Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping

Dutrow, Natalie; Nix, David A.; Holt, Derick G.; Milash, Brett; Dalley, Brian; Westbroek, Erick M.; Parnell, Timothy J.; Cairns, Bradley R.

doi:10.1038/ng.196

Cited by 101 publications

(110 citation statements)

References 38 publications

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“…The same threshold was applied in the first full annotation of the fission yeast genome (Wood et al 2002). However, the subsequent discovery of an additional 63 small protein-coding genes combines with the realization that 94% of the genome is transcribed (Dutrow et al 2008;Wilhelm et al 2008;Quintales et al 2010) to raise the distinct possibility that further small protein-coding genes await discovery.…”

Section: T He Fission Yeast Schizosaccharomyces Pombe Is a Widelymentioning

confidence: 99%

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Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

et al. 2011

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Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 59 and 39 RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.

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Section: T He Fission Yeast Schizosaccharomyces Pombe Is a Widelymentioning

confidence: 99%

“…It undergoes a limited, yet highly defined, differentiation program in its sexual cycle. The initial genome annotation (Wood et al 2002) has been refined to a complement of 5027 protein-coding genes (Dutrow et al 2008;Wilhelm et al 2008;Quintales et al 2010).…”

Section: T He Fission Yeast Schizosaccharomyces Pombe Is a Widelymentioning

confidence: 99%

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

et al. 2011

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“…To test this possibility we examined the insertion levels at the transcription start sites (TSSs) (annotated in the Sanger Center, February 2011 chromosome contigs based on Dutrow et al (2008) and Lantermann et al (2010) (Figure 3C). As expected, nucleosome occupancy was very low in the regions 150 nt upstream of TSSs and from the start of ORFs, nucleosomes were positioned in phased arrays.…”

Section: The Insertion Sites Favor Nucleosome-depleted Positionsmentioning

confidence: 99%

Integration Profiling of Gene Function With Dense Maps of Transposon Integration

et al. 2013

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Understanding how complex networks of genes integrate to produce dividing cells is an important goal that is limited by the difficulty in defining the function of individual genes. Current resources for the systematic identification of gene function such as siRNA libraries and collections of deletion strains are costly and organism specific. We describe here integration profiling, a novel approach to identify the function of eukaryotic genes based upon dense maps of transposon integration. As a proof of concept, we used the transposon Hermes to generate a library of 360,513 insertions in the genome of Schizosaccharomyces pombe. On average, we obtained one insertion for every 29 bp of the genome. Hermes integrated more often into nucleosome free sites and 33% of the insertions occurred in ORFs. We found that ORFs with low integration densities successfully identified the genes that are essential for cell division. Importantly, the nonessential ORFs with intermediate levels of insertion correlated with the nonessential genes that have functions required for colonies to reach full size. This finding indicates that integration profiles can measure the contribution of nonessential genes to cell division. While integration profiling succeeded in identifying genes necessary for propagation, it also has the potential to identify genes important for many other functions such as DNA repair, stress response, and meiosis.T HE accelerated rate of gene discovery in an increasing number of species has challenged the existing methods for determining the functions of genes. Traditional approaches for characterizing the function of genes rely on obtaining mutant alleles and testing them in individual experiments for phenotypes. Direct and systematic methods for evaluating gene function have been developed. Genomewide RNAi screens of cultured cells require the synthesis, validation, and refinement of large libraries of double stranded RNAs or vectors that express double stranded RNAs. While RNAi screens have successfully identified many genes that may contribute to key functions such as the replication of human immunodeficiency virus (Brass et al. 2008;Konig et al. 2008;Zhou et al. 2008), the production of RNAi libraries is resource intensive and substantial complications exist, such as off-target effects and incomplete mRNA knockdown.An alternate approach for characterizing gene function in haploid cells relies on targeted gene deletions. For Saccharomyces cerevisiae and Schizosaccharomyces pombe, collections of strains have been created that contain systematic deletions of the predicted coding sequences (Winzeler et al. 1999;Kim et al. 2010). These comprehensive collections of strains can be readily screened under a variety of conditions to probe the contributions of individual genes to specific processes. However, considerable effort and resources are required to generate deletion sets and once generated, it is difficult to study the deletions in combination with other mutations. Another limitation with deletion collec...

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“…G ENOME-WIDE surveys of eukaryotic transcriptomes have led to the identification of abundant noncoding transcription in plants, mammals (Lee et al 2009), and fungi (David et al 2006;Samanta et al 2006;Dutrow et al 2008;Nagalakshmi et al 2008;Sellam et al 2010). The noncoding transcriptome of higher eukaryotes includes a class of various small RNAs that were extensively studied and that were shown to directly modulate gene expression (reviewed by Lee et al 2009;Olejniczak et al 2010;Taft et al 2010).…”

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confidence: 99%

Transcriptional Regulatory Circuitries in the Human Pathogen Candida albicans Involving Sense–Antisense Interactions

Aḥmad¹,

Kravets

Rustchenko

2012

Genetics

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Candida albicans, a major human fungal pathogen, usually contains a diploid genome, but controls adaptation to a toxic alternative carbon source L-sorbose, by the reversible loss of one chromosome 5 (Ch5). We have previously identified multiple unique regions on Ch5 that repress the growth on sorbose. In one of the regions, the CSU51 gene determining the repressive property of the region was identified. We report here the identification of the CSU53 gene from a different region on Ch5. Most importantly, we find that CSU51 and CSU53 are associated with novel regulatory elements, ASUs, which are embedded within CSUs in an antisense configuration. ASUs act opposite to CSUs by enhancing the growth on sorbose. In respect to the CSU transcripts, the ASU long antisense transcripts are in lesser amounts, are completely overlapped, and are inversely related. ASUs interact with CSUs in natural CSU/ASU cis configurations, as well as when extra copies of ASUs are placed in trans to the CSU/ASU configurations. We suggest that ASU long embedded antisense transcripts modulate CSU sense transcripts.

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Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping

Cited by 101 publications

References 38 publications

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

Integration Profiling of Gene Function With Dense Maps of Transposon Integration

Transcriptional Regulatory Circuitries in the Human Pathogen Candida albicans Involving Sense–Antisense Interactions

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