Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis.
Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis.
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DOI：
10.1186/s13100-015-0049-1
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发表时间：
2015
期刊：
影响因子：
4.9
通讯作者：
Hu LT
中科院分区：
文献类型：
--
作者：
Klein BA;Chen T;Scott JC;Koenigsberg AL;Duncan MJ;Hu LT
DNA和转座因子的重复区域已被发现构成真核生物和原核生物基因组的很大百分比。已知这些元件参与转录调控、宿主-病原体相互作用和基因组进化。我们确定了一个微小卫星内的一个微型反向重复转座因子（MITE）牙龈卟啉单胞菌。牙龈卟啉单胞菌小卫星和相关的MITE，命名为“BrickBuild”，包含串联重复的23个核苷酸的DNA序列，在重复之间缺乏间隔区，并且具有包括小的反向重复末端的侧翼“前导”和“尾”亚基。BrickBuilt MITE的形式在牙龈卟啉单胞菌菌株ATCC 33277的基因组中发现了19次，并且在菌株W83、TDC 60、HG 66和JCVI SC 001中也发现了多次。BrickBuilt总是位于距离最近的上游和下游编码序列49至591个核苷酸之间的基因间范围内。BrickBuilt的片段含有具有双向转录能力的启动子元件。我们利用现有的全基因组测序、微阵列和RNAseq数据对BrickBuilt进行了生物信息学分析，并进行了体外启动子探针测定，以确定这些元件表达的潜在作用、机制和调控及其对周围基因座的影响。MITE和MITE样元件在牙龈卟啉单胞菌中的多样性、定位性和有限的宿主范围性质表明，这些元件可能在促进基因组进化以及调节转录调控系统中发挥重要作用。本文的在线版本（doi：10.1186/s13100-015-0049-1）包含补充材料，可供授权用户使用。
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. We 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. We 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. The online version of this article (doi:10.1186/s13100-015-0049-1) contains supplementary material, which is available to authorized users.