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Staying alive in adversity: transcriptome dynamics in the stress-resistant dauer larva

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Abstract

In response to food depletion and overcrowding, the soil nematode Caenorhabditis elegans can arrest development and form an alternate third larval stage called the dauer. Though nonfeeding, the dauer larva is long lived and stress resistant. Metabolic and transcription rates are lowered but the transcriptome of the dauer is complex. In this study, distribution analysis of transcript profiles generated by Serial Analysis of Gene Expression (SAGE) in dauer larvae and in mixed developmental stages is presented. An inverse relationship was observed between frequency and abundance/copy number of SAGE tag types (transcripts) in both profiles. In the dauer profile, a relatively greater proportion of highly abundant transcripts was counterbalanced by a smaller fraction of low to moderately abundant transcripts. Comparisons of abundant tag counts between the two profiles revealed relative enrichment in the dauer profile of transcripts with predicted or known involvement in ribosome biogenesis and protein synthesis, membrane transport, and immune responses. Translation-coupled mRNA decay is proposed as part of an immune-like stress response in the dauer larva. An influence of genomic region on transcript level may reflect the coordination of transcription and mRNA turnover.

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Acknowledgements

This research was supported in part by DHHS grants GM60151 and AG12689 to D. Riddle and by a Division of Biological Sciences Research Incentive Fund, University of Missouri—Columbia. Thanks are extended to S. Jones for SAGE tag correlations to predicted genes and to S. Jones and D. Blasiar for guidance in data mining, D. Riddle for the stimulating and thoughtful advisement and to D. Riddle and the reviewers for manuscript critiques, D. Baillie for helpful suggestions, and to R. Madsen for the biostatistics consultation services.

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    Suzan J. Holt

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Fig. S1

Transcript abundance distributions for dauer larvae and mixed stages. Transcript abundance classes/bins (theoretical minimum to maximum copies of each tag type per bin): 1 (1-5), 2 (6-10), 3 (11-20), 4 (21-40), 5 (41-80), 6 (81-160), 7 (161-320), 8 (321-640), 9 (641-1280), 10 (1281-2560). a. Relative frequency of transcripts (tag types) versus transcript abundance (copy number) class (log2 × log2). The theoretical maximum number of copies represents each transcript abundance class for either profile, i.e., the X-axis data points are fixed. b. Relative frequency of transcripts (tag types) versus average tag count per abundance class (log2 × log2). The X-axis data points can differ by profile (PDF 58 kb)

Fig. S2

Differential expression of PUF family genes. Encoded products contain the Pumilio/Puf RNA-binding domain IPR001313. Black bars: p 5 1.34E-05 (FDR 5 4.01E-05). Genes as shown and puf-8/C30G12.7, puf-9/W06B11.2, fbf-1/H12I13.4, fbf-2/F21H12.5, puf-3/Y45F10A.2, puf-5/F54C9.8 (PDF 65 kb)

Table S1

Abundant transcripts in the dauer larva or mixed-stage SAGE profiles (PDF 103 kb)

Table S2

Candidate genes for SAGA or TFIID regulation are differentially expressed in dauer larvae (D) and mixed stages (M) (PDF 66 kb)

Table S3

Transcription machinery genes (PDF 61 kb)

Table S4

Ribosomal protein genes (PDF 51 kb)

Table S5

Translation factor family genes (PDF 59 kb)

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Holt, S.J. Staying alive in adversity: transcriptome dynamics in the stress-resistant dauer larva. Funct Integr Genomics 6, 285–299 (2006). https://doi.org/10.1007/s10142-006-0024-5

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