Quantification of the yeast transcriptome by single-molecule sequencing

Lipson, Doron; Raz, Tal; Kieu, Alix; Jones, Dan; Giladi, Eldar; Thayer, Edward C.; Thompson, John F.; Letovsky, Stan; Milos, Patrice M.; Causey, Marie

doi:10.1038/nbt.1551

Cited by 182 publications

(190 citation statements)

References 24 publications

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“…Since RPs are needed in equimolar within the ribosome (Spahn et al 2001), and since pairs of duplicated RP genes encode nearly identical proteins and are thus functionally redundant within the ribosome (Lucioli et al 1988;Rotenberg et al 1988), we may expect their transcripts to have lower expression levels than transcripts of RP genes that have only one copy in the yeast genome. To test this hypothesis, we obtained mRNA abundance measurements from three different DNA microarray technologies (Holstege et al 1998;David et al 2006;Lipson et al 2009) and three different RNA-seq techniques (Nagalakshmi et al 2008;Lipson et al 2009;Yassour et al 2009). Indeed, in all six data sets, transcripts of singlecopy RP genes are expressed at significantly higher levels than transcripts of duplicated RP genes ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…RPs for which a measurement was missing in a given data set appear as gray bars and are sorted to the bottom of the list. The ranking is shown for our library of RP promoter fusions (leftmost column), for transcription rate measurements using DNA microarrays (Holstege et al 1998) (second column), and for mRNA abundance measurements using DNA microarrays (David et al 2006;Lipson et al 2009) or RNA-seq (Nagalakshmi et al 2008;Lipson et al 2009;Yassour et al 2009). For each data set, the rank-sum test P-value that tests whether the ranking of singlecopy RPs is higher than that of duplicated RPs is shown.…”

Section: Obtaining Accurate Measurements Of Rp Promoter Activitiesmentioning

confidence: 99%

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Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Zeevi¹,

Sharon²,

Lotan-Pompan³

et al. 2011

Genome Res.

105

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Coordinate regulation of ribosomal protein (RP) genes is key for controlling cell growth. In yeast, it is unclear how this regulation achieves the required equimolar amounts of the different RP components, given that some RP genes exist in duplicate copies, while others have only one copy. Here, we tested whether the solution to this challenge is partly encoded within the DNA sequence of the RP promoters, by fusing 110 different RP promoters to a fluorescent gene reporter, allowing us to robustly detect differences in their promoter activities that are as small as~10%. We found that single-copy RP promoters have significantly higher activities, suggesting that proper RP stoichiometry is indeed partly encoded within the RP promoters. Notably, we also partially uncovered how this regulation is encoded by finding that RP promoters with higher activity have more nucleosome-disfavoring sequences and characteristic spatial organizations of these sequences and of binding sites for key RP regulators. Mutations in these elements result in a significant decrease of RP promoter activity. Thus, our results suggest that intrinsic (DNA-dependent) nucleosome organization may be a key mechanism by which genomes encode biologically meaningful promoter activities. Our approach can readily be applied to uncover how transcriptional programs of other promoters are encoded.

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Section: Resultsmentioning

confidence: 99%

Section: Obtaining Accurate Measurements Of Rp Promoter Activitiesmentioning

confidence: 99%

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Zeevi¹,

Sharon²,

Lotan-Pompan³

et al. 2011

Genome Res.

105

View full text Add to dashboard Cite

show abstract

“…Bioinformatics-To compute digital gene expression (DGE) from the Helicos sequence data for the RefSeq genes, we used the DGE pipeline of HeliSphere 1.1.498.63 software using the Mouse.Txome reference files with default settings (14). To compute DGE for Repbase to deal with the fact that reads of repetitive sequence will often align to multiple locations in the genome, we used a method called Probabilistic Assessment of Sequencing Alignments that assigns weights to multiple alignments for a read.…”

Section: Methodsmentioning

confidence: 99%

The WTX Tumor Suppressor Interacts with the Transcriptional Corepressor TRIM28

Kim

Wittner

Amzallag

et al. 2015

Journal of Biological Chemistry

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Background:The Wilms tumor suppressor WTX localizes to both nucleus and cytoplasm, but its nuclear function is not understood. Results: Nuclear WTX co-immunoprecipitates with the transcriptional corepressor TRIM28, modulating its chromatin binding and coregulating the expression of DNA repeat elements. Conclusion: WTX contributes to silencing of heterochromatic repeats. Significance: WTX may modulate tumorigenesis and cell differentiation in part through its effect on chromatin regulation.

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“…Namely, next generation sequencing technologies, which are rapidly revolutionizing evolutionary biology research will be of paramount interest (Rokas & Abbot 2009). These approaches have already showed their efficiency in various applications, including rapid SNP (single nucleotide polymorphism) discovery (Barbazuk et al 2007), genome sequencing of ecologically important models (Vera et al 2008) as well as accurate gene expression analysis (Torres et al 2007;Lipson et al 2009). High throughput pyrosequencing (454 Life Sciences, Margulies et al 2005) is particularly relevant to the study of non-model organisms such as whitefish since it yields longer sequencing reads than any other method, allowing more accurate de novo sequence assemblies in the absence of reference genomes.…”

Section: Future Directions: Stepping Into the Next-generation Sequencmentioning

confidence: 99%

On the origin of species: insights from the ecological genomics of lake whitefish

Bernatchez

Renaut

Whiteley

et al. 2010

Phil. Trans. R. Soc. B

228

317

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In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on the ecological genomics of sympatric forms of whitefish (Coregonus spp.) engaged in the process of speciation. We present this system as an example of how applying a combination of approaches under the conceptual framework of the theory of adaptive radiation has yielded substantial insight into evolutionary processes in a non-model species. We also discuss how the joint use of recent biotechnological developments will provide a powerful means to address issues raised by observations made to date. Namely, we present data illustrating the potential offered by combining next generation sequencing technologies with other genomic approaches to reveal the genomic bases of adaptive divergence and reproductive isolation. Given increasing access to these new genomic tools, we argue that non-model species studied in their ecological context such as whitefish will play an increasingly important role in generalizing knowledge of speciation.

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Quantification of the yeast transcriptome by single-molecule sequencing

Cited by 182 publications

References 24 publications

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

The WTX Tumor Suppressor Interacts with the Transcriptional Corepressor TRIM28

On the origin of species: insights from the ecological genomics of lake whitefish

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