Ontology highlight
ABSTRACT:
PROVIDER: PRJNA418101 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6282634.fastq.gz | Fastqsanger.gz | |||
| SRR6282635.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD.
2010-12-01 | GSE25209 | GEO
Project description:ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD. Epitope tagged strains were compared to untagged control strains. Two biological replicates were preformed for the RME1 ChIP. For the MATa1 and MATalpha2 ChIP, peaks were considered indicative of binding if both MATa1 and MATalpha2 showed enrichment above the untagged control.
2010-12-01 | E-GEOD-25209 | biostudies-arrayexpress
Project description:Ogataea polymorpha draft genome sequencing
| PRJDB3035 | ENA
Project description:This is genome-scale metabolic model of Komagataella pastoris as the representative yeast species for the clade Pichiaceae. This model was generated through homology search using a fungal pan-GEM largely based on Yeast8 for Saccharomyces cerevisiae, in addition to manual curation. This model has been produced by the Yeast-Species-GEMs project from Sysbio (www.sysbio.se). This is model version 1.0.0 accompanying the publication (DOI: 10.15252/msb.202110427), currently hosted on BioModels Database and identified by MODEL2109130009. Further curations of this model will be tracked in the GitHub repository: https://github.com/SysBioChalmers/Yeast-Species-GEMs Models for species of the same clade includes: Ambrosiozyma kashinagacola; Ambrosiozyma monospora; Brettanomyces anomalus; Candida arabinofermentans; Candida boidinii; Candida sorboxylosa; Candida succiphila; Brettanomyces bruxellensis; Komagataella pastoris; Kuraishia capsulata; Ogataea methanolica; Ogataea parapolymorpha; Ogataea polymorpha; Pichia membranifaciens; Ogataea henricii; Ambrosiozyma ambrosiae; Citeromyces matritensis; Ambrosiozyma vanderkliftii; Brettanomyces custersianus; Komagataella populi; Saturnispora hagleri; Saturnispora mendoncae; Saturnispora saitoi; Saturnispora serradocipensis; Saturnispora silvae; Saturnispora zaruensis; Pichia occidentalis; Pichia norvegensis; Pichia nakasei; Pichia kudriavzevii; Pichia heedii; Pichia exigua; Martiniozyma abiesophila; Ogataea nitratoaversa; Ogataea populialbae; Ogataea zsoltii; Ogataea trehalophila; Ogataea trehaloabstinens; Ogataea ramenticola; Ogataea pini; Ogataea pilisensis; Ogataea philodendri; Ogataea glucozyma; Ogataea kodamae; Ogataea methylivora; Ogataea minuta; Ogataea naganishii; Ogataea nonfermentans; Kuraishia ogatae; Kuraishia molischiana; Komagataella pseudopastoris; Ambrosiozyma oregonensis; Ambrosiozyma philentoma; Citeromyces hawaiiensis; Citeromyces siamensis; Ambrosiozyma maleeae; Ambrosiozyma pseudovanderkliftii; Pichia terricola; Saturnispora dispora; Kregervanrija delftensis; Kregervanrija fluxuum. These models are available in the zip file. To cite BioModels, please use: V Chelliah et al; BioModels: ten-year anniversary. Nucleic Acids Res 2015; 43 (D1): D542-D548. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to MIT License for more information.
2021-11-01 | MODEL2109130009 | BioModels
Project description:Ogataea polymorpha species complex population genomics
| PRJNA706707 | ENA
Project description:Eukaryotic genomic DNA is packaged in the nucleus as chromatin – a DNA-protein aggregate regulating genome function, including transcription. Chromatin is classified as either active euchromatin or silent heterochromatin, with each marked by distinct histone post-translational modifications (PTMs). Chromatin composition also mediates genome organization, including how heterochromatin aggregates at the nuclear periphery while euchromatin localizes to the nucleus center. In fungi, heterochromatic loci cluster, including independent centromere and telomere clusters that form the Rabl chromosome conformation. However, it is unknown if chromatin composition and genome organization are conserved in closely related fungi, including some yeast species. Here, we examined differences in histone PTM deposition, gene expression, and genome organization in two yeast species from the order Pichiales, which diverged from a common ancestor with Saccharomyces cerevisiae more than 200 million years ago. We focused on Ogataea polymorpha, which is used for industrial protein production, and Ogataea haglerorum, an isolate of which harbors a translocation between chromosomes 1 and 6. We show that the enrichment of three activating PTMs – the trimethylation of lysine 4 of histone H3 (H3K4me3) and the acetylation of lysine 9 of histone H3 (H3K9ac) or lysine 16 of histone H4 (H4K16ac) – are similar genome-wide yet individual gene orthologs have distinct chromatin and expression patterns. While both Ogataea genomes organize into a Rabl conformation, the O. haglerorum translocation alters subtelomeric chromatin composition and expression of genes affected by the translocation. Our work highlights the genome function differences that occur on a microevolutionary scale.
2026-03-05 | GSE318721 | GEO
Project description:Ogataea polymorpha strain:LTD 37.2 Genome sequencing
| PRJNA1292285 | ENA
Project description:Rme1, a conserved transcription factor among members of the ascomycete lineage, regulates meiosis and pseudohyphal growth in baker’s yeast. The genome of the meiosis-defective fungal pathogen Candida albicans encodes a Rme1 homolog, which we previously mapped within a transcriptional circuitry that controls hyphal growth. To delineate a possible role of Rme1 in C. albicans morphogenesis, we combined genome-wide expression and location analyses of Rme1. Strikingly, Rme1 bound upstream and activated the expression of markers of chlamydosporulation, a process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolished chlamydosporulation in three chlamydospore-forming Candida species, whereas its overexpression bypassed the requirement for chlamydosporulation cues and regulators, indicating that Rme1 is central to chlamydospore development. Moreover, RME1 expression levels correlated with chlamydosporulation efficiency among clinical isolates, further highlighting Rme1 importance in this process. Interestingly, RME1 displayed a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase depending upon Rme1 function and independent of chlamydospore-inducing cues. We suggest that Rme1 function spans from the regulation of meiosis in sexual yeasts to the control of an epigenetic switch necessary for asexual spore formation in meiosis-defective Candida species.
2020-10-07 | GSE142159 | GEO