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Updated: Aug 25, 2025
A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
Published on: March 7, 2019
Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely
Yu Ono1, Kenta Katayama1,2, Tomoki Onuma1
1Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan.
Abstract:
Non-coding RNAs (ncRNAs) ubiquitously exist in normal and cancer cells. Despite their prevalent distribution, the functions of most long ncRNAs remain uncharacterized. The fission yeast Schizosaccharomyces pombe expresses >1800 ncRNAs annotated to date, but most unconventional ncRNAs (excluding tRNA, rRNA, snRNA and snoRNA) remain uncharacterized. To discover the functional ncRNAs, here we performed a combinatory screening of computational and biological tests. First, all S. pombe ncRNAs were screened in silico for those showing conservation in sequence as well as in secondary structure with ncRNAs in closely related species. Almost a half of the 151 selected conserved ncRNA genes were uncharacterized. Twelve ncRNA genes that did not overlap with protein-coding sequences were next chosen for biological screening that examines defects in growth or sexual differentiation, as well as sensitivities to drugs and stresses. Finally, we highlighted an ncRNA transcribed from SPNCRNA.1669, which inhibited untimely initiation of sexual differentiation. A domain that was predicted as conserved secondary structure by the computational operations was essential for the ncRNA to function. Thus, this study demonstrates that in silico selection focusing on conservation of the secondary structure over species is a powerful method to pinpoint novel functional ncRNAs.
Insights
Researchers screened fission yeast non-coding RNAs (ncRNAs) to find new functions. They identified a specific ncRNA that prevents premature sexual differentiation, highlighting the power of computational structure analysis for discovering functional ncRNAs.
Area of Science:
- Molecular Biology
- Genetics
- Fungal Biology
Background:
- Non-coding RNAs (ncRNAs) are abundant in cells, but the functions of most long ncRNAs are unknown.
- Fission yeast (Schizosaccharomyces pombe) has over 1800 annotated ncRNAs, with many unconventional ones lacking functional characterization.
Purpose of the Study:
- To discover novel functional ncRNAs in Schizosaccharomyces pombe.
- To investigate the role of conserved ncRNAs in cellular processes like growth and differentiation.
Main Methods:
- In silico screening of S. pombe ncRNAs for sequence and secondary structure conservation across related species.
- Biological screening of selected conserved ncRNA genes for defects in growth, sexual differentiation, and stress/drug sensitivity.
- Functional analysis of a specific ncRNA (SPNCRNA.1669) and its conserved structural domain.
Main Results:
- Identified 151 conserved ncRNA genes, with nearly half being uncharacterized.
- Selected 12 ncRNA genes for further biological screening.
- Discovered an ncRNA (SPNCRNA.1669) that inhibits premature sexual differentiation in fission yeast.
- Confirmed that a conserved secondary structure domain is crucial for this ncRNA's function.
Conclusions:
- In silico analysis focusing on conserved secondary structure is an effective strategy for identifying novel functional ncRNAs.
- The identified ncRNA (SPNCRNA.1669) plays a regulatory role in fission yeast sexual differentiation.
- This study expands the understanding of ncRNA functions in Schizosaccharomyces pombe.
