|
| Status |
Public on May 15, 2015 |
| Title |
Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development.
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| |
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| Overall design |
shRNA knock down of lncRNAs followed by DNA methylation profiling
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| |
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| Contributor(s) |
Kurian L, Aguirre A, Benner C, Izpisua-Belmonte JC |
| Citation(s) |
25739401 |
| Submission date |
Feb 13, 2014 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
|
| Organization name |
University of California, San Diego (UCSD)
|
| Department |
Medicine
|
| Street address |
9500 Gilman Dr. MC 0640
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE54969 |
Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development |
|
| Relations |
| BioProject |
PRJNA238181 |
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