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  Rapid evolutionary turnover underlies conserved lncRNA-genome interactions

Quinn, J. J., Zhang, Q. C., Georgiev, P., Ilik, I. A., Akhtar, A., & Chang, H. Y. (2016). Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes and Development, 30, 191-207. doi:10.1101/gad.272187.115.

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http://genesdev.cshlp.org/content/30/2/191 (Publisher version)
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 Creators:
Quinn, Jeffrey J.1, 2, Author
Zhang, Qiangfeng C.1, Author
Georgiev, Plamen3, Author              
Ilik, Ibrahim Avsar3, Author              
Akhtar, Asifa3, Author              
Chang, Howard Y.1, Author
Affiliations:
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA, ou_persistent22              
2Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA, ou_persistent22              
3Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, 79108 Freiburg, DE, ou_2243640              

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 Abstract: Many long noncoding RNAs (lncRNAs) can regulate chromatin states, but the evolutionary origin and dynamics driving lncRNA-genome interactions are unclear. We adapted an integrative strategy that identifies lncRNA orthologs in different species despite limited sequence similarity, which is applicable to mammalian and insect lncRNAs. Analysis of the roX lncRNAs, which are essential for dosage compensation of the single X chromosome in Drosophila males, revealed 47 new roX orthologs in diverse Drosophilid species across ∼40 million years of evolution. Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA-genome interactions.

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Language(s): eng - English
 Dates: 2016-01-15
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1101/gad.272187.115
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Title: Genes and Development
Source Genre: Journal
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Publ. Info: Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 30 Sequence Number: - Start / End Page: 191 - 207 Identifier: ISSN: 0890-9369
CoNE: https://pure.mpg.de/cone/journals/resource/954925557453