Universität zu Köln

Spaller, Thomas, Groth, Marco ORCID: 0000-0002-9199-8990, Gloeckner, Gernot and Winckler, Thomas (2017). TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element. PLoS One, 12 (4). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotran-sposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions similar to 47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only similar to 24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes. We determined that a tagged TRE5-A element (TRE5-A(bsr)) integrated at 384 of 405 tRNA genes, suggesting that expansion of the current natural TRE5-A population is not limited by the availability of targets. We further observed that TRE5-A(bsr) targets the ribosomal 5S gene on the multicopy extrachromosomal DNA element that carries the ribosomal RNA genes, indicating that TRE5-A integration may extend to the entire RNA polymerase III (Pol III) transcriptome. We determined that both natural TRE5-A and cloned TRE5-A(bsr) retrotranspose to locations on the extrachromosomal rDNA element that contain tRNA gene-typical A/B box promoter motifs without displaying any other tRNA gene context. Based on previous data suggesting that TRE5-A targets tRNA genes by locating Pol III transcription complexes, we propose that A/B box loci reflect Pol III transcription complex assembly sites that possess a function in the biology of the extrachromosomal rDNA element.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Spaller, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Groth, Marco UNSPECIFIED orcid.org/0000-0002-9199-8990 UNSPECIFIED Gloeckner, Gernot UNSPECIFIED UNSPECIFIED UNSPECIFIED Winckler, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-233907
DOI:	10.1371/journal.pone.0175729
Journal or Publication Title:	PLoS One
Volume:	12
Number:	4
Date:	2017
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language GENOME EVOLUTION; DISCOIDEUM GENOME; DNA-REPLICATION; MOBILE ELEMENTS; TARGET SITE; HUMAN-CELLS; INTEGRATION; GENES; SEQUENCE; INITIATION Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/23390