Functional heritage: the evolution of chimeric RNA into a gene
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA540701 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8998280_1.fastq.gz | Fastqsanger.gz | |||
| SRR8998280_2.fastq.gz | Fastqsanger.gz | |||
| SRR8998281_1.fastq.gz | Fastqsanger.gz | |||
| SRR8998281_2.fastq.gz | Fastqsanger.gz | |||
| SRR8998278_1.fastq.gz | Fastqsanger.gz |
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Project description:Once believed to be unique features of neoplasia, chimeric RNAs have been discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes and that forming chimeric RNA at the transcriptional level may be a “trial” mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to the pseudogene MRPS31P5. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmoset monkeys, which do not possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Here, we provide multiple lines of evidence supporting that MRPS31P5 is not truly a pseudogene, but a functional descendent of the H-S chimera. We also show that H-S is a product of cis-splicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.
2020-01-22 | GSE130594 | GEO
Project description:Once believed to be unique features of neoplasia, chimeric RNAs are now being discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes, and that forming chimeric RNA at the transcriptional level may be a 'trial' mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to that of a 'pseudogene' MRPS31P5. Sequence analysis revealed that MRPS31P5 transcript is more similar to H-S chimeric RNA than its 'parent' gene, MRPS31. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmosets, which do not yet possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Silencing H-S in marmoset cells resulted in similar phenotype as silencing MRPS31P5 in human cells. In addition, whole transcriptome analysis and candidate downstream target validation revealed common signalling pathways shared by the two transcripts. Interestingly, H-S failed to rescue the phenotype caused by silencing MPRS31P5 in human and rhesus cells, whereas MRPS31P5 can at least partially rescue the phenotype caused by silencing H-S in marmoset cells, suggesting that MRPS31P5 may have further evolved into a distinct entity. Thus, multiple lines of evidence support that MRPS31P5 is not truly a pseudogene of MRPS31, but a likely functional descendent of H-S chimera. Instead being a gene fusion product, H-S is a product of cis-splicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.
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Project description:Gene expression profiles generated from skeletal muscle biopsies taken from participants of the HERITAGE family study. Participants completed an endurance training regime in which a skeletal muscle biopsy was taken prior to the start and after the final session of the program. Biopsies were used to generate Affymetrix gene expression microarrays.
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Project description:Cultural heritage material Metagenome
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Project description:The overall objective of the heritage project is to study the role of the genotype in cardiovascular,metabolic and hormonal responses to aerobic exercise training and the contribution of regular exercise to changes in several cardiovascular disease and diabetes risk factors. PLEASE NOTE THE POST-TRAINING GENE CHIP FILES HAVE NEVER BEEN RELEASED ON GEO. PLEASE ALSO NOTE THAT DUE TO THE OUTDATED INSULIN ASSAY UTILISED IN THE HERITAGE STUDY, THE INSULIN DATA WAS NOT COMPARABLE WITH ANY MORE RECENT MODERN STUDIES.
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Project description:The Heritage family study - skeletal muscle gene expression
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Project description:The overall objective of the heritage project is to study the role of the genotype in cardiovascular,metabolic and hormonal responses to aerobic exercise training and the contribution of regular exercise to changes in several cardiovascular disease and diabetes risk factors. The study cohort in this analysis consists of 473 Caucasian subjects (230 male and 243 female) from 99 nuclear families who completed M-bM-^IM-%58 of the prescribed 60 exercise-training sessions.The phenotypic expression of each individualM-bM-^@M-^Ys genotype is assessed under two well-defined environmental conditions, the pre- and post-training conditions. Here we have made the pre-training data available as used in the article Phillips BE, Williams JP, Gustafsson T, Bouchard C, Rankinen T, et al. (2013) Molecular Networks of Human Muscle Adaptation to Exercise and Age. PLoS Genet 9(3): e1003389. doi:10.1371/journal.pgen.1003389 52 U133+2 profiles (17M-bM-^@M-^S63 yr) generated from pre-exercise muscle biopsy samples from the HERITAGE Family Study. Heritage_pre dataset.
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Project description:Here we present genome-wide genotyping data of 70 human samples from Europe (Balto-Slavic speakers, Greeks) that are used in addition to public data in a study of genetic heritage of the Balto-Slavic populations.
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