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| Status |
Public on Apr 14, 2010 |
| Title |
Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.
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| Overall design |
Use of ChIP-seq to identify genomic regions bound by RNA Polymerase III machinery in multiple cell types as well as RNA-seq in HeLa for gene expression analysis. See GSE20609 for whole human genome raw Pol III ChIP-array data. See link below for supplementary methods and analysis.
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| Contributor(s) |
Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR |
| Citation(s) |
20418882 |
| Submission date |
Feb 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Oler |
| E-mail(s) |
andrew.oler@nih.gov
|
| Organization name |
NIAID/NIH
|
| Department |
Bioinformatics and Computational Biosciences Branch (BCBB)
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| Lab |
Computational Biology Section
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| Street address |
31 Center Drive, Room 3B62E
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (11)
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| Relations |
| SRA |
SRP002001 |
| BioProject |
PRJNA125353 |
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