|
| Status |
Public on Nov 10, 2016 |
| Title |
The dynamic landscape of fission yeast meiosis alternative-splice isoforms |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop a computational tool, SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.
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| |
|
| Overall design |
2 replicates of 6 time points total RNA for pacbio sequencing
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| |
|
| Contributor(s) |
Kuang Z, Boeke JD, Canzar S |
| Citation(s) |
27856494 |
| |
| Submission date |
Mar 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zheng Kuang |
| Organization name |
UT Southwestern medical center
|
| Department |
Immunology
|
| Lab |
Lora Hooper
|
| Street address |
6000 Harry Hines Blvd. NA7.500
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21481 |
PacBio RS II (Schizosaccharomyces pombe) |
|
| Samples (18)
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|
| Relations |
| BioProject |
PRJNA317011 |
| SRA |
SRP072705 |
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