Fast evolution of gained essential function by a young gene through gained interaction with other essential genes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5750300_1.fastq.gz | Fastqsanger.gz | |||
| SRR5750300_2.fastq.gz | Fastqsanger.gz | |||
| SRR5750310_1.fastq.gz | Fastqsanger.gz | |||
| SRR5750310_2.fastq.gz | Fastqsanger.gz | |||
| SRR5750281_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
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Project description:New genes are those that originated relatively recently and are only present in a subset of species in a phylogeny. Evidence from humans and other species has demonstrated that, despite their young age, new genes can exhibit novel functions that are essential for the survival of an organism. One potential mechanism by which new genes gain essential functions is through the acquisition of many new interactions with pre-existing genes. This hypothesis is consistent with well-established observations that genes with many interaction partners are more likely to have essential functions. However, the accumulation of gene-gene interactions is, on average, a slow evolutionary process. This raises the question of how, in a short evolutionary time, new genes can acquire multiple novel interactions and how this might lead to their essential roles in the survival of an organism. In this study, we characterized the evolutionary history and function of a young duplicated gene that quickly became essential for the survival of Drosophila melanogaster. This young gene (CG7804) duplicated from another essential gene (TBPH) through retrotransposition less than four million years ago (Zhang et al. 2010), and is present in few Drosophila species. We found that unlike its evolutionarily conserved, broadly expressed parental gene, CG7804 has evolved rapidly under positive selection since its birth. Despite its young age, functional analyses show that CG7804 is essential for the survival of D. melanogaster. In particular, its expression is essential at different tissues from its parental gene. RNA-seq and ChIP-seq analysis suggests that CG7804 acquired essential function to survival through gaining new DNA binding targets that influence the expression of a suite of genes with other essential function and large number of protein-protein interaction. Our study is an important step towards deciphering the evolutionary trajectory by which duplicated genes functionally diverge from the parental gene and become essential.
2019-06-01 | GSE100419 | GEO
Project description:New genes are those that originated relatively recently and are only present in a subset of species in a phylogeny. Evidence from humans and other species has demonstrated that, despite their young age, new genes can exhibit novel functions that are essential for the survival of an organism. One potential mechanism by which new genes gain essential functions is through the acquisition of many new interactions with pre-existing genes. This hypothesis is consistent with well-established observations that genes with many interaction partners are more likely to have essential functions. However, the accumulation of gene-gene interactions is, on average, a slow evolutionary process. This raises the question of how, in a short evolutionary time, new genes can acquire multiple novel interactions and how this might lead to their essential roles in the survival of an organism. In this study, we characterized the evolutionary history and function of a young duplicated gene that quickly became essential for the survival of Drosophila melanogaster. This young gene (CG7804) duplicated from another essential gene (TBPH) through retrotransposition less than four million years ago (Zhang et al. 2010), and is present in few Drosophila species. We found that unlike its evolutionarily conserved, broadly expressed parental gene, CG7804 has evolved rapidly under positive selection since its birth. Despite its young age, functional analyses show that CG7804 is essential for the survival of D. melanogaster. In particular, its expression is essential at different tissues from its parental gene. RNA-seq and ChIP-seq analysis suggests that CG7804 acquired essential function to survival through gaining new DNA binding targets that influence the expression of a suite of genes with other essential function and large number of protein-protein interaction. Our study is an important step towards deciphering the evolutionary trajectory by which duplicated genes functionally diverge from the parental gene and become essential.
2019-06-01 | GSE100342 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-06-01 | GSE100420 | GEO
Project description:Fast evolution of gained essential function by a young gene through gained interaction with other essential genes [RNA-Seq]
| PRJNA391701 | ENA
Project description:Fast evolution of gained essential function by a young gene through gained interaction with other essential genes [ChIP-Seq]
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Project description:New genes are of recent origin and only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. Although there are detailed analyses of the mechanisms underlying new genes' gaining fertility functions, how new genes rapidly become essential for viability remains unclear. We focused on a young retro-duplicated gene (CG7804, which we named Cocoon) in Drosophila that originated between 4 and 10 Ma. We found that, unlike its evolutionarily conserved parental gene, Cocoon has evolved under positive selection and accumulated many amino acid differences at functional sites from the parental gene. Despite its young age, Cocoon is essential for the survival of Drosophila melanogaster at multiple developmental stages, including the critical embryonic stage, and its expression is essential in different tissues from those of its parental gene. Functional genomic analyses found that Cocoon acquired unique DNA-binding sites and has a contrasting effect on gene expression to that of its parental gene. Importantly, Cocoon binding predominantly locates at genes that have other essential functions and/or have multiple gene-gene interactions, suggesting that Cocoon acquired novel essential function to survival through forming interactions that have large impacts on the gene interaction network. Our study is an important step toward deciphering the evolutionary trajectory by which new genes functionally diverge from parental genes and become essential.
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Project description:This study was performed to compare transcriptomic changes in the heterogeneous mouse skin epidermal stem cells and hair follicle stem cells (HFSC) populations during chronological aging. Slow-cycling stem cells (label retaining cells, LRCs), fast-cycling stem cells (non-label retaining cells, nLRCs) and hair follicle stem cells express unique gene signatures in young age (2 months old) and have independent stem cell identities. The changes in aging stem cells lineage identities have been a topic of discussion and here we examined if distinct stem cells cycling speed affects their aging process by comparing the transcriptomes of slow-and fast-cycling epidermal stem cells. Our data indicates the loss of unique stem cell identities in aging slow or fast-cycling epidermal stem cells or HFSC at 2 years of age with intermediary effects seen at 1.5 year old.
2022-10-01 | GSE185087 | GEO
Project description:Fast skeletal myosin binding protein-C regulates fast skeletal muscle contraction
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Project description:Thousands of long intergenic noncoding RNAs (lincRNAs) are encoded by the mammalian genome, which were reported to have multiple biological functions as transcriptional activators acting in cis 1 or trans 2, transcriptional repressors 3,4 or miRNAs decoys 5,6. However, the function of most lincRNAs has not yet been identified in vivo. Here, we demonstrate a role for linc-MYH, a novel long intergenic noncoding RNA, in adult fast-type myofibre specialization. Skeletal myofibre fast and slow phenotypes are established through differential expression of numerous fibre-specific genes7. We show linc-MYH and the fast MYH genes share a common enhancer located in the fast MYH genes locus and regulated by the Six1 homeoproteins. Muscle-specific Six1 mutant mice show increased expression of slow-type genes, and downregulation of linc-MYH and fast-type genes. linc-MYH function revealed by in vivo knockdown and wide transcriptomic analysis, is in fine to prevent expression of genes ensuring slow muscle contractile properties, and to increase fast-type muscle gene expression in fast-type myofibres. Thus, formation of efficient fast sarcomeric units and appropriate Ca++ cycling and excitation/contraction/relaxation coupling in fast- myofibres is achieved through the coordiante control of fast MYHs and linc-MYH expression by a Six bound enhancer.
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