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Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi

Nature Structural & Molecular Biology volume 23, pages 450–455 (2016)Cite this article

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Abstract

Antisense long noncoding RNAs (ASlncRNAs) have been implicated in regulating gene expression in response to physiological cues. However, little is known about the evolutionary dynamics of ASlncRNA and what underlies the evolution of their expression. Here, using budding yeast Saccharomyces spp. and Naumovozyma castellii as models, we show that ASlncRNA repertoires have expanded since the loss of RNA interference (RNAi), in terms of their expression levels, their lengths and their degree of overlap with coding genes. Furthermore, we show that RNAi is inhibitory to ASlncRNA transcriptomes and that increased expression of ASlncRNAs in the presence of RNAi is deleterious to N. castellii, which has retained RNAi. Together, our results suggest that the loss of RNAi had substantial effects on the genome-wide increase in expression of ASlncRNAs during the evolution of budding yeasts.

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Figure 1: ASlncRNA expression patterns among budding yeast.
Figure 2: Elevation of ASlncRNA levels across the budding yeast phylogeny.
Figure 3: ASlncRNAs have increased in length and have overlapped mRNAs to a greater extent since the divergence of Saccharomyces from N. castellii.
Figure 4: RNAi constrains ASlncRNA expression.

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  • 15 April 2016

    This article was initially published as an Analysis. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank H. Malik, I.A. Drinnenberg and the members of the Tsukiyama laboratory for helpful discussions; H. Malik and I.A. Drinnenberg for critical reading of the manuscript; M. Dunham (University of Washington), D. Bartel (Massachusetts Institute of Technology) and D. Gottschling (Fred Hutchinson Cancer Research Center (FHCRC)) for yeast strains; and A. Marty and FHCRC for sharing resources for deep sequencing. This work was supported by a grant from the US National Institutes of Health (R01 GM058465 to T.T.) and a predoctoral fellowship from the US National Institutes of Health (F31 GM101944 to E.A.A.).

Author information

Authors and Affiliations

  1. Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

    Eric A Alcid & Toshio Tsukiyama

  2. Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

    Eric A Alcid

Authors
  1. Eric A Alcid
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Contributions

E.A.A. planned and performed experiments, analyzed and interpreted data, and wrote the manuscript. T.T. planned experiments, interpreted data and wrote the manuscript.

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Correspondence to Toshio Tsukiyama.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Sense RNA expression patterns among budding yeast.

a) Normalized read counts of IPP1 mRNA as measured by RNAseq. (b) as in (a), but for ACT1 mRNA. (c) Principal Component Analysis (PCA) of sense RNA transcriptomes in budding yeast. (d) Neighbor-joining tree of sense RNA transcriptomes based on pairwise distance matrices (Jensen-Shannon distance metric). Highlighted in blue are species of the genus Saccharomyces. Indicated is the bootstrap level between N. castellii and genus Saccharomyces species (out of 100)

Supplementary Figure 2 Pairwise comparisons of sense RNA transcriptomes and ASlncRNA transcriptomes among budding yeast.

(From left to right) (a) Cladogram representing the phylogenetic relationships among budding yeasts; pairwise scatter-plots of sense RNA transcriptomes comprised of 5031 orthologous ORFs for all studied budding yeast species (top), and corresponding Spearman’s rho values (bottom)

(b) as in (a), but for ASlncRNA transcriptomes.

Supplementary Figure 3 Antisense and sense RN-expression differences at tandem and convergent genes in budding yeast species.

(a) Ribbon Plots of antisense read density in log2-scale at genes arranged in convergent (blue) or tandem (pink) orientations for each species analyzed. Antisense read density mapping to the downstream gene has been lightened. (b) Ribbon Plots of sense read density in log2-scale at genes arranged in convergent orientation for (top to bottom) S. uvarum, S. kudriavzevii, S. mikatae, S. cerevisiae. N. castellii is represented in all the plots by the blue ribbon. The lines represent the antisense RNA-seq signal, while the outer borders of the ribbon represent 1 standard-error of the mean away from the mean. (c) As in (b), except for genes arranged in tandem orientation.

Supplementary Figure 4 RNAi constrains Rrp6-dependent transcripts in S. cerevisiae and N. castellii.

(a) Distribution of ASlncRNA levels in wild type S. cerevisiae and N.castellii (SUT-ASlncRNAs) (b) As in (a), but for CUT-ASlncRNAs. See Methods for identification of CUT-ASlncRNAs. (c) Box plots showing the distribution of log2 fold-changes of CUT-ASlncRNAs in an rrp6 background for S. cerevisiae (right) and N. castellii (left). (d) Boxplot representation of the distribution of log2 normalized read counts of ASlncRNAs in the N. castellii rrp6 (left) and rrp6 dcr1 (right) strains for all ASlncRNAs identified in the rrp6 dcr1 mutant (e) as in (d), but for ASlncRNAs with statistically significant steady-state levels.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Tables 8 and 9 (PDF 1739 kb)

Supplementary Table 1

RNA-seq libraries and the percentage of reads that map antisense (XLS 31 kb)

Supplementary Table 2

All orthologs shared between N. castellii and Saccharomyces species, with SGD/YGOB gene names (XLS 805 kb)

Supplementary Table 3

ASlncRNAs in S. cerevisiae (XLS 1310 kb)

Supplementary Table 4

ASlncRNAs in S. mikatae (XLS 326 kb)

Supplementary Table 5

ASlncRNAs in S. kudriavzevii (XLS 224 kb)

Supplementary Table 6

ASlncRNAs in S. uvarum (XLS 186 kb)

Supplementary Table 7

ASlncRNAs in N. castellii (XLS 92 kb)

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Alcid, E., Tsukiyama, T. Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. Nat Struct Mol Biol 23, 450–455 (2016). https://doi.org/10.1038/nsmb.3192

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