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| Status |
Public on Mar 13, 2021 |
| Title |
HMJSL C. Neoformans splicing factor knockout RNA-seq |
| Organism |
Cryptococcus neoformans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We determined that over 60 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. We found they govern splicing efficiency of introns with divergent spacing between intron elements. Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites. Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G-patch/helicase pair that promotes splicing fidelity. We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.
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| Overall design |
Examination of 13 splicing factor knockouts, and 1 exosome factor knockout in Cryptococcus neoformans.
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| Contributor(s) |
Sales-Lee J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 12, 2021 |
| Last update date |
Mar 15, 2021 |
| Contact name |
Hiten Madhani |
| Organization name |
UCSF
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| Department |
Biochemistry
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| Lab |
Madhani Lab
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| Street address |
600 16th St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL21073 |
Illumina HiSeq 4000 (Cryptococcus neoformans) |
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| Samples (36)
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| GSM5170660 |
KN99 - rbm5 day 1, replicate 2 |
| GSM5170661 |
KN99 - ccdc12 day 1, replicate 1 |
| GSM5170662 |
KN99 - ccdc12 day 1, replicate 2 |
| GSM5170663 |
KN99 - rbm17 day 1, replicate 1 |
| GSM5170664 |
KN99 - rbm17 day 1, replicate 2 |
| GSM5170665 |
KN99 - dhx35 day 1, replicate 1 |
| GSM5170666 |
KN99 - dhx35 day 1, replicate 2 |
| GSM5170667 |
KN99 - gpatch1 day 1, replicate 1 |
| GSM5170668 |
KN99 - gpatch1 day 1, replicate 2 |
| GSM5170669 |
KN99 - sap18 day 1, replicate 1 |
| GSM5170670 |
KN99 - sap18 day 1, replicate 2 |
| GSM5170671 |
KN99 - WT day 2, replicate 1 |
| GSM5170672 |
KN99 - WT day 2, replicate 2 |
| GSM5170673 |
KN99 - fam50a day 2, replicate 1 |
| GSM5170674 |
KN99 - fam50a day 2, replicate 2 |
| GSM5170675 |
KN99 - fam32a day 2, replicate 1 |
| GSM5170676 |
KN99 - fam32a day 2, replicate 2 |
| GSM5170677 |
KN99 - ik day 2, replicate 1 |
| GSM5170678 |
KN99 - ik day 2, replicate 2 |
| GSM5170679 |
KN99 - znf830 day 2, replicate 1 |
| GSM5170680 |
KN99 - znf830 day 2, replicate 2 |
| GSM5170681 |
KN99 - nosip day 2, replicate 1 |
| GSM5170682 |
KN99 - nosip day 2, replicate 2 |
| GSM5170683 |
KN99 - WT day 3, replicate 1 |
| GSM5170684 |
KN99 - WT day 3, replicate 2 |
| GSM5170685 |
KN99 - cxorf56 day 3, replicate 1 |
| GSM5170686 |
KN99 - cxorf56 day 3, replicate 2 |
| GSM5170687 |
KN99 - ctnnbl1 day 3, replicate 1 |
| GSM5170688 |
KN99 - ctnnbl1 day 3, replicate 2 |
| GSM5170689 |
KN99 - rrp6 day 3, replicate 1 |
| GSM5170690 |
KN99 - rrp6 day 3, replicate 2 |
| GSM5170691 |
KN99 - fra10ac1 day 3, replicate 1 |
| GSM5170692 |
KN99 - fra10ac1 day 3, replicate 2 |
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| Relations |
| BioProject |
PRJNA714086 |
| SRA |
SRP310427 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168814_AS_differential_JUM_output.tar.gz |
951.0 Kb |
(ftp)(http) |
TAR |
| GSE168814_RAW.tar |
1.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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