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| Status |
Public on Sep 28, 2023 |
| Title |
An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We previously showed that the germ cell specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility. RBMXL2 evolved from the X-linked RBMX gene, which is silenced during meiosis due to sex chromosome inactivation. It has been unknown whether RBMXL2 provides a direct replacement for RBMX in meiosis, or whether RBMXL2 evolved to deal with the transcriptionally permissive environment of meiosis. Here we find that RBMX primarily operates as a splicing repressor in somatic cells, and specifically regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and repress the selection of cryptic splice sites that would compromise gene function. These similarities in overall function suggested that RBMXL2 might replace the function of RBMX during meiosis. To test this prediction we carried out inducible expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing in response to RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMX and RBMXL2 have parallel roles in somatic tissues and the germline that must have have been conserved over at least 200 million years of mammalian evolution. We propose RBMX family proteins are particularly important for the splicing inclusion of ultra-long exons because these would be particularly susceptible to disruption by cryptic splice site selection.
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| Overall design |
RNA-Seq was performed on the following samples:
MDA-MB-231 cells treated with either control siRNAs (1 + 3 biological replicates) or siRNAs targeting RBMX (1 + 3 biological replicates);
HEK293 cells treated with either control siRNAs or siRNAs targeting RBMX, half of which were treated with tetracycline to induce RBMXL2 overexpression (1 biological replicate per condition)
**Please note that no suitable processed data was generated for GSM7429573-GSM7429576 samples. The processing produced BAMs which were examined in IGV to generate the conclusions that are described in the associated publication.
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| Contributor(s) |
Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara MR, Yonchev ID, James K, Chadegani MK, Ehrmann I, Smith GR, Cockell SJ, Munkley J, Wilson SA, Barash Y, Elliott DJ |
| Citation(s) |
39356106 |
| |
| Submission date |
Sep 29, 2020 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Graham Smith |
| E-mail(s) |
graham.smith3@newcastle.ac.uk
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| Organization name |
Newcastle University
|
| Department |
Bioinformatics Support Unit
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| Street address |
Framlington Place
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| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE233498 |
An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression |
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| Relations |
| BioProject |
PRJNA666447 |
| SRA |
SRP285823 |
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