0000000000074497
AUTHOR
Oreto Antúnez
showing 20 related works from this author
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression
2008
Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Δ cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice an…
iTRAQ and DIGE in the ecophysiological characterization of zebra mussel populations (Dreissena polymorpha) invading the Ebro and the Júcar hydrograph…
2012
Poster presentado en el 9th Iberian and 6th Iberoamerican Congress on Environmental Contamination and Toxicology "The environmental research: essential for sustainability" celebrado en Valencia del 1 al 3 de julio de 2013
MOESM2 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 2: Fig. S2. Gene set enrichment analysis (GSEA) for the highest ChIP-exo reads. The genes were ranked according to the number of mapped reads and searched for GO terms enriched at the top of the list in comparison with the rest of the list using GSEA. The resulting list of over-represented GO terms was reduced and visualized with the ReviGO web server ( http://revigo.irb.hr/ ). a) Binding at 25 °C. Left: Results at the Biological Process GO; right: Results at the Cellular Component GO. b) Binding at 37 °C, results are given for the Biological Process GO. The Cellular Component GO gave no results. The size of the circle for each GO term is proportional to the number of genes …
MOESM4 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 4: Fig. S4. Gene set enrichment analysis (GSEA) analysis of HL ratios (sus1Δ/WT). Gene Ontology (GO) terms (filtered by means of ReviGO software, see Fig, S2) over-represented at the top and at the bottom of the ranked list of HL ratio values.
MOESM5 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 5: Table S1. Is a table listing strain used in this study.
MOESM1 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 1: Fig. S1. Sus1 occupancy at TFIID-dependent genes was monitored by ChIP analysis of Sus1-TAP in a wild-type strain (Sus1-TAP). As a control, the signal of an isogenic strain bearing no-tagged Sus1 was monitored (No-tag). The occupancy level was calculated as the signal ratio of IP samples in relation to the input signal and relative to an internal control. The resulting normalized ratios were plotted. Error bars represent the SD from at least three independent experiments. Differences in means were assessed by Student’s independent-samples t test. P values
Mitochondrial inheritance and fermentative : oxidative balance in hybrids between Saccharomyces cerevisiae and Saccharomyces uvarum.
2008
Breeding between Saccharomyces species is a useful tool for obtaining improved wine yeast strains, combining fermentative features of parental species. In this work, 25 artificial Saccharomyces cerevisiae × Saccharomyces uvarum hybrids were constructed by spore conjugation. A multi-locus PCR‐restriction fragment length polymorphism (PCR‐RFLP) analysis, targeting six nuclear gene markers and the ribosomal region including the 5.8S rRNA gene and the two internal transcribed spacers, showed that the hybrid genome is the result of two chromosome sets, one coming from S. cerevisiae and the other from S. uvarum. Mitochondrial DNA (mtDNA) typing showed uniparental inheritance in all hybrids. Furth…
MOESM7 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 7. ChIP-exo data analysis.
MOESM3 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 3: Fig. S3. Gene set enrichment analysis (GSEA) of TR ratios (sus1Δ/WT). Gene Ontology (GO) terms (filtered by means of ReviGO software, see Fig, S2) over-represented at the top and at the bottom of the ranked list of TR ratio values.
MOESM6 of The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Additional file 6: Table S2. Is a table listing Primers for ChIP analysis and RT-qPCR.
Yeast HAT1 and HAT2 deletions have different life-span and transcriptome phenotypes
2005
AbstractHAT-B is a yeast histone acetyltransferase composed of Hat1, Hat2 and Hif1 proteins. We demonstrate that a hat2 mutant or a hat1hat2 double mutant, but not a hat1 mutant, have an extended life-span. Transcriptome analysis shows that the single hat mutants are not very different from wild type. However, the comparison of the hat1 and hat2 transcriptomes shows that they are different. The hat1hat2 double mutant shows a transcriptional phenotype similar to that of the hat1 mutant but strongly enhanced. These results indicate that Hat2p could have additional functions in the cell to those of Hat1p.
2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vent…
2011
Hydrothermal vent mussels Bathymodiolus azoricus are naturally exposed to toxic chemical species originated directly from vent chimneys. The amount of toxic elements varies significantly among vent sites along the Mid-Atlantic Ridge and B. azoricus must be able to adapt to changes in hydrothermal fluid composition, temperature and pressure. The aim of this work was to study changes in the proteome in the "gill-bacteria complex" of mussels B. azoricus from three hydrothermal vent sites with distinct environmental characteristics using 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE). Results showed that 31 proteins had different expression profiles among vent sites and both cluster…
Protein expression profiles in Bathymodiolus azoricus exposed to cadmium
2019
Proteomic changes in the "gill-bacteria complex" of the hydrothermal vent mussel B. azoricus exposed to cadmium in pressurized chambers ((Incubateurs Pressurises pour l'Observation en Culture d'Animaux Marins Profonds - IPOCAMP) were analyzed and compared with the non-exposed control group. 2-D Fluorescence Difference Gel Electrophoresis (2D-DIGE) showed that less than 1.5% of the proteome of mussels and symbiotic bacteria were affected by a short-term (24 h) Cd exposure. Twelve proteins of the more abundant differentially expressed proteins of which six were up-regulated and six were down-regulated were excised, digested and identified by mass spectrometry. The identified proteins included…
Screening trematodes for novel intervention targets: a proteomic and immunological comparison of Schistosoma haematobium, Schistosoma bovis and Echin…
2011
SUMMARYWith the current paucity of vaccine targets for parasitic diseases, particularly those in childhood, the aim of this study was to compare protein expression and immune cross-reactivity between the trematodes Schistosoma haematobium, S. bovis and Echinostoma caproni in the hope of identifying novel intervention targets. Native adult parasite proteins were separated by 2-dimensional gel electrophoresis and identified through electrospray ionisation tandem mass spectrometry to produce a reference gel. Proteins from differential gel electrophoresis analyses of the three parasite proteomes were compared and screened against sera from hamsters infected with S. haematobium and E. caproni fo…
A multicentric study to evaluate the use of relative retention times in targeted proteomics.
2016
Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results…
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome
2013
All participating laboratories are members of ProteoRed-ISCIII.-- et al.
The SAGA/TREX‑2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally
2018
Abstract Background Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt–Ada–Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. Results Here we find that the SAGA/TREX-2 subunit Sus1 associates with upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitmen…
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.
From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures
2017
Background Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time. Results High-strength liquor from acidified grass biomass exhibited a low biodiversity, which differed greatly depen…
A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses
2004
The yeast Saccharomyces cerevisiae has been widely used for the implementation of DNA chip technologies. For this reason and due to the extensive use of this organism for basic and applied studies, yeast DNA chips are being used by many laboratories for expression or genomic analyses. While membrane arrays (macroarrays) offer several advantages, for many laboratories they are not affordable. Here we report that a cluster of four Spanish molecular-biology yeast laboratories, with relatively small budgets, have developed a complete set of probes for the genome of S. cerevisiae. These have been used to produce a new type of macroarray on a nylon surface. The macroarrays have been evaluated and…