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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
Satellite DNA (sat-DNA), with high homogenous repeats, has been located in several organisms. In the pea, four fractions of rRNA were observed to hybridize with the main band.19 In Drosophila viridis sat-DNAs are very specific in location and are rich in A-T sequences. They are consistently located on the sides of the nuclei nearest to the vitelline membrane. Highly repetitive sat-DNA sequences have been found in Cucurbitaceous species. The restriction pattern suggests an internal Hind III sequence of repeats with 380 bp in Cucumis melo. In Cucumis sativus, on the other hand, excision results in repeated units of 180 bp. A certain amount of homology between the satellites of the two species has been recorded, together with the properties of amplification and dispersion. Sat-DNAs have also been traced through in situ hybridization in human acrocentrics, especially on the short arm. Some of them exhibit some heterogeneity in their DNA content. In this connection, the intensity of fluoresecence has not been considered a proper criterion for detecting homogeneity of satellites.18 A satellite is historically a CsCl-density satellite. In this case there is no density difference and a satellite is not observed on CsCl (as in the green monkey), but a reassociation or restriction enzyme is given for a family of repeats whose members are not exact copies of each other.
Nucleic Acids
Published in Danilo D. Lasic, LIPOSOMES in GENE DELIVERY, 2019
Satellite DNA contains very short sequences which are repeats or inverted repeats. They form circular molecules and hairpin loops (palindromes) which may also be important for organization of DNA within chromosomes and for maintaining its structural integrity.
A Survey of Newer Gene Probing Techniques
Published in Victor A. Bernstam, Pocket Guide to GENE LEVEL DIAGNOSTICS in Clinical Practice, 2019
Chromosome-specific probes containing only repetitive (satellite) DNA hybridize predominantly to the centromeric regions of the chromosome. Hybridization probes constructed from chromosome-specific libraries specifically stain individual chromosomes. In these protocols, total genomic DNA is used as a competitor to exclude the dispersed repetitive sequences from participation in ISH. Various chromosomal aberrations can thus be identified as demonstrated by the diagnosis of trisomy 18 with the probe LI.84. Likewise, the pericentric region of human chromosome 17 has been analyzed by a cDNA clone containing the entire alphoid repeat. Using a monomer of the higher order repeat, the chromosomal specificity of ISH was improved. Shorter probes can further improve the chromosome specificity, allowing the precise identification of individual chromosomes using alphoid repeats. Biotinylated DNA probes can be used for highresolution mapping of satellite DNA.
The use of qPCR in human Chagas disease: a systematic review
Published in Expert Review of Molecular Diagnostics, 2019
Luciana Hagström, Ana Luisa Pereira Marques, Nadjar Nitz, Mariana Machado Hecht
It has been observed that experimental design of the studies uses different DNA fragments for amplification. Some studies had shown that cPCR assays targeting nDNA had better results than targeting kDNA [68,90,91], although in cPCR the last one is the most commonly used [89]. In this systematic review, the nDNA as a target for amplification was more used than kDNA sequences. The use of nuclear satellite DNA for the T. cruzi detection was initially described by Moser et al in 1989 [92]. This material is extremely conserved and represents 104 to 105 copies in the parasite genome so may provide accurate qPCR results [55,56,60,93,94]. It has been indicated that PCR assays targeted the satellite DNA were more specific than those based on kDNA [56]. However, Ramírez et al [63] and Abras et al [84] suggested that kDNA qPCR have higher sensitivity than nDNA qPCR. In fact, the use of kDNA as a target in qPCR can be more sensitive at least to detect T. cruzi discrete typing units (DTU) I DNA [56]. Although the amount of satellite DNA changes between T. cruzi lineages [55,95,96] and this fact can alter the melting temperature and affect the interpretation of results of parasitic load [55], it has been suggested that PCR methods targeting nDNA might be useful for typing T. cruzi [55,97].
Effect of electromagnetic field exposure on the transcription of repetitive DNA elements in human cells
Published in Electromagnetic Biology and Medicine, 2019
Brunella Del Re, Ferdinando Bersani, Gianfranco Giorgi
(3) SAT sequences constitute about 15% of human genome. In particular, alpha satellite DNA (SATA), consisting of 171-bp monomeric repeat units, are present in all human chromosomes and enriched at all human centromere. The monomer arrays are chromosome specific but share a high homology in consensus sequence. Some monomers within the centromere contain a 17 bp CENP-B box, which is a binding site for the CENP-B protein, that is used for centromere assembly, so SATA are essential for centromere function during cell division. These sequences are transcribed into repetitive noncoding RNA and this transcription, tightly regulated, is needed for the accurate cell division (McNulty et al. 2018). Numerous evidences indicate that this transcriptional activity can be altered by various environmental chemical and physical agents (reviewed by Ferreira et al. 2015).
Heterochromatin extension: a possible cytogenetic fate of primary amenorrhea along with normal karyotype
Published in Journal of Obstetrics and Gynaecology, 2022
Bishal Kumar Dey, Shanoli Ghosh, Ajanta Halder, Somajita Chakraborty, Sanchita Roy
Reviewing the works of last decade, we have noticed that we have similar numerical and structural abnormalities found in the patients with PA (Table 3). Our previous study which was conducted by Ghosh et al. revealed 14% cases with structural chromosomal anomalies, out of 150 primary amenorrheic females and single case with heterochromatin extension for chromosome 9 (9qh+) along with normal karyotype. But in this present study, we found heterochromatin extension not only for 9qh+ but also for 16qh+. We found a case of age 14 with PA having 46, XX, 9qh+ karyotype with utero-vaginal abnormalities (Müllerian agenesis, hypoplastic ovaries, vaginal hypoplasia, etc.). For normal karyotype with extended heterochromatin, only FSH (p < .05) and TSH (p < .05) varied significantly. The increase in level of gonadotropins (FSH and LH) is higher in case of Turner’s syndrome karyotype with PA associated with increase in heterochromatin region. Perhaps, the concentration of TSH becomes elevated due to the neuro-endocrinological problems that may not be directly associated with PA. Analysis at the molecular level, may be needed to unveil any relationship between heteromorphism and PA taking in to consideration, the more crucial cellular effects of heterochromatin than previously thought. Chromosomal polymorphic variations, consisting of highly repetitive sequences of satellite DNA that do not encode any significant protein are considered to be normal variant. But chromosomal polymorphisms may cause certain clinical effects, such as infertility and recurrent miscarriages that comes from the data of recent studies (An et al. 2016). When infertility and adverse reproductive outcomes are found to be associated with karyotypic presentation with extended heteromorphic regions, it is not accurate to consider heteromorphic variants as being normal structural chromosomal aberrations. With refined molecular techniques, genes for fertility and viability are thought to reside in heterochromatin. DNA sequence analysis of human chromosome 9 has shown that it is highly structurally polymorphic with many intra-chromosomal and inter-chromosomal duplications. In response to environmental stress, there may be transcriptional activation of constitutive heterochromatin domains that lead to altered regulation of the genome and cause aberrations in chromosome pairing and cell division.