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| Status |
Public on Oct 01, 2016 |
| Title |
A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
The magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this question in a systematic manner, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally-based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson's R2 of 0.347 for predicting the results of chromosomally integrated reporter assays. This is substantially better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for how cis-regulatory elements are identified, prioritized and functionally validated.
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| Overall design |
We developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers and 204 controls in an episomal versus a chromosomally integrated context. By using integration-competent vs. integration-defective components of the lentiviral system, we directly compared the functional activities of 2,236 candidate liver enhancers in a chromosomally integrated versus an episomal context in the human liver hepatocellular carcinoma cell line, HepG2.
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| Contributor(s) |
Shendure J, Ahituv N |
| Citation(s) |
27831498 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA197139 |
Integrative interpretation of the organismal consequences of non-coding variation |
UNIVERSITY OF WASHINGTON |
Shendure |
| R01 HG006768 |
Massively parallel, in vivo functional testing of regulatory elements |
UNIVERSITY OF WASHINGTON |
Shendure |
| R01 MH109907 |
Massively parallel dissection of psychiatric regulatory networks |
J. DAVID GLADSTONE INSTITUTES |
Ahituv |
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| |
| Submission date |
Jun 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jay Shendure |
| Organization name |
University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Shendure
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA327312 |
| SRA |
SRP077617 |
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