MIR: Family of repeats common to vertebrate genomes

Korotkov, Eugene V.; Korotkova, Maria A.; Rudenko, V. М.

doi:10.1007/bf02759556

Cited by 8 publications

(2 citation statements)

References 27 publications

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“…SINEs are non-autonomous TEs that do not encode their own proteins but utilize those coded by LINEs [ 4 ]. In mammalian genomes, SINEs are wildly represented (mainly by the Alu and mammalian-wide interspersed repeat (MIR) families) and extensively studied [ 5 , 6 ]. However, even in mammals, it has been shown that only a part of all existing SINEs have been identified by standard repeat detection methods [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

“…It is known that the probability of substitution differs among nucleotides and that full sequence replacement does not occur immediately; at first, a purine-pyrimidine copy, which has low similarity to the initial sequence, is generated. This observation has helped to identify new copies of MIR-like elements in many genomes [ 5 ]. It is also known that cells use different repression mechanisms, including DNA methylation, to prevent further transposon movements across the genome, which in turn causes more frequent C → T substitutions [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

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Search for SINE repeats in the rice genome using correlation-based position weight matrices

2021

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Background Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes and also found in plants. After insertion in a new position in the genome, TEs quickly accumulate mutations, which complicate their identification and annotation by modern bioinformatics methods. In this study, we searched for highly divergent SINE copies in the genome of rice (Oryza sativa subsp. japonica) using the Highly Divergent Repeat Search Method (HDRSM). Results The HDRSM considers correlations of neighboring symbols to construct position weight matrix (PWM) for a SINE family, which is then used to perform a search for new copies. In order to evaluate the accuracy of the method and compare it with the RepeatMasker program, we generated a set of SINE copies containing nucleotide substitutions and indels and inserted them into an artificial chromosome for analysis. The HDRSM showed better results both in terms of the number of identified inserted repeats and the accuracy of determining their boundaries. A search for the copies of 39 SINE families in the rice genome produced 14,030 hits; among them, 5704 were not detected by RepeatMasker. Conclusions The HDRSM could find divergent SINE copies, correctly determine their boundaries, and offer a high level of statistical significance. We also found that RepeatMasker is able to find relatively short copies of the SINE families with a higher level of similarity, while HDRSM is able to find more diverged copies. To obtain a comprehensive profile of SINE distribution in the genome, combined application of the HDRSM and RepeatMasker is recommended.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Search for SINE repeats in the rice genome using correlation-based position weight matrices

2021

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2001

Comp Funct Genom

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large‐scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large‐scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted

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Korotkov

Korotkova

2001

Molecular Biology

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MIR: Family of repeats common to vertebrate genomes

Cited by 8 publications

References 27 publications

Search for SINE repeats in the rice genome using correlation-based position weight matrices

Search for SINE repeats in the rice genome using correlation-based position weight matrices

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