An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo. / Duch, Mogens R.; Carrasco, Maria L; Jespersen, Thomas; Aagaard, Lars; Pedersen, Finn Skou; Jespersen, Thomas.
In: Nucleic Acids Symposium Series, Vol. 32, No. 6, 01.01.2004, p. 2039-48.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo
AU - Duch, Mogens R.
AU - Carrasco, Maria L
AU - Jespersen, Thomas
AU - Aagaard, Lars
AU - Pedersen, Finn Skou
AU - Jespersen, Thomas
PY - 2004/1/1
Y1 - 2004/1/1
N2 - Murine leukemia viruses harboring an internal ribosome entry site (IRES)-directed translational cassette are able to replicate, but undergo loss of heterologous sequences upon continued passage. While complete loss of heterologous sequences is favored when these are flanked by a direct repeat, deletion mutants with junction sites within the heterologous cassette may also be retrieved, in particular from vectors without flanking repeats. Such deletion mutants were here used to investigate determinants of reverse transcriptase-mediated non-homologous recombination. Based upon previous structural analysis the individual recombination sites within the IRES could be assigned to either base-paired or unpaired regions of RNA. This assignment showed a significant bias (P = 0.000082) towards recombination within unpaired regions of the IRES. We propose that the events observed in this in vivo system result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes, especially in the absence of longer stretches of sequence similarity.
AB - Murine leukemia viruses harboring an internal ribosome entry site (IRES)-directed translational cassette are able to replicate, but undergo loss of heterologous sequences upon continued passage. While complete loss of heterologous sequences is favored when these are flanked by a direct repeat, deletion mutants with junction sites within the heterologous cassette may also be retrieved, in particular from vectors without flanking repeats. Such deletion mutants were here used to investigate determinants of reverse transcriptase-mediated non-homologous recombination. Based upon previous structural analysis the individual recombination sites within the IRES could be assigned to either base-paired or unpaired regions of RNA. This assignment showed a significant bias (P = 0.000082) towards recombination within unpaired regions of the IRES. We propose that the events observed in this in vivo system result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes, especially in the absence of longer stretches of sequence similarity.
KW - Animals
KW - Base Sequence
KW - Cell Line
KW - Mice
KW - Molecular Sequence Data
KW - Nucleic Acid Conformation
KW - RNA, Viral
KW - RNA-Directed DNA Polymerase
KW - Recombination, Genetic
KW - Regulatory Sequences, Ribonucleic Acid
KW - Retroviridae
KW - Sequence Deletion
KW - Sequence Homology, Nucleic Acid
KW - Virus Replication
U2 - 10.1093/nar/gkh513
DO - 10.1093/nar/gkh513
M3 - Journal article
C2 - 15069126
VL - 32
SP - 2039
EP - 2048
JO - Nucleic acids symposium series
JF - Nucleic acids symposium series
SN - 0261-3166
IS - 6
ER -
ID: 33018575