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| Status |
Public on Apr 26, 2021 |
| Title |
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. When transcribed, pseudogenes may encode proteins or enact RNA-intrinsic regulatory mechanisms. However, the extent, characteristics and functional relevance of the human pseudogene transcriptome are unclear. Short-read sequencing platforms have limited power to resolve and accurately quantify pseudogene transcripts owing to the high sequence similarity of pseudogenes and their parent genes. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes. Pseudogene transcripts are expressed in tissue-specific patterns, exhibit complex splicing patterns and contribute to the coding sequences of known genes. We survey pseudogene transcripts encoding intact open reading frames (ORFs), representing potential unannotated protein-coding genes, and demonstrate their efficient translation in cultured cells. To assess the impact of noncoding pseudogenes on the cellular transcriptome, we delete the nucleus-enriched pseudogene PDCL3P4 transcript from HAP1 cells and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the transcriptional landscape underpinning human biology and disease.
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| |
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| Overall design |
Identification of full-length pseudogene transcripts
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| |
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| Contributor(s) |
Troskie RL, Jafrani Y, Mercer TR, Ewing AD, Faulkner GJ, Cheetham SW |
| Citation(s) |
33971925 |
| |
| Submission date |
Oct 29, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Seth Cheetham |
| E-mail(s) |
seth.cheetham@mater.uq.edu.au
|
| Organization name |
Mater Research Institute-University of Queensland
|
| Street address |
Level 4, 37 Kent St
|
| City |
Wooloongabba |
| State/province |
QLD |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
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| Platforms (2) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA673144 |
| SRA |
SRP289711 |
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