Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation

Ramamoorthy, Senthilkumar; Garapati, Hita Sony; Mishra, Rakesh K.

doi:10.1016/j.gene.2014.08.052

Cited by 12 publications

(14 citation statements)

References 41 publications

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“…Benefiting from these advances, cross-species comparisons of SSR distribution revealed the following features: (1) SSRs are non-randomly distributed, and dinucleotide repeats are the most abundant type in the genomes of various species; (2) exons contain more trinucleotide and hexanucleotide SSRs than other kinds of repeats; (3) trinucleotide repeats in exons display different motif preference in different biological kingdoms, e.g., AGC triplets were more abundant in animals, whereas AAG triplets were the dominant motif in some plants 1, 12, 13 . In recent years, next-generation sequencing technologies have developed rapidly, promoting the high-throughput discovery of EST-SSR markers in various plant species, such as adzuki beans 14 and wheat 15 , based on transcriptome sequencing data.…”

Section: Introductionmentioning

confidence: 99%

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Liu

Zhang

et al. 2017

Sci Rep

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Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.

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Section: Introductionmentioning

confidence: 99%

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Liu

Zhang

et al. 2017

Sci Rep

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“…More recently, a 2014 study [22] identified dinucleotide repeat motifs (DRMs) as general features that can render a nonfunctional sequence into an active enhancer element. Another comprehensive study of the simple sequence repeats in 2014 [23] suggests their potential role in genome regulation and organization. Variable number tandem repeats (VNTRs), as these sequence repeats are broadly termed, have already been implicated in many complex neurological disorders (e.g., Huntington disease [24]) and are generally known to be polymorphic [25].…”

Section: Resultsmentioning

confidence: 99%

Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization

Nikumbh

Pfeifer

2017

BMC Bioinformatics

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BackgroundKnowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions — the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin.ResultsWe present a method that can be trained on 5C data using the genetic sequence of the candidate loci to predict potential genome-wide interaction partners of a particular locus of interest. We have built locus-specific support vector machine (SVM)-based predictors using the oligomer distance histograms (ODH) representation. The method shows good performance with a mean test AUC (area under the receiver operating characteristic (ROC) curve) of 0.7 or higher for various regions across cell lines GM12878, K562 and HeLa-S3. In cases where any locus did not have sufficient candidate interaction partners for model training, we employed multitask learning to share knowledge between models of different loci. In this scenario, across the three cell lines, the method attained an average performance increase of 0.09 in the AUC. Performance evaluation of the models trained on 5C data regarding prediction on an independent high-resolution Hi-C dataset (which is a rather hard problem) shows 0.56 AUC, on average. Additionally, we have developed new, intuitive visualization methods that enable interpretation of sequence signals that contributed towards prediction of locus-specific interaction partners. The analysis of these sequence signals suggests a potential general role of short tandem repeat sequences in genome organization.ConclusionsWe demonstrated how our approach can 1) provide insights into sequence features of locus-specific interaction partners, and 2) also identify their cell-line specificity. That our models deem short tandem repeat sequences as discriminative for prediction of potential interaction partners, suggests that they could play a larger role in genome organization. Thus, our approach can (a) be beneficial to broadly understand, at the sequence-level, chromatin interactions and higher-order structures like (meta-) topologically associating domains (TADs); (b) study regions omitted from existing prediction approaches using various information sources (e.g., epigenetic information); and (c) improve methods that predict the 3D structure of the chromatin.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1624-x) contains supplementary material, which is available to authorized users.

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“…The frequency of an SSR is expected to decline with increasing repeat length. We have demonstrated earlier that certain SSRs, however, show a preference for occurring at higher lengths in some organisms (Ramamoorthy, et al 2014). A length preference is therefore defined as a sudden increase in the frequency of occurrence seen at a particular range of SSR length (Additional File 2, Figure S5).…”

Section: Length Ranges Of Ssrsmentioning

confidence: 99%

“…A length preference is therefore defined as a sudden increase in the frequency of occurrence seen at a particular range of SSR length (Additional File 2, Figure S5). Our earlier work has indicated that 45 bp repeat size is the optimum length for a majority of the SSRs, especially in the human genome (Ramamoorthy, et al 2014). Here we confirm that length preference is seen for relatively longer SSR size ranges in all genomes (~50 bp), except in fungi where SSR preferred lengths are generally smaller (~20 bp) (Table 3.3).…”

Section: Length Ranges Of Ssrsmentioning

confidence: 99%

Patterns of microsatellite distribution reflect the evolution of biological complexity

Surabhi

Avvaru

Sowpati

et al. 2018

Preprint

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Microsatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been nonexhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.peer-reviewed)

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Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation

Cited by 12 publications

References 41 publications

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization

Patterns of microsatellite distribution reflect the evolution of biological complexity

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