Literature DB >> 12711681

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium.

Richard Sucgang1, Guokai Chen, Wen Liu, Ryan Lindsay, Jing Lu, Donna Muzny, Gad Shaulsky, William Loomis, Richard Gibbs, Adam Kuspa.   

Abstract

Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.

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Year:  2003        PMID: 12711681      PMCID: PMC154234          DOI: 10.1093/nar/gkg348

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  37 in total

1.  Electrophoretic karyotype for Dictyostelium discoideum.

Authors:  E C Cox; C D Vocke; S Walter; K Y Gregg; E S Bain
Journal:  Proc Natl Acad Sci U S A       Date:  1990-11       Impact factor: 11.205

2.  Tandem repeats in extrachromosomal ribosomal DNA of Dictyostelium discoideum, resulting from chromosomal mutations.

Authors:  R A Cole; K L Williams
Journal:  Genetics       Date:  1992-04       Impact factor: 4.562

3.  Regulatory sequences for the amplification and replication of the ribosomal DNA minichromosome in Tetrahymena thermophila.

Authors:  P Blomberg; C Randolph; C H Yao; M C Yao
Journal:  Mol Cell Biol       Date:  1997-12       Impact factor: 4.272

4.  Cultivation and synchronous morphogenesis of Dictyostelium under controlled experimental conditions.

Authors:  M Sussman
Journal:  Methods Cell Biol       Date:  1987       Impact factor: 1.441

5.  The replication of ribosomal DNA in Physarum polycephalum.

Authors:  V M Vogt; R Braun
Journal:  Eur J Biochem       Date:  1977-11-01

6.  Higher-order association of extrachromosomal rDNA genes in Dictyostelium discoideum.

Authors:  I Simon; D E Olins
Journal:  Cell Biol Int       Date:  1994-11       Impact factor: 3.612

7.  Electrophoretic isolation of nucleosomes from Dictyostelium nuclei and nucleoli: proteins associated with monomers and dimers.

Authors:  R W Parish; S Schmidlin; S Fuhrer; R Widmer
Journal:  FEBS Lett       Date:  1980-02-11       Impact factor: 4.124

8.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum.

Authors:  Gernot Glöckner; Ludwig Eichinger; Karol Szafranski; Justin A Pachebat; Alan T Bankier; Paul H Dear; Rüdiger Lehmann; Cornelia Baumgart; Genís Parra; Josep F Abril; Roderic Guigó; Kai Kumpf; Budi Tunggal; Edward Cox; Michael A Quail; Matthias Platzer; André Rosenthal; Angelika A Noegel
Journal:  Nature       Date:  2002-07-04       Impact factor: 49.962

9.  A "double adaptor" method for improved shotgun library construction.

Authors:  B Andersson; M A Wentland; J Y Ricafrente; W Liu; R A Gibbs
Journal:  Anal Biochem       Date:  1996-04-05       Impact factor: 3.365

10.  The cell cycle during the vegetative stage of Dictyostelium discoideum and its response to temperature change.

Authors:  I M Zada-Hames; J M Ashworth
Journal:  J Cell Sci       Date:  1978-08       Impact factor: 5.285

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  29 in total

1.  The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes.

Authors:  Bill Wickstead; Klaus Ersfeld; Keith Gull
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

2.  Novel non-coding RNAs in Dictyostelium discoideum and their expression during development.

Authors:  Anders Aspegren; Andrea Hinas; Pontus Larsson; Anders Larsson; Fredrik Söderbom
Journal:  Nucleic Acids Res       Date:  2004-08-27       Impact factor: 16.971

3.  Reevaluation of the predicted gene structure of Dictyostelium cystatin A3 (cpiC) by nucleotide sequence determination of its cDNA* and its phylogenetic position in the cystatin superfamily.

Authors:  Medhat S El-Halawany; Hideki Shibata; Kiyotaka Hitomi; Masatoshi Maki
Journal:  Mol Biol Rep       Date:  2005-12       Impact factor: 2.316

4.  Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.

Authors:  Carsten Boesler; Janis Kruse; Fredrik Söderbom; Christian Hammann
Journal:  J Biol Chem       Date:  2011-03-18       Impact factor: 5.157

Review 5.  dictyBase and the Dicty Stock Center (version 2.0) - a progress report.

Authors:  Petra Fey; Robert J Dodson; Siddhartha Basu; Eric C Hartline; Rex L Chisholm
Journal:  Int J Dev Biol       Date:  2019       Impact factor: 2.203

6.  Role of RNA polymerase III transcription factors in the selection of integration sites by the dictyostelium non-long terminal repeat retrotransposon TRE5-A.

Authors:  Oliver Siol; Moustapha Boutliliss; Thanh Chung; Gernot Glöckner; Theodor Dingermann; Thomas Winckler
Journal:  Mol Cell Biol       Date:  2006-09-18       Impact factor: 4.272

7.  One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.

Authors:  Petra Fey; Robert J Dodson; Siddhartha Basu; Rex L Chisholm
Journal:  Methods Mol Biol       Date:  2013

8.  Template jumping by a LINE reverse transcriptase has created a SINE-like 5S rRNA retropseudogene in Dictyostelium.

Authors:  K Szafranski; T Dingermann; G Glöckner; T Winckler
Journal:  Mol Genet Genomics       Date:  2003-12-02       Impact factor: 3.291

9.  De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring.

Authors:  Pontus Larsson; Andrea Hinas; David H Ardell; Leif A Kirsebom; Anders Virtanen; Fredrik Söderbom
Journal:  Genome Res       Date:  2008-03-17       Impact factor: 9.043

Review 10.  Revamp a model-status and prospects of the Dictyostelium genome project.

Authors:  Ludwig Eichinger
Journal:  Curr Genet       Date:  2003-07-11       Impact factor: 3.886

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