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Keywords = short-interrupted repeats cassette

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13 pages, 1731 KB  
Article
Short Interrupted Repeat Cassette (SIRC)—Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana
by Igor V. Gorbenko, Ivan S. Petrushin, Andrey B. Shcherban, Yuriy L. Orlov and Yuri M. Konstantinov
Int. J. Mol. Sci. 2023, 24(13), 11116; https://doi.org/10.3390/ijms241311116 - 5 Jul 2023
Cited by 2 | Viewed by 2270
Abstract
Short interrupted repeat cassette (SIRC)—a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC’s distribution are located within pericentromeric regions. We suggest that originally SIRC was [...] Read more.
Short interrupted repeat cassette (SIRC)—a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC’s distribution are located within pericentromeric regions. We suggest that originally SIRC was a special case of the complex internal structure of the miniature inverted repeat transposable element (MITE), and further MITE amplification, transposition, and loss of terminal inverted repeats gave rise to SIRC as an independent DNA element. SIRC sites were significantly enriched with several histone modifications associated with constitutive heterochromatin and mobile genetic elements. The majority of DNA-binding proteins, strongly associated with SIRC, are related to histone modifications for transcription repression. A part of SIRC was found to overlap highly inducible protein-coding genes, suggesting a possible regulatory role for these elements, yet their definitive functions need further investigation. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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