Search results for "RNA Polymerase II"
showing 10 items of 76 documents
A complete set of nascent transcription rates for yeast genes
2010
The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) a…
Genome-wide studies of mRNA synthesis and degradation in eukaryotes
2012
In recent years, the use of genome-wide technologies has revolutionized the study of eukaryotic transcription producing results for thousands of genes at every step of mRNA life. The statistical analyses of the results for a single condition, different conditions, different transcription stages, or even between different techniques, is outlining a totally new landscape of the eukaryotic transcription process. Although most studies have been conducted in the yeast Saccharomyces cerevisiae as a model cell, others have also focused on higher eukaryotes, which can also be comparatively analyzed. The picture which emerges is that transcription is a more variable process than initially suspected,…
Genome wide studies of mRNA synthesis and degradation in eukaryotes
2012
In recent years, the use of genome-wide technologies has revolutionized the study of eukaryotic transcription producing results for thousands of genes at every step of mRNA life. The statistical analyses of the results for a single condition, different conditions, different transcription stages, or even between different techniques, is outlining a totally new landscape of the eukaryotic transcription process. Although most studies have been conducted in the yeast Saccharomyces cerevisiae as a model cell, others have also focused on higher eukaryotes, which can also be comparatively analyzed. The picture which emerges is that transcription is a more variable process than initially suspected,…
Chromatin structure of the yeast FBP1 gene: transcription-dependent changes in the regulatory and coding regions.
1993
We have studied the chromatin structure of the Saccharomyces cerevisiae FBP1 gene, which codes for fructose-1,6-bisphosphatase. A strong, constitutive, DNase I, micrococcal nuclease and S1 nuclease hypersensitive site is present close to the 3′ end of the coding region. In the repressed state, positioned nucleosomes exist around this site, and subtle changes occur in this nucleosomal organization upon derepression. A DNase I hypersensitive region is located within the promoter between positions −540 and −400 and it extends towards the gene in the derepressed state, leading to an alteration of nucleosomal positioning. Psoralen crosslinking of chromatin, which is used for the first time to st…
External conditions inversely change the RNA polymerase II elongation rate and density in yeast.
2013
Elongation speed is a key parameter in RNA polymerase II (RNA pol II) activity. It affects the transcription rate, while it is conditioned by the physicochemical environment it works in at the same time. For instance, it is well-known that temperature affects the biochemical reactions rates. Therefore in free-living organisms that are able to grow at various environmental temperatures, such as the yeast Saccharomyces cerevisiae, evolution should have not only shaped the structural and functional properties of this key enzyme, but should have also provided mechanisms and pathways to adapt its activity to the optimal performance required. We studied the changes in RNA pol II elongation speed …
Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe
2021
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery
2004
12 páginas, 7 figuras, 1 tabla. Material suplementario en: https://doi.org/10.1016/S0092-8674(03)01025-0. The SUS1 sequences have been deposited in GenBank with the accession number AY278445.
Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae.
2014
Abstract Background Specific histone modifications play important roles in chromatin functions; i.e., activation or repression of gene transcription. This participation must occur as a dynamic process. Nevertheless, most of the histone modification maps reported to date provide only static pictures that link certain modifications with active or silenced states. This study, however, focuses on the global histone modification variation that occurs in response to the transcriptional reprogramming produced by a physiological perturbation in yeast. Results We did a genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after saline stress. The most…
The Pisum sativum psp54 gene requires ABI3 and a chromatin remodeller to switch from a poised to a transcriptionally active state
2011
Summary •Aspects of transcriptional regulation in plants, such as the order in which transcriptional factors and the preinitiation complex are assembled, are obscure because studies carried out under conditions in which native chromatin structure is preserved are still few in comparison with those carried out under other conditions. •In vivo chromatin immunoprecipitation (ChIP) experiments were used here to study the regulation of Pisum sativum psp54, which codes for the precursor of a chromatin-associated protein in dry seeds. •Antibodies against PsSNF5, a component of the SWI/SNF remodelling complex, and against the transcriptional factor Pisum sativum abscisic acid insensitive 3 (PsABI3)…
The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field
2014
Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an…