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@article{1419826,
author = {Gerasimov, E.S. and Gasparyan, A.A. and Kaurov, I. and Tichý, Boris and Logacheva, M.D. and Kolesnikov, A.A. and Lukes, J. and Yurchenko, V. and Zimmer, S.L. and Flegontov, P.},
article_location = {Oxford},
article_number = {2},
doi = {http://dx.doi.org/10.1093/nar/gkx1202},
keywords = {AUG INITIATION CODONS; MESSENGER-RNA; INSECT TRYPANOSOMATIDS; LEISHMANIA-TARENTOLAE; LEPTOMONAS-PYRRHOCORIS; CRITHIDIA-FASCICULATA; GENE-EXPRESSION; BRUCEI; EVOLUTION; CRYPTOGENE},
language = {eng},
issn = {0305-1048},
journal = {Nucleic Acids Research},
title = {Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool},
url = {https://watermark.silverchair.com/gkx1202.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbEwggGtBgkqhkiG9w0BBwagggGeMIIBmgIBADCCAZMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMBNUArG-Efs-5so1GAgEQgIIBZHlJiUZ_ep3ZlMPsc_UR4wpdnYomIHGEXoCUTkCVABoZyU},
volume = {46},
year = {2018}
}
TY - JOUR
ID - 1419826
AU - Gerasimov, E.S. - Gasparyan, A.A. - Kaurov, I. - Tichý, Boris - Logacheva, M.D. - Kolesnikov, A.A. - Lukes, J. - Yurchenko, V. - Zimmer, S.L. - Flegontov, P.
PY - 2018
TI - Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool
JF - Nucleic Acids Research
VL - 46
IS - 2
SP - 765-781
EP - 765-781
PB - Oxford University Press
SN - 03051048
KW - AUG INITIATION CODONS
KW - MESSENGER-RNA
KW - INSECT TRYPANOSOMATIDS
KW - LEISHMANIA-TARENTOLAE
KW - LEPTOMONAS-PYRRHOCORIS
KW - CRITHIDIA-FASCICULATA
KW - GENE-EXPRESSION
KW - BRUCEI
KW - EVOLUTION
KW - CRYPTOGENE
UR - https://watermark.silverchair.com/gkx1202.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbEwggGtBgkqhkiG9w0BBwagggGeMIIBmgIBADCCAZMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMBNUArG-Efs-5so1GAgEQgIIBZHlJiUZ_ep3ZlMPsc_UR4wpdnYomIHGEXoCUTkCVABoZyU
N2 - RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded. Thus, analysis of kinetoplastid mitochondrial transcriptomes has proven frustratingly complex. Here we present our analysis of Leptomonas pyrrhocoris mitochondrial cDNA deep sequencing reads using T-Aligner, our new tool which allows comprehensive characterization of RNA editing, not relying on targeted transcript amplification and on prior knowledge of final edited products. T-Aligner implements a pipeline of read mapping, visualization of all editing states and their coverage, and assembly of canonical and alternative translatable mRNAs. We also assess T-Aligner functionality on a more challenging deep sequencing read input from Trypanosoma cruzi. The analysis reveals that transcripts of cryptogenes of both species undergo very complex editing that includes the formation of alternative open reading frames and whole categories of truncated editing products.
ER -
GERASIMOV, E.S., A.A. GASPARYAN, I. KAUROV, Boris TICHÝ, M.D. LOGACHEVA, A.A. KOLESNIKOV, J. LUKES, V. YURCHENKO, S.L. ZIMMER and P. FLEGONTOV. Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2018, vol.~46, No~2, p.~765-781. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkx1202.
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