Project description:We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. nucleosome mapping for 3 strains bearing yeast artificial chromosomes from Kluyveromyces lactis and 2 strains with Debaryomyces hansenii artificial chromosomes in Saccharomyces cerevisiae
Project description:We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit.
Project description:In contrast to the desiccation tolerant (DT) ‘orthodox’ seeds, the so-called ‘intermediate’ seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds but show a considerable variability for the seed DT level, which may help to decipher the molecular basis of seed DT in plants. We thus led a comparative transcriptome analysis of developing seeds in three coffee species with contrasting seed DT levels. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were upregulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, an upregulation of numerous players of the metabolism, transport and perception of auxin was observed in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT levels are better prepared to cease respiration and avoid oxidative stresses.
2020-05-26 | PXD015806 | Pride
Project description:New species description
| PRJNA369468 | ENA
Project description:DT-DYLC &DT-DYLCJ
| PRJNA1237704 | ENA
Project description:Taxonomy and description of new species and reclassification of some bacterial strains
Project description:We report RNA-seq data for S. cerevisiae strains following temperature shift using oligo dT purified, ribo-depleted, or 3'-TAG sequencing libraries.
