pharmacology, DEAD-box RNA Helicases physiology, Eukaryotic Initiation Factor-4A physiology, Transcriptome drug effects
- Abstract
Background: Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amplify production of pro-growth and pro-survival factors. Convergence of these signals on eIF4F positions this factor as a gatekeeper of malignant fate. While the oncogenic properties of eIF4F have been characterized, genome-wide evaluation of eIF4F translational output is incomplete yet critical for developing novel translation-targeted therapies., Results: To understand the impact of eIF4F on malignancy, we utilized a genome-wide ribosome profiling approach to identify eIF4F-driven mRNAs in MDA-MB-231 breast cancer cells. Using Silvestrol, a selective eIF4A inhibitor, we identify 284 genes that rely on eIF4A for efficient translation. Our screen confirmed several known eIF4F-dependent genes and identified many unrecognized targets of translation regulation. We show that 5′UTR complexity determines Silvestrol-sensitivity and altering 5′UTR structure modifies translational output. We highlight physiological implications of eIF4A inhibition, providing mechanistic insight into eIF4F pro-oncogenic activity., Conclusions: Here we describe the transcriptome-wide consequence of eIF4A inhibition in malignant cells, define mRNA features that confer eIF4A dependence, and provide genetic support for Silvestrol’s anti-oncogenic properties. Importantly, our results show that eIF4A inhibition alters translation of an mRNA subset distinct from those affected by mTOR-mediated eIF4E inhibition. These results have significant implications for therapeutically targeting translation and underscore a dynamic role for eIF4F in remodeling the proteome toward malignancy.
- Published
- 2014
- Full Text
- View/download PDF
3. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
- Author
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Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, and Chan SW
- Subjects
- Animals, Base Sequence, Molecular Sequence Data, Plants genetics, Species Specificity, Centromere genetics, Evolution, Molecular, Tandem Repeat Sequences
- Abstract
Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data., Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution., Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.
- Published
- 2013
- Full Text
- View/download PDF
4. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.
- Author
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Shock JL, Fischer KF, and DeRisi JL
- Subjects
- Animals, Genome, Protozoan, Half-Life, RNA, Messenger metabolism, RNA, Protozoan metabolism, Erythrocytes parasitology, Gene Expression Regulation, Developmental, Genes, Protozoan, Plasmodium falciparum genetics, Plasmodium falciparum growth & development, RNA Stability
- Abstract
Background: The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression., Results: We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes., Conclusion: Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.
- Published
- 2007
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5. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
- Author
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Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, and DeRisi JL
- Subjects
- Algorithms, DNA, Viral genetics, HeLa Cells, Humans, Phylogeny, Research Design, Species Specificity, Computational Biology methods, Oligonucleotide Array Sequence Analysis, Software
- Abstract
DNA microarrays may be used to identify microbial species present in environmental and clinical samples. However, automated tools for reliable species identification based on observed microarray hybridization patterns are lacking. We present an algorithm, E-Predict, for microarray-based species identification. E-Predict compares observed hybridization patterns with theoretical energy profiles representing different species. We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications.
- Published
- 2005
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6. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.
- Author
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Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, and DeRisi JL
- Subjects
- Animals, Blotting, Northern, Plasmodium falciparum growth & development, RNA, Protozoan genetics, RNA, Protozoan metabolism, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis methods, Plasmodium falciparum genetics
- Abstract
Background: The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development., Results: We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages., Conclusions: DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.
- Published
- 2003
- Full Text
- View/download PDF
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