Abstract
BackgroundRepetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, host-pathogen interactions and genome evolution.ResultsWe identified a minisatellite contained within a miniature inverted-repeat transposable element (MITE) in Porphyromonas gingivalis. The P. gingivalis minisatellite and associated MITE, named ‘BrickBuilt’, comprises a tandemly repeating twenty-three nucleotide DNA sequence lacking spacer regions between repeats, and with flanking ‘leader’ and ‘tail’ subunits that include small inverted-repeat ends. Forms of the BrickBuilt MITE are found 19 times in the genome of P. gingivalis strain ATCC 33277, and also multiple times within the strains W83, TDC60, HG66 and JCVI SC001. BrickBuilt is always located intergenically ranging between 49 and 591 nucleotides from the nearest upstream and downstream coding sequences. Segments of BrickBuilt contain promoter elements with bidirectional transcription capabilities.ConclusionsWe performed a bioinformatic analysis of BrickBuilt utilizing existing whole genome sequencing, microarray and RNAseq data, as well as performing in vitro promoter probe assays to determine potential roles, mechanisms and regulation of the expression of these elements and their affect on surrounding loci. The multiplicity, localization and limited host range nature of MITEs and MITE-like elements in P. gingivalis suggest that these elements may play an important role in facilitating genome evolution as well as modulating the transcriptional regulatory system.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-015-0049-1) contains supplementary material, which is available to authorized users.
Highlights
Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes
Identification of a repetitive element in Porphyromonas gingivalis We identified a DNA element, ‘BrickBuilt’, in the genome of P. gingivalis strain ATCC 33277
The element was initially identified as a tandemly-repeated sequence of 23 nt located intergenically at a single site (Additional file 1: Figure S1)
Summary
Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, host-pathogen interactions and genome evolution. Repetitive Elements (REs) are DNA sequences present in multiple copies throughout a genome, chromosome or vector. They are broadly classified into ‘terminal’, ‘tandem’ and ‘interspersed’ repeats, each of these classifications encompasses several sub-types of REs. Tandem repeats are classified as either identical or nonidentical based on the level of nucleic acid matching. They are further classified as either micro, mini or macro
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