Abstract
The role of 3′-end stem-loops in retrotransposition was experimentally demonstrated for transposons of various species, where LINE-SINE retrotransposons share the same 3′-end sequences, containing a stem-loop. We have discovered that 62–68% of processed pseduogenes and mRNAs also have 3′-end stem-loops. We investigated the properties of 3′-end stem-loops of human L1s, Alus, processed pseudogenes and mRNAs that do not share the same sequences, but all have 3′-end stem-loops. We have built sequence-based and structure-based machine-learning models that are able to recognize 3′-end L1, Alu, processed pseudogene and mRNA stem-loops with high performance. The sequence-based models use only sequence information and capture compositional bias in 3′-ends. The structure-based models consider physical, chemical and geometrical properties of dinucleotides composing a stem and position-specific nucleotide content of a loop and a bulge. The most important parameters include shift, tilt, rise, and hydrophilicity. The obtained results clearly point to the existence of structural constrains for 3′-end stem-loops of L1 and Alu, which are probably important for transposition, and reveal the potential of mRNAs to be recognized by the L1 machinery. The proposed approach is applicable to a broader task of recognizing RNA (DNA) secondary structures. The constructed models are freely available at github (https://github.com/AlexShein/transposons/).
Highlights
Transposons are pieces of DNA, which are able to multiply and move inside a genome
Solution 3D-structures of stem-loops for long interspersed nuclear elements (LINEs) transposons in eel and zebrafish revealed some characteristic structural stem-loop properties that, together with mutagenesis analysis, showed which nucleotide positions are vitally important for retrotransposition
As we showed earlier, despite the absence of similarity at the sequence level, all L1 and Alu transposons possess a 3′-end stem-loop structure[12]. This observation raises a question about the evolutionary importance of this structure in the process of transposition and whether evolutionary structural constrains exist that can be detected by computational methods
Summary
Transposons are pieces of DNA, which are able to multiply and move inside a genome. Transposons have been found in all eukaryotes and usually occupy a considerable part of any genome (46% of a human, 37% of a mouse, 10% of a fruit fly, and 85% of a corn genome)[1,2]. Transposons started to be considered as a “tool” of evolution, because they cause large-scale genome re-arrangements (for example, recombination between two non-allelic elements in two different chromosomes) as well as minor genome changes (duplications, inversions, deletions)[7] Transposons can influence their own expression as well as the expression of the nearby genes[8]. For several species it was experimentally shown that the LINE protein recognizes a secondary structure, such as a stem-loop, at the 3′-end of a transposon RNA. It was shown that in some organisms, LINEs and SINEs have identical 3′-end sequences containing a stem-loop structure, which is essential for transposon RNA recognition by transposon proteins[9,10,11]. Mutational analysis showed that this flexibility is somehow required for transposition
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