Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae

Kyriakou, Dimitris; Stavrou, Emmanouil; Demosthenous, Panayiota; Angelidou, Georgia; Luis, Bryan-Joseph San; Boone, Charles; Promponas, Vasilis J.; Kirmizis, Antonis

doi:10.1186/s12915-016-0325-7

Cited by 20 publications

(22 citation statements)

References 87 publications

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“…Determining how ncRNAs fit into the genetic networks identified using the protein deletion collection and the synthetic genetic array technology (Baryshnikova et al 2010) will provide a comprehensive map of protein/ ncRNA interactions and elucidate further the global role of ncRNA in the cell. Indeed, scientists have already begun to explore the interplay between ncRNAs and proteins (Kyriakou et al 2016). Finally, this resource will open up a new facet for large-scale biotechnological applications.…”

Section: Resultsmentioning

confidence: 99%

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

Parker¹,

Fraczek²,

et al. 2017

RNA

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Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research.

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Section: Resultsmentioning

confidence: 99%

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

Parker¹,

Fraczek²,

et al. 2017

RNA

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“…In the budding yeast S. cerevisiae , a trans -mechanism was stated for the stable unannotated transcript (SUT) SUT457, which physically interacts with 12 genes essential for telomere organization and homeostasis (Kyriakou et al 2016) . Another example is SPNCRNA.1164 , a regulator of atf1 expression in response to oxidative stress in S. pombe (Leong et al 2014).…”

Section: The Challenge Of Classifying Lncrnasmentioning

confidence: 99%

A current view on long noncoding RNAs in yeast and filamentous fungi

Till

Mach

Mach-Aigner

2018

Appl Microbiol Biotechnol

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Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.

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“…The ability of 50 CUT, 93 SUT, 61 snoRNA and 168 tRNA deletion mutant strains to utilize different carbon sources, and to tolerate extreme pH and oxidative stress was scored. The colony size was used as a proxy for fitness and normalized to the wild-type strain according to Tong and Boone [9]. The ncRNA deletion mutants showing similar behaviour across the 23 different conditions were grouped, generating 42 distinct functional clusters (Fig 1).…”

Section: Resultsmentioning

confidence: 99%

“…These results suggest that SUT126, SUT126, SUT035 and SUT532 can act in trans , which may underlie the altered regulation of large numbers of genes in these mutants. There are only a handful of examples of trans acting ncRNAs in yeast but a CUT that affects gene regulation, CUT281, can act both in cis and trans to repress the PHO84 gene [6, 36], while SUT457 can act in trans to rescue the phenotype of telomeric overhang accumulation observed in SUT457Δ cells [9].…”

Section: Resultsmentioning

confidence: 99%

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Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and widespreadin transeffects on the protein regulatory network

Balarezo-Cisneros

Parker

Fraczek

et al. 2020

Preprint

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24Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated 25 Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to 26 play pivotal roles in the transcriptional and post-transcriptional regulation of genes in 27 eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces 28 cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA 29 deletion strains in 23 different growth conditions were collected, identifying ncRNAs 30 responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 31 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided 32 by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding 33 genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and 34 SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we 35 described the impact of SUTs and CUTs in modulating coding gene expression in response 36 of different environmental conditions, regulating important biological process such as 37 respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT530, 38 SUT468) or rRNA processing (SUT075 and snR30). Overall, this data captures and integrates 39 the regulatory and phenotypic network of ncRNAs and protein coding genes, providing 40 genome-wide evidence of the impact of ncRNAs on cellular homeostasis. 41 42 Author Summary 43 44 The yeast genome contains 25% of non-coding RNA molecules (ncRNAs), which do not 45 translate into proteins but are involved in regulation of gene expression. ncRNAs can affect 46 nearby genes by physically interfering with their transcription (cis mode of action), or they 50 regulation are still lacking. Here, we used the ncRNA yeast deletion collection to score their 51 impact on cellular function in different environmental conditions. A group of 20 ncRNAs 52 mutants with broad fitness diversity were selected to investigate their effect on the protein and 53 ncRNA expression network. We showed a high correlation between altered phenotypes and 54 global transcriptional changes, in an environmental dependent manner. We confirmed the 55 widespread trans acting expressional regulation of ncRNAs in the genome and their role in 56 affecting transcription factors. These findings support the notion of the involvement on ncRNAs 57 in fine tuning the cellular expression via regulations of TFs, as an advantageous RNA-58 mediated mechanism that can be fast and cost-effective for the cells. 59 65 expression. More recently, RNA transcripts which are not translated into protein, have been 66 described to have a prominent role as epigenetic modifiers [1,2]. There are an increasing 67 number of examples of these non-coding RNA (ncRNA) transcripts regulating gene 68 expression positively and negatively [3-10]. 69 RNA interference (RNAi) was the first understood example of ncRNA involvement in 70 epigene...

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Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae

Cited by 20 publications

References 87 publications

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

A current view on long noncoding RNAs in yeast and filamentous fungi

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and widespreadin transeffects on the protein regulatory network

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