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A Critical Review of Some Terminologies used for Additional DNA in Plant Chromosomes
Published in S. K. Dutta, DNA Systematics, 2019
Inverted repeats or palindromes, in view of their occurrence in clusters at specific loci, have been assigned certain functions.77 The term fold back or snapback DNA has been used and involvement in the formation of micronuclear DNA in ciliates has been suggested. Polymorphisms in inverted repeats are common and may have an evolutionary importance. Several functions have been attributed to palindromes. Their role in DNA replication at chromosome end has been suggested by Cavalier-Smith78 and Heumanns.79 Hartman et al.80 have ascribed more than one function to these sequences.
Mobile DNA Sequences and Their Possible Role in Evolution
Published in S. K. Dutta, DNA Systematics, 2019
Georgii P. Georgiev, Yurii V. Ilyin, Alexei P. Ryskov, Tatiana I. Gerasimova
If the existence of inverted repeats at the termini is important for excision, one should consider the case where two oppositely oriented short ubiquitous repeats (B1, B2, or Alu) may be inserted close to each other. In this case, they may create, together with the sequence located in between, an element potentially excisible by transposase. Recently, genome instability in the region of human DNA enriched in Alu repeat sequences has been clearly demonstrated.117 In this case, DNA rearrangements, involving restriction fragment length polymorphism and variations in copy number, are detected in the human genome by blot hybridization with a cloned segment of human DNA initially present in a cluster of Alu repeat sequences. These rearrangements involve both extrachromosomal, circular duplex DNAs and integrated sequences, indicating the presence of transposable elements in human cells.
Nucleic Acids
Published in Danilo D. Lasic, LIPOSOMES in GENE DELIVERY, 2019
Bending of DNA, which is a necessary condition for its tight packing, can also be increased by specific sequences, such as the AA dinucleotide that can become an AATT stack that acts as a wedge in the DNA. Such wedge elements introduce bending anisotropy. Highly repeated sequences may induce turns; inverted repeats (also known as palindromes) may form hairpins, while moderately repetitive DNA may be responsible for winding around histones or protamines. Additionally, bending can be enhanced if only one side of DNA has its charges neutralized (Strauss and Maher, 1995). In addition to natural DNA condensation into nucleosomes, DNA can also be condensed artificially.
Flagellum and toxin phase variation impacts intestinal colonization and disease development in a mouse model of Clostridioides difficile infection
Published in Gut Microbes, 2022
Dominika Trzilova, Mercedes A. H. Warren, Nicole C. Gadda, Caitlin L. Williams, Rita Tamayo
Previous studies showed that the site-specific recombinase RecV is required for inversion of the flg, cwpV, cmrRST, and CDR20291_0963 switches, and overexpression of recV influences the inversion of the pdcB and pdcC switches.24,44 Interestingly, the inverted repeats for a given invertible sequence vary in length and in position relative to the determined site of DNA recombination.24 Further, sequence conservation among the inverted repeats of RecV-invertible sequences is modest, making the identification of a core RecV-binding sequence difficult. We found that substitution of three residues that are conserved among most of the RIRs (flg-3sub) reduced flagellar switch inversion from ON to OFF and OFF to ON but did not eliminate inversion. However, deleting the residue previously determined to be the site of flagellar switch inversion in the RIR and the two flanking residues (flg-Δ3), prevented inversion as effectively as deleting the RIR. These results validate the approach of identifying the recombination site by evaluating enrichment of 5’ end clipped reads generated by whole genome sequencing.24 Future work will determine whether changes to the site of recombination impair RecV binding and/or the ability to catalyze DNA inversion.
Selective release of circRNAs in platelet-derived extracellular vesicles
Published in Journal of Extracellular Vesicles, 2018
Christian Preußer, Lee-Hsueh Hung, Tim Schneider, Silke Schreiner, Martin Hardt, Anna Moebus, Sentot Santoso, Albrecht Bindereif
Regarding the genomic structure of Plt-circR4, we identified, based on RNA-seq data, a novel transcript with 4 exons, which mapped to the minus strand of chromosome 4 (Figure 2(b); for exon positions, see Supplementary Table S3). In addition to the predominant circular form of exon 3, a very minor proportion of linear-spliced isoforms could be detected. Around exon 3, a DNA mariner transposon (Hsmar1) was recognised by RepeatMasker (http://www.repeatmasker.org) [26]. This class of transposons encodes a mariner transposase that is flanked by inverted terminal repeats [27], which we identified 140 bp upstream of the 5’ end and 195 bp downstream of the 3’ end of the Plt-circR4 exon. We note that inverted repeat elements can modulate RNA circularisation [11,14].
Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the in silico approach
Published in Pathogens and Global Health, 2018
Navaneethan Palanisamy, Dario Akaberi, Johan Lennerstrand, Åke Lundkvist
The RactIP server was used to predict long-range RNA-RNA interactions. The 5’ UTR and 3’ UTR sequences were given as input in separate fields. The server predicted the following interactions: 5’ GGAGAACAAG 3’ in the 5’ UTR with 5’ CUUGUUCUCC 3’ in the 3’ UTR. These sequences are inverted repeats. We found these sequences conserved in AFHV (114–123 in the 5’ UTR and 10695–10704 in the 3’ UTR; accession number: JF416957.1), KFDV (114–123 in the 5’ UTR and 10694–10703 in the 3’ UTR; accession number: JF416958.1 or HM055369.1) and TBEV (115–124 in the 5’ UTR and 11062–11071 in the 3’ UTR; accession number: NC_001672.1). This sequence has 50% GC content (total = 10 nucleotides). In all the three viruses, the repeat sequence in the 5’ UTR was found in one of the hairpin loops. In the 3’ UTR, on the other hand, the repeat sequence was predicted to be in one of the hairpin loops in KFDV (Figure 5, bottom), in one of the broken stems (bulges) in AFDV (Figure 5, bottom), and in one of the internal loops in TBEV (Figure 5, bottom).