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| Status |
Public on Aug 09, 2023 |
| Title |
Genome-wide CRISPR interference screen identifies long non-coding RNA DARS1-AS1 as a novel regulator of glioblastoma tumorigenesis. |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
There are over 15,000 long (>200 nucleotides) noncoding RNA (lncRNAs) genes in the human genome, but only few of them has been functionally characterized. Emerging evidence has shown that long non-coding RNAs (lncRNAs) modulate diverse biological processes and mediate tumor-promoting/suppressing effects and serve as independent diagnostic/prognostic biomarkers in cancer. However, the role and function mechanism of the lncRNA/RBP-mediated regulatory circuits in determining the functional characteristics of GSCs underlying GBM pathogenesis remains poorly understood. To fill this gap, we combined CRISPR (clustered regularly interspaced short palindromic repeat) interference (CRISPRi), with large-scale computational analysis of The Cancer Genome Atlas (TCGA) to systematically identify the functional lncRNAs with clinically relevant expression in GBM.
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| Overall design |
To identify the GBM dependency on lncRNAs with clinically relevant expression, the CRISPR interference (CRISPRi) screens on lncRNAs that showed differential expression between GBM tumors and low-grade glioma (LGG) tumors or normal brain tissues were performed in two GBM cell lines U251 and U87. RNA-seq experiments in the absence/presence of siRNA-mediated DARS1-AS1/YBX1 knockdown U251 cells were performed to explore the up/down-regulated genes by DARS1-AS1/YBX1. eCLIP-seq experiments were conducted in U251 cells to identify YBX1 directly binding mRNA.
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| Contributor(s) |
Chen Y, Zheng C, Wei Y |
| Citation(s) |
37540752 |
| |
| Submission date |
Sep 09, 2022 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Yiwen Chen |
| E-mail(s) |
YChen26@mdanderson.org
|
| Phone |
713-745-9283
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| Organization name |
UT MD Anderson Cancer Center
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| Department |
Bioinformatics & Comp Biology
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| Street address |
1400 Pressler Street, Unit 1410
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA878831 |
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