Genomics. Transcriptomics. Proteomics

Molecular Biology

, Volume 41, Issue 6, pp 886-893

First online:

Homology-dependent inactivation of LTR retrotransposons in Aspergillus fumigatus and A. nidulans genomes

  • O. S. NovikovaAffiliated withInstitute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences Email author 
  • , V. FetAffiliated withMarshall University
  • , A. G. BlinovAffiliated withInstitute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences

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Abstract

The repeat-induced point mutation mechanism (RIP) is the most intriguing among the known mechanisms of homology-dependent gene inactivation (silencing) because of its ability to produce irreversible mutations in repetitive DNA sequences. Discovered for the first time in Neurospora crassa, RIP is characterized by C:G to T:A transitions in duplicated sequences. The mechanisms and range of occurrence of RIP are still poorly understood. Mobile elements, including retrotransposons, are a common target for the processes that lead to homology-dependent silencing because of their ability to propagate themselves. Comparative analysis of LTR retrotransposons was performed throughout the genomes of two ascomycetes, Aspergillus fumigatus and A. nidulans. “De-RIP” retroelements were reconstructed on the basis of several copies. CpG, CpA, and TpG sites, which are potential targets for mutagenesis, were found at a much lower frequency in mobile elements than in structural genes. The dinucleotide targets of the two species are affected by RIP at different frequencies: mutagenesis occurs at both CpG and CpA sites in A. fumigatus and is confined to CpG dinucleotides in A. nidulans. This work provides a theoretical background for planning the experimental investigation of RIP inactivation in aspergilli.

Key words

Aspergillus LTR retrotransposons in silico analysis mutagenesis RIP inactivation