|
Status |
Public on Dec 15, 2020 |
Title |
An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq) |
Organism |
Saccharomyces cerevisiae |
Experiment type |
Expression profiling by high throughput sequencing Other
|
Summary |
Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. Here, we use a high-resolution quantitative approach to study alternative TSS and transcript end site (TES) usage during three different cell fate transitions in yeast: entry into gametogenesis, commitment to meiotic divisions and return to vegetative growth. We propose that an alternative transcriptome of mRNA isoforms and lncRNAs shapes local gene expression during cell fate transitions. Hence, changes in the types and proportions of different RNAs transcribed at a locus are important inputs for gene expression at distinct stages of development.
|
|
|
Overall design |
Transcript Isoform sequencing (TIF) analysis of Saccharomyces cerevisiae SK1 strains. All strains used in this study harbor the IME1gene controlled by a copper inducible promoter (pCUP1), the NDT80 gene controlled by a galactose inducible promoter (pGAL) and a constitutively expressed Gal4 transcription factor fused to the hormone binding domain of the estrogen receptor (Gal4-ER). For the sporulation time course, cells were grown overnight in YPD medium, diluted, and shifted to sporulation media (SPO). IME1 was induced after 2h in Spo by adding 50 μM CuSO4. Time points for each cell fate transition were pooled in equal proportions for library construction and sequencing. Two independent replicates were sequenced.. Details for library preparation are described below.
|
|
|
Contributor(s) |
Chia M, Li C, van Werven F, Marques S, Pelechano V |
Citation(s) |
33446241 |
|
Submission date |
Dec 02, 2019 |
Last update date |
Jan 19, 2021 |
Contact name |
Folkert van Werven |
E-mail(s) |
Folkert.vanWerven@crick.ac.uk
|
Organization name |
Francis Crick Institute
|
Street address |
1 Midland Road
|
City |
London |
ZIP/Postal code |
NW1 1AT |
Country |
United Kingdom |
|
|
Platforms (1) |
GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
Samples (8)
|
GSM4200179 |
Wild-type TIFseq premeiotic replicate 1 |
GSM4200180 |
Wild-type TIFseq premeiotic replicate 2 |
GSM4200181 |
Wild-type TIFseq early meiotic replicate 1 |
GSM4200182 |
Wild-type TIFseq early meiotic replicate 2 |
GSM4200183 |
Wild-type TIFseq mid-late meiotic replicate 1 |
GSM4200184 |
Wild-type TIFseq mid-late meiotic replicate 2 |
GSM4200185 |
Wild-type TIFseq return to growth replicate 1 |
GSM4200186 |
Wild-type TIFseq return to growth replicate 2 |
|
This SubSeries is part of SuperSeries: |
GSE137711 |
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts |
|
Relations |
BioProject |
PRJNA592981 |
SRA |
SRP234421 |