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A short RNA stem-loop is necessary and sufficient for repression of gene expression during early logarithmic phase in trypanosomes.

Fernández-Moya SM, Carrington M, Estévez AM - Nucleic Acids Res. (2014)

Bottom Line: We have compared the transcriptomes of cultured procyclic Trypanosoma brucei cells in early and late logarithmic phases and found that ∼200 mRNAs were differentially regulated.When placed in the 3'-UTR of an unregulated transcript, the cis-element is sufficient to confer regulation in response to purines.To our knowledge, this is the first example of a discrete RNA element that can autonomously regulate gene expression in trypanosomes in response to an external factor and reveals an unprecedented purine-dependent signaling pathway that controls gene expression in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento, s/n, 18016 Armilla, Granada, Spain.

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The transcriptome of procyclic T. brucei is remodeled during the growth curve. (A) Typical growth curve of procyclic T. brucei cells. RNA samples were obtained from cells in early and late logarithmic phases, and subjected to high-throughput sequencing. (B) List of mRNAs whose abundance is altered at least ± 2.5-fold (log2 = ±1.3) in late log phase. Transcripts encoding hypothetical proteins are not shown. A complete list can be found in Supplementary Table S1. (C) Gene Ontology (GO) analysis of mRNAs upregulated in late log phase. Only significantly enriched categories (P < 0.01) are shown.
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Figure 1: The transcriptome of procyclic T. brucei is remodeled during the growth curve. (A) Typical growth curve of procyclic T. brucei cells. RNA samples were obtained from cells in early and late logarithmic phases, and subjected to high-throughput sequencing. (B) List of mRNAs whose abundance is altered at least ± 2.5-fold (log2 = ±1.3) in late log phase. Transcripts encoding hypothetical proteins are not shown. A complete list can be found in Supplementary Table S1. (C) Gene Ontology (GO) analysis of mRNAs upregulated in late log phase. Only significantly enriched categories (P < 0.01) are shown.

Mentions: To analyze how the transcriptome of procyclic trypanosomes is remodeled during the growth cycle in culture, we prepared RNA samples from early and late logarithmic phase cells (Figure 1A) and compared them using deep sequencing. There were ∼200 transcripts with at least 2-fold altered abundance in late logarithmic phase, of which 80 were upregulated and 117 downregulated. A list of the top (>2.5-fold) regulated transcripts with known or predicted functions is shown in Figure 1B. The complete list of all regulated transcripts, including hypothetical proteins, can be found in Supplementary Table S1.


A short RNA stem-loop is necessary and sufficient for repression of gene expression during early logarithmic phase in trypanosomes.

Fernández-Moya SM, Carrington M, Estévez AM - Nucleic Acids Res. (2014)

The transcriptome of procyclic T. brucei is remodeled during the growth curve. (A) Typical growth curve of procyclic T. brucei cells. RNA samples were obtained from cells in early and late logarithmic phases, and subjected to high-throughput sequencing. (B) List of mRNAs whose abundance is altered at least ± 2.5-fold (log2 = ±1.3) in late log phase. Transcripts encoding hypothetical proteins are not shown. A complete list can be found in Supplementary Table S1. (C) Gene Ontology (GO) analysis of mRNAs upregulated in late log phase. Only significantly enriched categories (P < 0.01) are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4066783&req=5

Figure 1: The transcriptome of procyclic T. brucei is remodeled during the growth curve. (A) Typical growth curve of procyclic T. brucei cells. RNA samples were obtained from cells in early and late logarithmic phases, and subjected to high-throughput sequencing. (B) List of mRNAs whose abundance is altered at least ± 2.5-fold (log2 = ±1.3) in late log phase. Transcripts encoding hypothetical proteins are not shown. A complete list can be found in Supplementary Table S1. (C) Gene Ontology (GO) analysis of mRNAs upregulated in late log phase. Only significantly enriched categories (P < 0.01) are shown.
Mentions: To analyze how the transcriptome of procyclic trypanosomes is remodeled during the growth cycle in culture, we prepared RNA samples from early and late logarithmic phase cells (Figure 1A) and compared them using deep sequencing. There were ∼200 transcripts with at least 2-fold altered abundance in late logarithmic phase, of which 80 were upregulated and 117 downregulated. A list of the top (>2.5-fold) regulated transcripts with known or predicted functions is shown in Figure 1B. The complete list of all regulated transcripts, including hypothetical proteins, can be found in Supplementary Table S1.

Bottom Line: We have compared the transcriptomes of cultured procyclic Trypanosoma brucei cells in early and late logarithmic phases and found that ∼200 mRNAs were differentially regulated.When placed in the 3'-UTR of an unregulated transcript, the cis-element is sufficient to confer regulation in response to purines.To our knowledge, this is the first example of a discrete RNA element that can autonomously regulate gene expression in trypanosomes in response to an external factor and reveals an unprecedented purine-dependent signaling pathway that controls gene expression in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento, s/n, 18016 Armilla, Granada, Spain.

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