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Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

ABSTRACT: It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments.

ORGANISM(S): Saccharomyces cerevisiae Saccharomyces paradoxus Saccharomyces mikatae

PROVIDER: GSE81320 | GEO | 2017/07/01

REPOSITORIES: GEO

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Project description:ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available. ArrayExpress Release Date: 2010-07-05 Publication Title: ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification Publication Author List: Matthew Biery,Heather Bouzek,Ronghua Chen,Stuart Jackson,Jason M. Johnson,Carol A. Rohl,Chris K. Raymond,David Haynor,Christopher D. Armour,John C. Castle Person Roles: submitter Person Last Name: Loewer Person First Name: Martin Person Mid Initials: Person Email: martin.loewer@tron-mainz.de Person Phone: +49 6131-720298-11 Person Address: TRON Translationale Onkologie gGmbH, Langenbeckstr. 8, D-55131 Mainz Person Affiliation: TRON

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Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

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