1,720,964 research outputs found
Developmentally regulated expression and expression strategies of Drosophila snoRNAs
No full textSmall nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, we analysed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and show by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. We also defined by quantitative RT-PCR the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. We found that most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an update outline of the fly snoRNA transcriptome, our data highlight that expression of these versatile ncRNAs can be finely regulated
Human dyskerin: beyond telomeres
No full textHuman dyskerin is an evolutively conserved protein
that participates in diverse nuclear complexes: the
H/ACA snoRNPs, that control ribosome biogenesis, RNA
pseudouridylation, and stability of H/ACA snoRNAs; the
scaRNPs, that control pseudouridylation of snRNAs; and the
telomerase active holoenzyme, which safeguards telomere
integrity. The biological importance of dyskerin is further
outlined by the fact that its deficiency causes the X-linked
dyskeratosis congenita disease, while its over-expression
characterizes several types of cancers and has been proposed
as prognostic marker. The role of dyskerin in telomere
maintenance has widely been discussed, while its functions
as H/ACA sno/scaRNP component has been so far mostly
overlooked and represent the main goal of this review. Here
we summarize how increasing evidence indicates that the
snoRNA/microRNA pathways can be interlaced, and that
dyskerin-dependent RNA pseudouridylation represents a
flexible mechanism able to modulate RNA function in different
ways, including modulation of splicing, change of
mRNA coding properties, and selective regulation of IRESdependent translation. We also propose a speculative model that suggests that the dynamics of pre-assembly and nuclear import of H/ACA RNPs are crucial regulatory steps that can be finely controlled in the cytoplasm in response to developmental, differentiative and stress stimuli
Intron retention: a human DKC1 gene common splicing event.
No full textIdentification of alternatively spliced transcripts produced by a gene is a crucial step in deciphering the bulk of its
biological roles and the overall processes that regulate its activity. By using a combination of bioinformatic and molecular
approaches we identified, cloned, and characterized 3 novel alternative splice isoforms derived from human dyskeratosis
congenita 1 (hDKC1), an essential human gene causative of the X-linked dyskeratosis congenita disease and involved in multiple
functions related to cell growth, proliferation, and telomere maintenance. Expression of the new isoforms, all characterized by
intron retention, was confirmed by RT-PCR in a panel of diverse cell lines and normal human tissues, and despite the presence
of premature termination codons, was not down-regulated by the mechanism of nonsense-mediated decay. Accumulation of
these transcripts fluctuated distinctly in the diverse tissues and during in vitro differentiation of Caco2 cells, suggesting that
their ratio may contribute to the gene functional diversity across different cell types. Intriguingly, the structure of one isoform
leads to exonize an intronically encoded small nucleolar RNA (snoRNA), highlighting an additional layer of complexity that can
contribute to overall gene regulation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
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