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| Status |
Public on Dec 16, 2015 |
| Title |
The life history of retrocopies illuminates the evolution of new mammalian genes |
| Organism |
Pongo pygmaeus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as useful models for the study of new gene origination. Here we combine extensive mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, the majority evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers or bivalent regulatory elements, as well as from CpG islands not associated to other genes. Altogether, these mechanisms facilitated the birth of up to 280 retrogenes in each therian species. Furthermore, the regulatory evolution of the originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated the cooption of distant promoters and in many cases allowed the expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute their parents during the process of male (meiotic) X inactivation, while others even rendered parental functions completely superfluous, allowing for parental gene loss. Overall, our reconstruction of the complete “life history” of mammalian retrogenes highlights the usefulness of retroposition as a general model for understanding new gene birth and functional evolution.
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| Overall design |
Assembly and expression of vertebrate retrogene transcripts
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| Contributor(s) |
Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H |
| Citation(s) |
26728716 |
| Submission date |
Aug 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesco Nicola Carelli |
| E-mail(s) |
fr.carelli@gmail.com
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| Organization name |
University of Cambridge
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| Lab |
Julie Ahringer
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| Street address |
Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL20833 |
Illumina MiSeq (Pongo pygmaeus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA293451 |
| SRA |
SRP062673 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE72236_RAW.tar |
330.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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