1,720,968 research outputs found
Acetylation and accessibility of rDNA chromatin in Saccharomices cerevisiae in Dtop1 and Dsir2 mutants.
No full textThe insertion of reporter genes in the ribosomal DNA (rDNA) locus of Saccharomyces cerevisiae causes their transcriptional repression. This kind of transcriptional silencing depends on proteins such as Sir2p and Top1p, and has been shown to be mediated by chromatin. While Sir2p modifies nucleosomes directly through its histone deacetylase activity, little is known about changes in the chromatin structure that occur at the rDNA locus when TOP1 is deleted. Here, we show that the absence of Top1p causes increased histone acetylation at the rDNA locus. Moreover, rDNA chromatin becomes more accessible in a similar manner in both top1 and sir2 mutant strains
DNA protein-interactions at the Saccharomyces cerevisiae 35s rRNA promoter and in its surrounding region.
No full textThis study represents a detailed analysis of the structural context of the RNA polymerase I promoter of Saccharomyces cerevisiae. We determined the presence of regularly spaced nucleosomes in the non-transcribed spacer (NTS) and found that five of them have well defined positions. We show that this nucleosome positioning is restricted to the region between the 35 S and 5 S rRNA promoters, beyond which a more delocalized chromatin structure is evident. A more refined analysis detects the DNA-protein interactions on the RNA polymerase I promoter at nucleotide resolution and provides the first in vivo footprints, attributable to factors like REB1, CF, UAF and an additional protection that seems to be sensitive to the topological context. Moreover, when this analysis is extended to different growth media (YPD versus YNB), some of these protections show a growth condition dependent behaviour
In vivo binding and hierarchy of assembly of the yeast RNA polymerase I transcription factors
No full textTranscription by RNA polymerase I in Saccharomyces cerevisiae requires a series of transcription factors that have been genetically and biochemically identified. In particular, the core factor (CF) and the upstream activation factor (UAF) have been shown in vitro to bind the core element and the upstream promoter element, respectively. We have analyzed in vivo the DNAse I footprinting of the 35S promoter in wild-type and mutant strains lacking one specific transcription factor at the time. In this way we were able to unambiguously attribute the protections by the CF and the UAF to their respective putative binding sites. In addition, we have found that in vivo a binding hierarchy exists, the UAF being necessary for CF binding. Because the CF footprinting is lost in mutants lacking a functional RNA polymerase I, we also conclude that the final step of preinitiation-complex assembly affects binding of the CF, stabilizing its contact with DNA. Thus, in vivo, the CF is recruited to the core element by the UAF and stabilized on DNA by the presence of a functional RNA polymerase I
In vivo studies of the Non Transcribed Spacer region of rDNA in S.cerevsiae
No full textThe rDNA is the genetic locus that encodes the ribosomal RNAs and physically defines where ribosomes start to assemble. In the yeast Saccharomyces cerevisiae, its highly repetitive structure makes it a very interesting target for studies about genome stability, chromatin mediated transcriptional silencing and progression of aging. In fact, recombination among the repeated units is suppressed in a WT cell. Moreover, when genes transcribed by RNA polymerase II are inserted in the rDNA cluster, their transcription is silenced. Finally, the formation of rDNA minicircles has been shown to be one of the causes of aging in yeast. DNA topoisomerase I has been shown to suppress recombination specifically at the rDNA of S. cerevisiae. Moreover, also the chromatin structure of this locus is affected in a top1 strain, because rDNA specific transcriptional silencing is abolished. Nonetheless, the molecular basis of how this enzyme interferes with these functions is yet unknown. Here are reported results obtained by in vivo studies of DNA-protein interactions occurring on the rDNA locus. The analyses include mapping of: nucleosome positioning; RNA polymerase I transcription factors and DNA topoisomerase I cleavage sites. Important conclusions can be drawn: nucleosome postitioning in the Non-transcribed Spacer (NTS) is not affected by RNA polymerase I transcription; the RNA polymerase I transcription factors bind DNA in vivo with a defined hierarchy, the DNA topoisomerase I cleaves the NTS in very specific sites, but cleavage is not induced by RNA polymerase I transcription. These in vivo studies help to characterize, the molecular basis of important phenomena as the transcriptional silencing and genome stability in yeast
SIR2 affects superhelicity of S. cerevisiae DNA plasmids and acts as replicative silencer
No full text
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
- …
