A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing.

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Research Abstract Details 

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A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Abstract Text:

Sean Thomas,L L Isadora Trejo Martinez,Scott J Westenberger,Nancy R Sturm,

BACKGROUND: The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for Trypanosoma cruzi, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised. RESULTS: Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from T. cruzi whole genome shotgun sequencing data. With these sequences and all published T. cruzi minicircle sequences, 108 unique guide RNAs from all known T. cruzi minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in T. cruzi minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found. CONCLUSION: The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. Based on these preferences, a method of predicting T. cruzi guide RNAs using only primary minicircle sequence data was created.

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Publishing Authors By Initials

S Thomas,LL Martinez,SJ Westenberger,NR Sturm,

For similar animals: invertebrates: protozoa: sarcomastigophora: mastigophora: zoomastigophora: kinetoplastida: trypanosomatina: trypanosoma: trypanosoma cruzi research abstracts see: animals: invertebrates: protozoa: sarcomastigophora: mastigophora: zoomastigophora: kinetoplastida: trypanosomatina: trypanosoma: trypanosoma cruzi research

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A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: BMC genomics

VOLUME: 8

Page Numbers: 133

Journal Abbreviation: BMC Genomics

ISSN: 1471-2164

DAY: 24

MONTH: 05

YEAR: 2007

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965258

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Keywords Mesh Terms:

KEYWORDS: Trypanosoma cruzi

MESH TERMS: genetics

Chemical & Substance for Abstract: A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. Information

Substance Name: RNA, Protozoan

Registry Number: 0

Grant and Affiliation Information for A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing.

AFFILIATION: Molecular Biology Institute, UCLA, Los Angeles, CA, USA. sean.thomas@sbri.org <sean.thomas@sbri.org>

Country: England

AGENCY: United States NIAID

GRANT: AI056034

ACRONYM: AI

MEDLINETA: BMC Genomics

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