Intron evolution in Saccharomycetaceae
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE58884
PROVIDER: PRJNA253808 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1481525.fastq.gz | Fastqsanger.gz | |||
| SRR1481526.fastq.gz | Fastqsanger.gz | |||
| SRR1481527.fastq.gz | Fastqsanger.gz | |||
| SRR1481528.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Purpose: Saccharomyceatacea yeast are intron-poor species and they contain on average 300 introns in their genomes. We designed RNAseq experiment to investigate if splicing patterns in related yeast species are similar. Methods: Total RNA was extracted from wild type cells and processed by the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA. cDNA libraries were prepared according to manufacturer's protocol and sequenced by SOLiD. Sequence reads were filtered and processed by TopHat. Results: We found 216, 163, 200 and 155 predicted introns with canonical splice signals in S. cerevisiae, S. kudriavzevii, S. bayanus and N. castellii respectively. Three introns in S. cerevisiae, four in S. bayanus and ten in S. castellii are novel compared to Saccharomyces Genome Database (SGD) annotations. The expression of introns and splicing shows very high correlation between species. Conclusion: Transcripts with introns in yeast species tested show similar levels of expression and splicing. We found few novel introns, which are conserved in yeast genomes.
2014-09-15 | GSE58884 | GEO
Project description:Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit. Splicing specific microarrays were used to assess the genome-wide defects in gene expression and pre-mRNA splicing that result from a deletion of a single ribosomal protein gene intron.
2012-03-01 | E-GEOD-35541 | biostudies-arrayexpress
Project description:Intron evolution may be readily imaged through the combined use of the "dot plot" function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate "Multiz" alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.
| S-EPMC9326662 | biostudies-literature
Project description:Intron-mediated induction of phenotypic heterogeneity
| PRJNA809314 | ENA
Project description:Intron retention analysis using isogrowth profiling
| PRJNA648363 | ENA
Project description:Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit.
2012-03-01 | GSE35541 | GEO
Project description:We present an analysis of intron retention under stress from two different drugs and their combinations in yeast Saccharomyces cerevisiae. We previously established isogrowth profiling, a method to abstract the non-specific effects of growth rate inhibition from the specific effect of perturbation by a small molecule: two drugs are used at varied ratios, but at fixed overall growth inhibition. Here, cycloheximide and LiCl were used at seven different ratios along the 50% growth inhibition isobole and the total ribodepleted RNA was sequenced. This allowed us to gauge the changes in intron retention due to the used drugs, while ensuring that the effects are not caused by growth inhibition. We found a prominent increase in intron retention under LiCl treatment that preferentially affects introns contained in the transcripts of ribosomal proteins.
2022-02-15 | GSE155060 | GEO
Project description:Exon-intron circRNA (EIciRNA) is a subclass of backsplicing-generated circRNAs featured with intron retention, among which some play roles in transcriptional regulation. We aim to characterize EIciRNAs by developing pipeline and investigate the factors involved in regulating EIciRNA biogenesis using CRISPR-Cas9 screen, as well as the physiology functions of EIciRNAs during neuronal differentiation.
2024-03-04 | GSE253233 | GEO
Project description:Introns in protein-coding genes are very rare in hemiascomycetous yeast genomes. It has been suggested that these species have experienced extensive intron loss during their evolution from the postulated intron-rich fungal ancestor. However, no intron-devoidy east species have been identified and some of the introns remaining within the genomes of intron-poor species, such as Saccharomyces cerevisiae, appear to be beneficial during growth under stress conditions. In order to reveal the pattern of intron retention within intron-poor yeast species and better understand the mechanisms of intron evolution, we generated a comprehensive set of 250 orthologous introns in the 20 species that comprise the Saccharomycetaceae, by analyzing RNA deep-sequencing data and alignments of intron-containing genes. Analysis of these intron sets shows that intron loss is at least two orders of magnitude more frequent than intron gain. Fine mapping of intron positions shows that intron sliding is rare, and that introns are almost always removed without changing the primary sequence of the encoded protein. The latter finding is consistent with the prevailing view that homologous recombination between reverse-transcribed mature mRNAs and the corresponding genomic locus is the primary mechanism of intron loss. However, we also find evidence that loss of a small number of introns is mediated by micro-homology, and that the number of intron losses is diminished in yeast species that have lost the microhomology end joining and nonhomologous end joining machinery.
| S-EPMC4202332 | biostudies-literature
Project description:In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. Correlation with splicing outcomes demonstrate that these associations are functional. The interactions between 5 splice sites, U1 snRNP, and elongating RNA polymerase II occurs genome-wide. Our findings reveal that during intron synthesis the upstream 5 splice site remains attached to the transcriptional machinery and is thus brought into proximity of the 3 splice site to enable rapid splicing.
2021-06-16 | GSE144874 | GEO