Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome.
The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription. The RNA editing process is directed by guide RNAs (gRNAs) that encode the information for the specific insertion and deletion of uridylates required to generate translata...
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ftdoajarticles:oai:doaj.org/article:dd977516774740f587916e8a5f96efcc 2023-05-15T15:10:31+02:00 Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. Laura E Kirby Yanni Sun David Judah Scooter Nowak Donna Koslowsky 2016-07-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0004793 https://doaj.org/article/dd977516774740f587916e8a5f96efcc EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4939953?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0004793 https://doaj.org/article/dd977516774740f587916e8a5f96efcc PLoS Neglected Tropical Diseases, Vol 10, Iss 7, p e0004793 (2016) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2016 ftdoajarticles https://doi.org/10.1371/journal.pntd.0004793 2022-12-31T13:04:06Z The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription. The RNA editing process is directed by guide RNAs (gRNAs) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRNAs. We have deep sequenced the gRNA transcriptome from the bloodstream form of the EATRO 164 cell line. Using conventionally accepted fully edited mRNA sequences, ~1 million gRNAs were identified. In contrast, over 3 million reads were identified in our insect stage gRNA transcriptome. A comparison of the two life cycle transcriptomes show an overall ratio of procyclic to bloodstream gRNA reads of 3.5:1. This ratio varies significantly by gene and by gRNA populations within genes. The variation in the abundance of the initiating gRNAs for each gene, however, displays a trend that correlates with the developmental pattern of edited gene expression. A comparison of related major classes from each transcriptome revealed a median value of ten single nucleotide variations per gRNA. Nucleotide variations were much less likely to occur in the consecutive Watson-Crick anchor region, indicating a very strong bias against G:U base pairs in this region. This work indicates that gRNAs are expressed during both life cycle stages, and that differential editing patterns observed for the different mitochondrial mRNA transcripts are not due to the presence or absence of gRNAs. However, the abundance of certain gRNAs may be important in the developmental regulation of RNA editing. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 10 7 e0004793 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Laura E Kirby Yanni Sun David Judah Scooter Nowak Donna Koslowsky Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription. The RNA editing process is directed by guide RNAs (gRNAs) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRNAs. We have deep sequenced the gRNA transcriptome from the bloodstream form of the EATRO 164 cell line. Using conventionally accepted fully edited mRNA sequences, ~1 million gRNAs were identified. In contrast, over 3 million reads were identified in our insect stage gRNA transcriptome. A comparison of the two life cycle transcriptomes show an overall ratio of procyclic to bloodstream gRNA reads of 3.5:1. This ratio varies significantly by gene and by gRNA populations within genes. The variation in the abundance of the initiating gRNAs for each gene, however, displays a trend that correlates with the developmental pattern of edited gene expression. A comparison of related major classes from each transcriptome revealed a median value of ten single nucleotide variations per gRNA. Nucleotide variations were much less likely to occur in the consecutive Watson-Crick anchor region, indicating a very strong bias against G:U base pairs in this region. This work indicates that gRNAs are expressed during both life cycle stages, and that differential editing patterns observed for the different mitochondrial mRNA transcripts are not due to the presence or absence of gRNAs. However, the abundance of certain gRNAs may be important in the developmental regulation of RNA editing. |
format |
Article in Journal/Newspaper |
author |
Laura E Kirby Yanni Sun David Judah Scooter Nowak Donna Koslowsky |
author_facet |
Laura E Kirby Yanni Sun David Judah Scooter Nowak Donna Koslowsky |
author_sort |
Laura E Kirby |
title |
Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
title_short |
Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
title_full |
Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
title_fullStr |
Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
title_full_unstemmed |
Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. |
title_sort |
analysis of the trypanosoma brucei eatro 164 bloodstream guide rna transcriptome. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2016 |
url |
https://doi.org/10.1371/journal.pntd.0004793 https://doaj.org/article/dd977516774740f587916e8a5f96efcc |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 10, Iss 7, p e0004793 (2016) |
op_relation |
http://europepmc.org/articles/PMC4939953?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0004793 https://doaj.org/article/dd977516774740f587916e8a5f96efcc |
op_doi |
https://doi.org/10.1371/journal.pntd.0004793 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
10 |
container_issue |
7 |
container_start_page |
e0004793 |
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