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| Status |
Public on Apr 30, 2024 |
| Title |
A first comprehensive analysis of Transcribed Ultra Conserved Regions uncovers important regulatory functions of novel non-coding transcripts in gliomas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Transcribed Ultra-Conserved Regions (TUCRs) represent a severely understudied class of putative non-coding RNAs (ncRNAs) that are 100% conserved across multiple species. We performed the first-ever analysis of TUCRs in glioblastoma (GBM) and low-grade gliomas (LGG). We leveraged large human datasets to identify the genomic locations, chromatin accessibility, transcription, differential expression, correlation with survival, and predicted functions of all 481 TUCRs, and identified TUCRs that are relevant to glioma biology. Of these, we investigated the expression, function, and mechanism of action of the most highly upregulated intergenic TUCR, uc.110, identifying it as a new oncogene. Uc.110 was highly overexpressed in GBM and LGG, where it promoted malignancy and tumor growth. Uc.110 activated the WNT pathway by upregulating the expression of membrane frizzled-related protein (MFRP), by sponging the tumor suppressor microRNA miR-544. This pioneering study shows important roles for TUCRs in gliomas and provides an extensive database and novel methods for future TUCR research.
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| Overall design |
To identify genes that are deregulated when the ultraconserved region uc.110 is knocked down, we performed RNA-Seq on GBM A172 cells treated with siRNAs targeting uc.110 or with scrambled control siRNA
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| Contributor(s) |
Abounader R, Gibert M Jr |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA1103342 |
| Submission date |
Apr 23, 2024 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Roger Abounader |
| E-mail(s) |
ra6u@virginia.edu, mkg7x@virginia.edu
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| Phone |
434-982-6634
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| Organization name |
University of Virginia
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| Department |
Microbiology
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| Lab |
Abounader Lab
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| Street address |
21 Hospital Drive
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22901 |
| Country |
USA |
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| Platforms (1) |
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| Samples (12)
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| GSM8226539 |
A172 cells, scrambled control siRNA, sample 1 |
| GSM8226540 |
A172 cells, scrambled control siRNA, sample 2 |
| GSM8226541 |
A172 cells, scrambled control siRNA, sample 3 |
| GSM8226542 |
A172 cells, scrambled control siRNA, sample 4 |
| GSM8226543 |
A172 cells, uc.110 siRNA-1, sample 1 |
| GSM8226544 |
A172 cells, uc.110 siRNA-1, sample 2 |
| GSM8226545 |
A172 cells, uc.110 siRNA-1, sample 3 |
| GSM8226546 |
A172 cells, uc.110 siRNA-1, sample 4 |
| GSM8226547 |
A172 cells, uc.110 siRNA-2, sample 1 |
| GSM8226548 |
A172 cells, uc.110 siRNA-2, sample 2 |
| GSM8226549 |
A172 cells, uc.110 siRNA-2, sample 3 |
| GSM8226550 |
A172 cells, uc.110 siRNA-2, sample 4 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE264713_seq_mergedcounts.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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