The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
Open accessAbstract
African trypanosomes are major pathogens of humans and livestock and represent a model for studies of unusual protozoal biology. We describe a high-throughput phenotyping approach termed RNA interference (RNAi) target sequencing, or RIT-seq that, using Illumina sequencing, maps fitness-costs associated with RNAi. We scored the abundance of >90,000 integrated RNAi targets recovered from trypanosome libraries before and after induction of RNAi. Data are presented for 7435 protein coding sequences, >99% of a non-redundant set in the Trypanosoma brucei genome. Analysis of bloodstream and insect life-cycle stages and differentiated libraries revealed genome-scale knockdown profiles of growth and development, linking thousands of previously uncharacterized and “hypothetical” genes to essential functions. Genes underlying prominent features of trypanosome biology are highlighted, including the constitutive emphasis on post-transcriptional gene expression control, the importance of flagellar motility and glycolysis in the bloodstream, and of carboxylic acid metabolism and phosphorylation during differentiation from the bloodstream to the insect stage. The current data set also provides much needed genetic validation to identify new drug targets. RIT-seq represents a versatile new tool for genome-scale functional analyses and for the exploitation of genome sequence data.
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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
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The Genome of the African Trypanosome Trypanosoma brucei
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Self-citationThe Genome Sequence of Trypanosoma cruzi , Etiologic Agent of Chagas Disease
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Self-citationThe Genome of the Kinetoplastid Parasite, Leishmania major
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Self-citationThe Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes
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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
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SSAHA: A Fast Search Method for Large DNA Databases
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Comparative Genomics of Trypanosomatid Parasitic Protozoa
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Tissue tropism in parasitic diseases
Silva Pereira, S., Trindade, S., De Niz, M., & Figueiredo, L. M. (2019) · Open Biology · doi:10.1098/rsob.190036 · Cited by 85
Trypanosomatid parasites rescue heme from endocytosed hemoglobin through lysosomal HRG transporters
Cabello‐Donayre, M., Malagarie‐Cazenave, S., Campos‐Salinas, J., Gálvez, F. J., Rodríguez‐Martínez, A., Pineda‐Molina, E., Orrego, L. M., Martínez‐García, M., Sánchez‐Cañete, M. P., Estévez, A. M., et al. (2016) · Molecular Microbiology · doi:10.1111/mmi.13430 · Cited by 37
Mechanisms of life cycle simplification in African trypanosomes
Oldrieve, G. R., Venter, F., Cayla, M., Verney, M., Hébert, L., Geerts, M., Van Reet, N., & Matthews, K. R. (2024) · Nature Communications · doi:10.1038/s41467-024-54555-w · Cited by 5
Metadata
- Authors
- Alsford, S., Turner, D. J., Obado, S. O., Sanchez-Flores, A., Glover, L., Berriman, M., Hertz-Fowler, C., & Horn, D.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-03-01
- Volume
- 21
- Issue
- 6
- Pages
- 915-924
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2158427156
- Cited by
- 470
- References
- 41
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Alsford, S., Turner, D. J., Obado, S. O., Sanchez-Flores, A., Glover, L., Berriman, M., Hertz-Fowler, C., & Horn, D. (2011). High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Research. https://doi.org/10.1101/gr.115089.110
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