Transcriptomics,Genomics

Dataset Information

159

The dynamic landscape of fission yeast meiosis alternative-splice isoforms


ABSTRACT: 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. Overall design: 2 replicates of 6 time points total RNA for pacbio sequencing

INSTRUMENT(S): PacBio RS II (Schizosaccharomyces pombe)

SUBMITTER: Zheng Kuang 

PROVIDER: GSE79802 | GEO | 2016-11-10

SECONDARY ACCESSION(S): PRJNA317011

REPOSITORIES: GEO

altmetric image

Publications

The dynamic landscape of fission yeast meiosis alternative-splice isoforms.

Kuang Zheng Z   Boeke Jef D JD   Canzar Stefan S  

Genome research 20161117 1


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 an open-source software program called SpliceHunter to characterize the transcriptome in the meiosis of fission yeast. We reveal 14,353 alternative splicing events in 17,669 novel isoforms at different stages of meiosis,  ...[more]

Similar Datasets

2007-08-08 | GSE7952 | GEO
2007-08-07 | E-GEOD-7952 | ArrayExpress
| PRJNA317011 | ENA
2013-07-29 | E-GEOD-49293 | ArrayExpress
2007-12-08 | GSE9734 | GEO
2006-01-19 | GSE3063 | GEO
2008-01-13 | GSE9372 | GEO
2017-08-02 | PXD003278 | Pride
2014-02-21 | E-GEOD-55213 | ArrayExpress
2011-05-05 | E-GEOD-26341 | ArrayExpress