IF 2.2 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2024-03-03 DOI: 10.1002/yea.3931

Shidong Xi, Tania Nguyen, Struan Murray, Phil Lorenz, Jane Mellor

{"title":"Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.","authors":"Shidong Xi, Tania Nguyen, Struan Murray, Phil Lorenz, Jane Mellor","doi":"10.1002/yea.3931","DOIUrl":"10.1002/yea.3931","url":null,"abstract":"Genomes from yeast to humans are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes gives the expected reference pattern. Bioinformatic pattern matching to the reference pattern identified 9542 transcription units in Saccharomyces cerevisiae, of which 47% are coding and 53% are noncoding. In total, 3113 (33%) are unannotated noncoding transcription units. Anchoring all transcription units to the TSS or polyadenylation site (PAS) of annotated genes reveals distinctive architectures of linked pairs of divergent transcripts approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS -60nt with respect to PAS) noncoding transcription unit co-occurs with a downstream (TSS +150nt) coding transcription unit and acts to limit levels of upstream antisense transcripts. The potential for extensive transcriptional interference is evident from low abundance unannotated transcription units with variable TSS (median -240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein-coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"222-241"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Implication of polymerase recycling for nascent transcript quantification by live cell imaging. 聚合酶循环对通过活细胞成像定量新生转录本的影响。

IF 2.2 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2024-02-22 DOI: 10.1002/yea.3929

Olivia Kindongo, Guillaume Lieb, Benjamin Skaggs, Yves Dusserre, Vincent Vincenzetti, Serge Pelet

{"title":"Implication of polymerase recycling for nascent transcript quantification by live cell imaging.","authors":"Olivia Kindongo, Guillaume Lieb, Benjamin Skaggs, Yves Dusserre, Vincent Vincenzetti, Serge Pelet","doi":"10.1002/yea.3929","DOIUrl":"10.1002/yea.3929","url":null,"abstract":"Transcription enables the production of RNA from a DNA template. Due to the highly dynamic nature of transcription, live-cell imaging methods play a crucial role in measuring the kinetics of this process. For instance, transcriptional bursts have been visualized using fluorescent phage-coat proteins that associate tightly with messenger RNA (mRNA) stem loops formed on nascent transcripts. To convert the signal emanating from a transcription site into meaningful estimates of transcription dynamics, the influence of various parameters on the measured signal must be evaluated. Here, the effect of gene length on the intensity of the transcription site focus was analyzed. Intuitively, a longer gene can support a larger number of transcribing polymerases, thus leading to an increase in the measured signal. However, measurements of transcription induced by hyper-osmotic stress responsive promoters display independence from gene length. A mathematical model of the stress-induced transcription process suggests that the formation of gene loops that favor the recycling of polymerase from the terminator to the promoter can explain the observed behavior. One experimentally validated prediction from this model is that the amount of mRNA produced from a short gene should be higher than for a long one as the density of active polymerase on the short gene will be increased by polymerase recycling. Our data suggest that this recycling contributes significantly to the expression output from a gene and that polymerase recycling is modulated by the promoter identity and the cellular state.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"279-294"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139933150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differing SAGA module requirements for NCR-sensitive gene transcription in yeast. 酵母中对 NCR 敏感基因转录的不同 SAGA 模块要求。

IF 2.2 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2023-06-25 DOI: 10.1002/yea.3885

Isabelle Georis, Aria Ronsmans, Fabienne Vierendeels, Evelyne Dubois

引用次数: 0

Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance. 对酿酒酵母线粒体转录组的长读程直接 RNA 测序揭示了内含子丰度的条件依赖性。

IF 2.2 4区生物学

Yeast Pub Date : 2024-04-01 Epub Date: 2023-08-29 DOI: 10.1002/yea.3893

Charlotte C Koster, Askar A Kleefeldt, Marcel van den Broek, Marijke Luttik, Jean-Marc Daran, Pascale Daran-Lapujade

{"title":"Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance.","authors":"Charlotte C Koster, Askar A Kleefeldt, Marcel van den Broek, Marijke Luttik, Jean-Marc Daran, Pascale Daran-Lapujade","doi":"10.1002/yea.3893","DOIUrl":"10.1002/yea.3893","url":null,"abstract":"Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene expression and splicing remain unresolved, even in the model eukaryote Saccharomyces cerevisiae. Long-read sequencing could address these fundamental questions. Therefore, a method for the enrichment of mitochondrial RNA and sequencing using Nanopore technology was developed, enabling the resolution of splicing of polycistronic genes and the quantification of spliced RNA. This method successfully captured the full mitochondrial transcriptome and resolved RNA splicing patterns with single-base resolution and was applied to explore the transcriptome of S. cerevisiae grown with glucose or ethanol as the sole carbon source, revealing the impact of growth conditions on mitochondrial RNA expression and splicing. This study uncovered a remarkable difference in the turnover of Group II introns between yeast grown in either mostly fermentative or fully respiratory conditions. Whether this accumulation of introns in glucose medium has an impact on mitochondrial functions remains to be explored. Combined with the high tractability of the model yeast S. cerevisiae, the developed method enables to monitor mitochondrial transcriptome responses in a broad range of relevant contexts, including oxidative stress, apoptosis and mitochondrial diseases.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"256-278"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10112265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast. 多孔裂殖酵母代表了裂殖酵母的一个独特进化系。

