Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms

Wilkinson, Derek; Váchová, Libuše; Hlaváček, Otakar; Maršíková, Jana; Gilfillan, Gregor D.; Palková, Zdena

doi:10.1155/2018/4950591

Cited by 8 publications

(10 citation statements)

References 73 publications

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“…ncRNAs are derived from sense or antisense coding regions and intergenic regions in yeast (Tudek et al, 2015). They also possess regulatory functions, such as regulating yeast colonies and biofilms (Wilkinson et al, 2018). We asked how the expression of wild-type yeast genes was affected by the inserted dChr.…”

Section: Discussionmentioning

confidence: 99%

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Zhou

Zhang

Wei

et al. 2021

Sci. China Life Sci.

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Yeast artificial chromosomes (YACs) are important tools for sequencing, gene cloning, and transferring large quantities of genetic information. However, the structure and activity of YAC chromatin, as well as the unintended impacts of introducing foreign DNA sequences on DNA-associated biochemical events, have not been widely explored. Here, we showed that abundant genetic elements like TATA box and transcription factor-binding motifs occurred unintentionally in a previously reported data-carrying chromosome (dChr). In addition, we used state-of-the-art sequencing technologies to comprehensively profile the genetic, epigenetic, transcriptional, and proteomic characteristics of the exogenous dChr. We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels. The dChr also displayed highly pervasive transcriptional ability and transcribed hundreds of noncoding RNAs. The results demonstrated that exogenous artificial chromosomes formed chromatin structures and did not remain as naked or loose plasmids. A better understanding of the YAC chromatin nature will improve our ability to design better data-storage chromosomes.

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Section: Discussionmentioning

confidence: 99%

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Zhou

Zhang

Wei

et al. 2021

Sci. China Life Sci.

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Section: Accepted Manuscriptmentioning

confidence: 99%

“…In addi on, Wilkinson et al used RNA sequencing to study the differen al expression of lncRNAs within differen ated cell subpopula ons of colonies and biofilms and found significant differences between cells located at upper (U) and lower (L) parts of a 15-day-old colony (Wilkinson et al 2018). A large number of mRNA/lncRNA pairs were either co-or an -regulated in U as opposed to L cells, which included genes with roles in cell wall organiza on (Wilkinson et al 2018). This supports a role for noncoding transcripts in cell wall remodeling, as U cells are known to resemble starved and quiescent cells which have thickened cell walls, which is in contrast to L cells that mobilize carbohydrates stored in the cell wall by ac va ng cell wall-degrading enzymes (Traven et al 2012).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Non-coding RNAs as cell wall regulators inSaccharomyces cerevisiae

Novačić

Vučenović

Primig

et al. 2020

Critical Reviews in Microbiology

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The cell wall of Saccharomyces cerevisiae is an extracellular organelle crucial for preserving its cellular integrity and detec ng environmental cues. The cell wall is composed of mannoproteins a ached to a polysaccharide network and is con nuously remodeled as cells undergo cell division, ma ng, gametogenesis or adapt to stressors. This makes yeast an excellent model to study the regula on of genes important for cell wall forma on and maintenance. Given that certain yeast strains are pathogenic, a be er understanding of their life cycle is of clinical relevance. This is why transcrip onal regulatory mechanisms governing genes involved in cell wall biogenesis or maintenance have been the focus of numerous studies. However, li le is known about the roles of long non-coding RNAs (lncRNAs), a class of transcripts that are thought to possess li le or no protein coding poten al, in controlling the expression of cell wall-related genes. This review outlines currently known mechanisms of lncRNAmediated regula on of gene expression in S. cerevisiae and describes examples of lncRNA-regulated genes encoding cell wall proteins. We suggest that the associa on of currently annotated lncRNAs with the coding sequences and/or promoters of cell wall-related genes highlights a poten al role for lncRNAs as important regulators of the yeast cell wall structure.

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“…The transition from colonies to biofilms by Saccharomyces cerevisiae is orchestrated in part by the opposing actions of two transcription factors Tup1, which promotes biofilm formation, and Cyc8/Ssn6, which inhibits Flo11 expression and represses biofilm formation [69]. Long non-coding RNAs (lncRNAs) are differentially expressed in Saccharomyces cerevisiae colonies versus biofilms [70].…”

Section: Rationale For the Existence Of Cell Death In Multi-and Unicementioning

confidence: 99%

Targeting intrinsic cell death pathways to control fungal pathogens

Kulkarni

Stolp

Hardwick

2019

Biochemical Pharmacology

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Fungal pathogens pose an increasing threat to public health. Limited clinical drug regimens and emerging drug-resistant isolates challenge infection control. The global burden of human fungal pathogens is estimated at 1 billion infections and 1.5 million deaths annually. In addition, plant fungal pathogens increasingly threaten global food resources. Novel strategies are needed to combat emerging fungal diseases and pan-resistant fungi. An untapped mechanistically novel approach is to pharmacologically activate the intrinsic cell death pathways encoded by pathogenic fungi. This strategy is analogous to new anti-cancer therapeutics now entering the clinic. Here we summarize the best understood examples of cell death mechanisms encoded by pathogenic fungi, contrast these to mammalian cell death pathways, and highlight the gaps in knowledge towards identifying potential death effectors as druggable targets.

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Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms

Cited by 8 publications

References 73 publications

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Non-coding RNAs as cell wall regulators inSaccharomyces cerevisiae

Targeting intrinsic cell death pathways to control fungal pathogens

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