Literature DB >> 17123956

KISS: the kinetoplastid RNA editing sequence search tool.

Torsten Ochsenreiter1, Michael Cipriano, Stephen L Hajduk.   

Abstract

Kinetoplastid mitochondrial mRNA editing is a post-transcriptional process of uridine insertion and deletion. Editing is mediated by small RNA molecules termed guide RNAs (gRNAs). Most gRNAs are encoded by numerous small circular DNA minicircles, while the protein coding mitochondrial genes are encoded on a separate, larger genome called the maxicircle. In order to provide a workbench for the analysis of RNA editing in kinetoplastids and a well-annotated set of guide RNAs for Trypanosoma brucei, we generated the kinetoplastid RNA editing sequence search tool (KISS) (http://gmod.mbl.edu/kiss/). KISS is a pipeline and database that uses BLAST comparisons and minicircle sequence motifs to annotate potential gRNAs and cognate mRNA editing sequence. KISS 1.0 contains all previously known minicircle and maxicircle data from Trypanosoma brucei plus >400 new minicircle sequences. Using an online format, KISS 1.0 allows the mapping and visualization of all known T. brucei gRNAs to minicircle genes and to potential mRNA substrates for RNA editing.

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Year:  2006        PMID： 17123956      PMCID： PMC1705751          DOI： 10.1261/rna.232907

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


  14 in total

1.  EMBOSS: the European Molecular Biology Open Software Suite.

Authors:  P Rice; I Longden; A Bleasby
Journal:  Trends Genet       Date:  2000-06       Impact factor: 11.639

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  In vitro guide RNA/mRNA chimaera formation in Trypanosoma brucei RNA editing.

Authors:  D J Koslowsky; H U Göringer; T H Morales; K Stuart
Journal:  Nature       Date:  1992-04-30       Impact factor: 49.962

4.  Guide RNAs in kinetoplastid mitochondria have a nonencoded 3' oligo(U) tail involved in recognition of the preedited region.

Authors:  B Blum; L Simpson
Journal:  Cell       Date:  1990-07-27       Impact factor: 41.582

5.  U-insertion/deletion Edited Sequence Database.

Authors:  L Simpson; S H Wang; O H Thiemann; J D Alfonzo; D A Maslov; H A Avila
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

Review 6.  The genomic organization of guide RNA genes in kinetoplastid protozoa: several conundrums and their solutions.

Authors:  L Simpson
Journal:  Mol Biochem Parasitol       Date:  1997-06       Impact factor: 1.759

7.  The guide RNA database.

Authors:  A E Souza; T Hermann; H U Göringer
Journal:  Nucleic Acids Res       Date:  1997-01-01       Impact factor: 16.971

8.  Organization of minicircle genes for guide RNAs in Trypanosoma brucei.

Authors:  V W Pollard; S P Rohrer; E F Michelotti; K Hancock; S L Hajduk
Journal:  Cell       Date:  1990-11-16       Impact factor: 41.582

9.  Multiple guide RNAs for identical editing of Trypanosoma brucei apocytochrome b mRNA have an unusual minicircle location and are developmentally regulated.

Authors:  G R Riley; R A Corell; K Stuart
Journal:  J Biol Chem       Date:  1994-02-25       Impact factor: 5.157

10.  Trypanosoma brucei minicircles encode multiple guide RNAs which can direct editing of extensively overlapping sequences.

Authors:  R A Corell; J E Feagin; G R Riley; T Strickland; J A Guderian; P J Myler; K Stuart
Journal:  Nucleic Acids Res       Date:  1993-09-11       Impact factor: 16.971
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  25 in total

1.  TbRGG2 facilitates kinetoplastid RNA editing initiation and progression past intrinsic pause sites.

Authors:  Michelle L Ammerman; Vladimir Presnyak; John C Fisk; Bardees M Foda; Laurie K Read
Journal:  RNA       Date:  2010-09-20       Impact factor: 4.942

2.  Aminoacylating urzymes challenge the RNA world hypothesis.

Authors:  Li Li; Christopher Francklyn; Charles W Carter
Journal:  J Biol Chem       Date:  2013-07-18       Impact factor: 5.157

3.  Emerging roles of PPR proteins in trypanosomes: switches, blocks, and triggers.

Authors:  Ruslan Aphasizhev; Inna Aphasizheva
Journal:  RNA Biol       Date:  2013-08-29       Impact factor: 4.652

4.  Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei.

Authors:  Bhaskara Reddy Madina; Gokulan Kuppan; Ajay A Vashisht; Yu-He Liang; Kurtis M Downey; James A Wohlschlegel; Xinhua Ji; Sing-Hoi Sze; James C Sacchettini; Laurie K Read; Jorge Cruz-Reyes
Journal:  RNA       Date:  2011-08-02       Impact factor: 4.942

5.  RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei.

Authors:  Inna Aphasizheva; Ruslan Aphasizhev
Journal:  Mol Cell Biol       Date:  2010-01-19       Impact factor: 4.272

6.  3' adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria.

Authors:  Ronald D Etheridge; Inna Aphasizheva; Paul D Gershon; Ruslan Aphasizhev
Journal:  EMBO J       Date:  2008-05-08       Impact factor: 11.598

7.  The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.

Authors:  Blaine H M Mooers; Amritanshu Singh
Journal:  RNA       Date:  2011-08-30       Impact factor: 4.942

8.  Mechanism of U insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex.

Authors:  Gene-Errol Ringpis; Inna Aphasizheva; Xiaorong Wang; Lan Huang; Richard H Lathrop; G Wesley Hatfield; Ruslan Aphasizhev
Journal:  J Mol Biol       Date:  2010-04-01       Impact factor: 5.469

9.  Kinetoplastid genomics: the thin end of the wedge.

Authors:  Nancy R Sturm; L L Isadora Trejo Martinez; Sean Thomas
Journal:  Infect Genet Evol       Date:  2008-07-15       Impact factor: 3.342

Review 10.  Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes.

Authors:  Inna Aphasizheva; Juan Alfonzo; Jason Carnes; Igor Cestari; Jorge Cruz-Reyes; H Ulrich Göringer; Stephen Hajduk; Julius Lukeš; Susan Madison-Antenucci; Dmitri A Maslov; Suzanne M McDermott; Torsten Ochsenreiter; Laurie K Read; Reza Salavati; Achim Schnaufer; André Schneider; Larry Simpson; Kenneth Stuart; Vyacheslav Yurchenko; Z Hong Zhou; Alena Zíková; Liye Zhang; Sara Zimmer; Ruslan Aphasizhev
Journal:  Trends Parasitol       Date:  2020-02-28
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