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Series GSE76955 Query DataSets for GSE76955
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.
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
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)
GSM2041442 TFIIB PIP-seq Rep1
GSM2041443 TFIIB PIP-seq Rep2
GSM2041444 TFIIB PIP-seq Rep3
BioProject PRJNA309133
SRA SRP068569

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Supplementary file Size Download File type/resource
GSE76955_RAW.tar 146.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE76955_TFIIB_PIP-seq_peaks.bed.gz 110.3 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file

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