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Epigenetic regulation of genes mediated by satellite DNA
No full textEpigenetic regulation of genes mediated by satellite DNA
Isidoro Feliciello, Ivana Akrap, Đurđica Ugarković
Satellite DNA is a highly repetitive DNA, organized in long tandem arrays, located in the heterochromatic regions of chromosomes. Due to intrastrand homologous recombination, elements of satellite DNAs can be excised from their heterochromatin loci and integrate into euchromatin. This scenario was proposed to describe euchromatic dispersion of TCAST, the species-specific major satellite DNA of beetle Tribolium castaneum, which is found associated with numerous protein-coding genes. Dispersed repeats of TCAST (dTcast) were present as monomeric or multimeric repeat units in intragenic (introns), as well as, intergenic regions. Our assumption was that dTcast can influence the expression of associated genes.
Our results show that dTcast does not significantly affect the level of gene expression under physiological condition but induces a transient downregulation of gene transcription after heat stress. Interestingly, also the level of TCAST satellite transcripts in the form of siRNAs and TCAST satellite DNA methylation as well as H3K9 met2/3 in heterochromatin are temperature modulated. We showed a temporary formation of heterochromatic state characterized by increased level of H3K9met2/3 at dTcast insertion sites and their spreading to the proximal regions. Such “heterochromatinization” occurs after heat stress and correlates with transcriptional downregulation of nearby genes. In conclusion, dTcast satellite elements influence the level of expression of their associated genes through RNA interference-based “heterochromatinization” which occurs transiently after heat stress. What is the physiological consequence of this satellite DNA-mediated modulation of gene expression remains to be elucidated
Epigenetic regulation of genes mediated by satellite DNA
No full textSatellite DNA is a highly repetitive DNA, organized in long tandem arrays, located in the heterochromatic regions of chromosomes. Repeats of satellite DNAs can be excised from their heterochromatin loci and integrate into euchromatin. This scenario was proposed to describe euchromatic dispersion of TCAST1, the species-specific major satellite DNA of beetle Triboliumcastaneum, which is associated with numerous protein-coding genes. Dispersed repeats of TCAST1 (dTcast1) were present as monomeric or multimeric repeat units in intragenic (introns), as well as, intergenic regions. Our assumption was that dTcast1can influence the expression of associated genes.
Our results show that dTcast1 affects the adjacent genes under physiological condition by inducing a slight downregulation of gene expression. The effect is more pronounced after heat stress when transient increase of satellite DNA transcripts processed into TCAST1-siRNAs is induced. We showed that a temporary formation of heterochromatic state characterized by increased level of H3K9met2/3 at dTcast insertion sites and their spreading to the proximal regions is responsible for downregulation of nearby genes. In conclusion, dTcast1 satellite elements influence the level of expression of their associated genes through RNA interference-based „heterochromatinization“and the level of suppression is positively correlated with the amount of transcripts of TCAST1 satellite DNA. Insertion of satellite DNA repeats within euchromatin provides genes with regulatory elements that modulate their activity in particular in response to environmental stress. Variation in satellite repeats insertion among individuals can in some cases provide phenotypic variation that could be acted upon by selection enabling satellite DNA to contribute to the evolution of gene regulatory networks
Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum
Get PDFTandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization and subfamily-specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin while Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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