Characterisation of Caenorhabditis eleganssperm transcriptome and proteome

Ma, Xuan; Zhu, Yingjie; Li, Chunfang; Xue, Peng; Zhao, Yanmei; Chen, Shilin; Yang, Fuquan; Liu, Miao

doi:10.1186/1471-2164-15-168

Cited by 56 publications

(73 citation statements)

References 56 publications

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“…As a result, low abundance lncRNAs expressed in only a fraction of cells are difficult to detect by RNA-seq of whole worm bodies (56). Supporting this hypothesis, a transcriptome of worm sperm revealed and validated 8 novel lncRNAs that the whole-body gene expression profile generated by the modENCODE Consortium failed to identify (57). Similarly, our muscle transcriptome revealed 461 novel transcripts with high confidence.…”

Section: Discussionmentioning

confidence: 88%

Analysis ofC. elegansmuscle transcriptome using trans-splicing-based RNA tagging (SRT)

Zhan

Sleumer

et al. 2016

Nucleic Acids Res

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Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. We have developed an easy and robust method for tissue-specific RNA-seq by taking advantage of the endogenous trans-splicing process. In this method, transgenic worms are generated in which a spliced leader (SL) RNA gene is fused with a sequence tag and driven by a tissue-specific promoter. Only in the tissue of interest, the tagged SL RNA gene is transcribed and then trans-spliced onto mRNAs. The tag allows enrichment and sequencing of mRNAs from that tissue only. As a proof of principle, we profiled the muscle transcriptome, which showed high coverage and efficient enrichment of muscle specific genes, with low background noise. To demonstrate the robustness of our method, we profiled muscle gene expression in dauer larvae and aging worms, revealing gene expression changes consistent with the physiology of these stages. The resulting muscle transcriptome also revealed 461 novel RNA transcripts, likely muscle-expressed long non-coding RNAs. In summary, the splicing-based RNA tagging (SRT) method provides a convenient and robust tool to profile trans-spliced genes and identify novel transcripts in a tissue-specific manner, with a low false positive rate.

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Section: Discussionmentioning

confidence: 88%

Analysis ofC. elegansmuscle transcriptome using trans-splicing-based RNA tagging (SRT)

Zhan

Sleumer

et al. 2016

Nucleic Acids Res

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“…Microarray studies indicated sperm expression (Reinke et al 2004), while later transcriptome and proteome profiling did not (Ma et al 2014). RT-PCR from fem-3(q23) mutant hermaphrodites (producing only sperm) amplified a prominent spe-47 product, whereas only a very faint product was amplified from fem-1(hc17) mutant animals, which produce only oocytes (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

“…Only two genes with novel mutations were found in the map region for hc198: Y23H5A.4 and F28B3.6 (Table 1 and Figure 1). Microarray data suggested that Y23H5A.4 is upregulated in sperm (Reinke et al 2000(Reinke et al , 2004, while transcriptome profiling showed that F28B3.6 is expressed in sperm (Ma et al 2014) (Table 1).…”

Section: Resultsmentioning

confidence: 99%

A New Player in the Spermiogenesis Pathway of Caenorhabditis elegans

et al. 2015

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Precise timing of sperm activation ensures the greatest likelihood of fertilization. Precision in Caenorhabditis elegans sperm activation is ensured by external signaling, which induces the spherical spermatid to reorganize and extend a pseudopod for motility. Spermatid activation, also called spermiogenesis, is prevented from occurring prematurely by the activity of SPE-6 and perhaps other proteins, termed "the brake model." Here, we identify the spe-47 gene from the hc198 mutation that causes premature spermiogenesis. The mutation was isolated in a suppressor screen of spe-27(it132ts), which normally renders worms sterile, due to defective transduction of the activation signal. In a spe-27(+) background, spe-47(hc198) causes a temperature-sensitive reduction of fertility, and in addition to premature spermiogenesis, many mutant sperm fail to activate altogether. The hc198 mutation is semidominant, inducing a more severe loss of fertility than do null alleles generated by CRISPR-associated protein 9 (Cas9) technology. The hc198 mutation affects an major sperm protein (MSP) domain, altering a conserved amino acid residue in a b-strand that mediates MSP-MSP dimerization. Both N-and C-terminal SPE-47 reporters associate with the forming fibrous body (FB)-membranous organelle, a specialized sperm organelle that packages MSP and other components during spermatogenesis. Once the FB is fully formed, the SPE-47 reporters dissociate and disappear. SPE-47 reporter localization is not altered by either the hc198 mutation or a C-terminal truncation deleting the MSP domain. The disappearance of SPE-47 reporters prior to the formation of spermatids requires a reevaluation of the brake model for prevention of premature spermatid activation.

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“…Thus, the proteome covers a considerable amount of the transcriptome with 59% of all identified KO IDs. Using mass spectrometry, Bai et al [53] identified about 40% of the genes in Aspergillus flavus , while [52] show for the sperm cells of Caenorhabditis elegans that 1080 of 2511 (approx. 30%) protein annotations overlap with the transcriptome.…”

Section: Resultsmentioning

confidence: 99%

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

et al. 2017

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Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.

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Characterisation of Caenorhabditis eleganssperm transcriptome and proteome

Cited by 56 publications

References 56 publications

Analysis ofC. elegansmuscle transcriptome using trans-splicing-based RNA tagging (SRT)

Analysis ofC. elegansmuscle transcriptome using trans-splicing-based RNA tagging (SRT)

A New Player in the Spermiogenesis Pathway of Caenorhabditis elegans

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

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