|
| Status |
Public on Oct 19, 2016 |
| Title |
Genome-wide uniformity of human “open” pre-initiation complexes |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5’ ends, and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the pre-initiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally “best” initiator (INR) sequence and/or shape. These finding reveal a common core to pervasive Pol II initiation throughout the human genome.
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| |
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| Overall design |
Genome-wide analysis of pre-initiation complex using PIP-seq
|
| |
|
| Contributor(s) |
Lai WK, Pugh BF |
| Citation(s) |
27927716 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM059055 |
REGULATION OF TBP DIMERS: Genome-wide Regulation of the TATA Binding Protein: REGULATION OF TBP DIMERS: REGULATION OF TBP DIMERS: Genome-wide Regulation of the TATA Binding Protein: Genome-wide Regulation of the TATA Binding Protein: Genome-wide Regulation of the TATA Binding Protein: REGULATION OF TBP DIMERS |
PENNSYLVANIA STATE UNIVERSITY-UNIV PARK |
B FRANKLIN PUGH |
|
| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bongsoo Park |
| E-mail(s) |
bxp12@psu.edu
|
| Phone |
814-441-3861
|
| Organization name |
Penn State University
|
| Street address |
453 North Frear Building
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA309133 |
| SRA |
SRP068569 |
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