MAK, a computational tool kit for automated MITE analysis

Abstract

Miniature inverted repeat transposable elements (MITEs) are ubiquitous and numerous in higher eukaryotic genomes. Analysis of MITE families is laborious and time consuming, especially when multiple MITE families are involved in the study. Based on the structural characteristics of MITEs and genetic principles for transposable elements (TEs), we have developed a computational tool kit named MITE analysis kit (MAK) to automate the processes (http://perl.idmb.tamu.edu/mak.htm). In addition to its ability to routinely retrieve family member sequences and to report the positions of these elements relative to the closest neighboring genes, MAK is a powerful tool for revealing anchor elements that link MITE families to known transposable element families. Implementation of the MAK is described, as are genetic principles and algorithms used in its derivation. Test runs of the programs for several MITE families yielded anchor sequences that retain TIRs and coding regions reminiscent of transposases. These anchor sequences are consistent with previously reported putative autonomous elements for these MITE families. Furthermore, analysis of two MITE families with no known links to any transposon family revealed two novel transposon families, namely Math and Kid, belonging to the IS5/Harbinger/PIF superfamily.

Figure 1

Diagram of pipelines for MAK.

Figure 2

Distance of members in MITE families MathE1, MathE2 and Tc8 to their closest genes. The names and positions of the genes closest to the MITEs retrieved with MAK are sorted ascendingly with Microsoft Excel. The distance of a MITE inside a coding sequence (CDS) to the gene is considered 0 and the distance of a MITE at the 5′ end of a CDS to the CDS is changed into a negative value. The sorted elements are numbered consecutively, starting from 1. The distance values of MITEs to a CDS are plotted against their numbering. Each unit of x-axis on the chart represents a MITE element and the distance of that MITE to a CDS is shown as the value on the y-axis.

Figure 3

Schematic presentation of TE family Math (A) and Kid (B). Anchor elements are aligned with similar long elements and corresponding MITE families. Vertical lines in internal regions of long elements (long gray bars) indicate dissimilar regions and vertical lines connected by dotted lines in MITE elements indicate similar sequence blocks on MITEs to the anchor elements. Dotted lines indicate deletion regions (blank regions). The elements are drawn to scale. The triangles at the ends represent TIRs. The accession number on the left of the elements indicate the accession on which the elements are located and the positions for these elements on the accessions are described in Results.

Figure 4

Putative gene structure for A-MathE1 and A-Kiddo (A). Dotted regions indicate putative coding exons. Exons showing similarity to putative PIFa transposase are indicated in densely dotted regions. Bridged regions indicate putative introns. Sequence alignment between A-MathE1 putative translation product (from 808–1642 on the DNA sequence) and maize PIFa putative transposase (from 70 to 296 on AF412282 protein sequence) (upper panel), and sequence alignment between A-Kiddo putative translation product (2044–2956 on the DNA sequence) and PIFa putative transposase (from 18 to 296 on AF412282) (B). Letters in black indicate identical residues and letters in gray indicate similar residues. Alignment of left TIRs and right TIRs from PIFa, MathE1 and KiddoE (C). Dotted lines denote omitted internal sequences.