IF 2.2 4区生物学

Yeast Pub Date : 2024-03-01 Epub Date: 2023-12-26 DOI: 10.1002/yea.3919

Graham J Etherington, Elisa Gomez Gil, Wilfried Haerty, Snezhana Oliferenko, Conrad A Nieduszynski

{"title":"Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast.","authors":"Graham J Etherington, Elisa Gomez Gil, Wilfried Haerty, Snezhana Oliferenko, Conrad A Nieduszynski","doi":"10.1002/yea.3919","DOIUrl":"10.1002/yea.3919","url":null,"abstract":"The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"95-107"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139037982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features. 端粒到端粒日本裂殖酵母基因组组装揭示了迄今未知的基因组特征。

IF 2.2 4区生物学

Yeast Pub Date : 2024-03-01 Epub Date: 2024-03-07 DOI: 10.1002/yea.3912

Graham J Etherington, Pei-Shang Wu, Snezhana Oliferenko, Frank Uhlmann, Conrad A Nieduszynski

{"title":"Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features.","authors":"Graham J Etherington, Pei-Shang Wu, Snezhana Oliferenko, Frank Uhlmann, Conrad A Nieduszynski","doi":"10.1002/yea.3912","DOIUrl":"10.1002/yea.3912","url":null,"abstract":"Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as \"fission yeasts.\" As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"73-86"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New species, genome assemblies, and tools shed fresh light on fission yeasts. 新物种、基因组组装和工具为裂殖酵母带来了新的启示。

IF 2.2 4区生物学

Yeast Pub Date : 2024-03-01 DOI: 10.1002/yea.3930

Melania D'Angiolo, Jürg Bähler

引用次数: 0

Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus. 恢复裂殖酵母物种 Schizosaccharomyces versatilis Wickerham et Duprat，它是日本裂殖酵母的一个兄弟物种。

IF 2.2 4区生物学

Yeast Pub Date : 2024-03-01 Epub Date: 2024-03-07 DOI: 10.1002/yea.3922

Michael Brysch-Herzberg, Guo-Song Jia, Matthias Sipiczki, Martin Seidel, Wen-Cai Zhang, Li-Lin Du

{"title":"Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus.","authors":"Michael Brysch-Herzberg, Guo-Song Jia, Matthias Sipiczki, Martin Seidel, Wen-Cai Zhang, Li-Lin Du","doi":"10.1002/yea.3922","DOIUrl":"10.1002/yea.3922","url":null,"abstract":"Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"108-127"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140050447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The rise of single-cell transcriptomics in yeast 酵母中单细胞转录组学的兴起

IF 2.6 4区生物学

Yeast Pub Date : 2024-02-25 DOI: 10.1002/yea.3934

Mariona Nadal-Ribelles, Carme Solé, Eulalia de Nadal, Francesc Posas

引用次数: 0

Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions. 在营养不良饥饿条件下氨基酸营养不良菌群的特征。

IF 2.2 4区生物学

Yeast Pub Date : 2024-01-01 Epub Date: 2023-11-23 DOI: 10.1002/yea.3910

Alisha G Lewis, Laurin Carmichael, Rebecca Y Wang, Patrick A Gibney

{"title":"Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions.","authors":"Alisha G Lewis, Laurin Carmichael, Rebecca Y Wang, Patrick A Gibney","doi":"10.1002/yea.3910","DOIUrl":"10.1002/yea.3910","url":null,"abstract":"Auxotrophic strains starving for their cognate nutrient, termed auxotrophic starvation, are characterized by a shorter lifespan, higher glucose wasting phenotype, and inability to accomplish cell cycle arrest when compared to a \"natural starvation,\" where a cell is starving for natural environmental growth-limiting nutrients such as phosphate. Since evidence of this physiological response is limited to only a subset of auxotrophs, we evaluated a panel of auxotrophic mutants to determine whether these responses are characteristic of a broader range of amino acid auxotrophs. Based on the starvation survival kinetics, the panel of strains was grouped into three categories-short-lived strains, strains with survival similar to a prototrophic wild type strain, and long-lived strains. Among the short-lived strains, we observed that the tyrosine, asparagine, threonine, and aspartic acid auxotrophs rapidly decline in viability, with all strains unable to arrest cell cycle progression. The three basic amino acid auxotrophs had a survival similar to a prototrophic strain starving in minimal media. The leucine, tryptophan, methionine, and cysteine auxotrophs displayed the longest lifespan. We also demonstrate how the phenomenon of glucose wasting is limited to only a subset of the tested auxotrophs, namely the asparagine, leucine, and lysine auxotrophs. Furthermore, we observed pleiotropic phenotypes associated with a subgroup of auxotrophs, highlighting the importance of considering unintended phenotypic effects when using auxotrophic strains especially in chronological aging experiments.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"5-18"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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