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| Status |
Public on Nov 10, 2016 |
| Title |
Genome-wide mapping of autonomous promoter activity in human cells |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of sequences that could be tested. Here we present Survey of Regulatory Elements (SuRE), a method to assay more than 10^8 DNA fragments, each 0.2-2kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library is constructed of random genomic fragments upstream of a 20bp barcode and decoded by paired-end sequencing. This library is then transfected into cells and transcribed barcodes are quantified in the RNA by high throughput sequencing. When applied to the human genome, we achieved a 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide. By computational modeling we delineated subregions within promoters that are relevant for their activity. For instance, we show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.
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| Overall design |
SuRE-seq assays in K562 cell-line; 1 experiment using library SuRE23 covering the entire K562 genome, with 2 biological replicates (with 4 and 2 PCR replicates resp.); 1 experiment using a library derived from
9 BACs covering in total 1.3Mb of the genome (SuRE BAC library), including hemin treated and control samples, with 1 biological replicate (each with 2 PCR replicates).
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| Contributor(s) |
van Arensbergen J, Pagie L, FitzPatrick VD, Bussemaker H, van Steensel B, de Haas M |
| Citation(s) |
28024146 |
| Submission date |
Feb 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
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| Phone |
+ 31 20 512 2040
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| Fax |
+31 20 669 1383
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| URL |
http://www.nki.nl/nkidep/vansteensel
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| Organization name |
Netherlands Cancer Institute
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| Department |
division of Molecular Biology
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| Lab |
van Steensel group
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (18)
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| GSM2262570 |
plasmid library, PCR rep2 |
| GSM2262571 |
SuRE K562 cDNA, Biorep1, PCRrep1 |
| GSM2262572 |
SuRE K562 cDNA, Biorep1, PCRrep2 |
| GSM2262573 |
SuRE K562 cDNA, Biorep1, PCRrep3 |
| GSM2262574 |
SuRE K562 cDNA, Biorep1, PCRrep4 |
| GSM2262575 |
SuRE K562 cDNA, Biorep2, PCRrep1 |
| GSM2262576 |
SuRE K562 cDNA, Biorep2, PCRrep2 |
| GSM2262577 |
BAC plasmid library, PCR rep1 |
| GSM2262578 |
BAC plasmid library, PCR rep2 |
| GSM2262579 |
SuRE BAC library K562 cDNA, Biorep1 |
| GSM2262580 |
SuRE BAC library K562 cDNA, Biorep2 |
| GSM2262581 |
BAC library K562 solvent control PCRrep1 |
| GSM2262582 |
BAC library K562 solvent control PCRrep2 |
| GSM2262583 |
BAC library K562 hemin control PCRrep1 |
| GSM2262584 |
BAC library K562 hemin control PCRrep2 |
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| Relations |
| BioProject |
PRJNA313292 |
| SRA |
SRP070893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE78709_SuRE-counts-K562_B45_B55_LP170105.txt.gz |
1.1 Gb |
(ftp)(http) |
TXT |
| GSE78709_SuRE23.iPCR.flat.count.160502.bw |
3.7 Gb |
(ftp)(http) |
BW |
| GSE78709_SuRE34.counts.JvA170901.txt.gz |
10.9 Mb |
(ftp)(http) |
TXT |
| GSE78709_gencode.based.tss.SuRE.170828.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE78709_sure23.plasmid.norm.combined.45.55.minus.160504.bw |
4.0 Gb |
(ftp)(http) |
BW |
| GSE78709_sure23.plasmid.norm.combined.45.55.plus.160504.bw |
4.0 Gb |
(ftp)(http) |
BW |
| GSE78709_sure34.flat.ipcr.coverage.160503.bw |
13.7 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.k562.norm.minus.160718.bw |
6.6 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.k562.norm.plus.160718.bw |
6.6 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.plasmid.norm.hemin_minus.160704.bw |
3.5 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.plasmid.norm.hemin_plus.160704.bw |
3.5 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.plasmid.norm.hemin_solvent_control_minus.160704.bw |
3.5 Mb |
(ftp)(http) |
BW |
| GSE78709_sure34.plasmid.norm.hemin_solvent_control_plus.160704.bw |
3.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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