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| Status |
Public on Apr 30, 2019 |
| Title |
The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
|
| Summary |
Abstract: A network of interactions between functional DNA elements regulates gene expression in a precise spatio-temporal pattern during development. This regulation is implemented through many-to-many looping interactions of DNA elements mediated by specific transcription factors such as Ctcf, Gata1 and Yy1. We carried out RNA polymerase II ChIA-PET and DNase-seq in Mouse Erythroleukemia (MEL) cells to capture genomewide changes in the resulting chromatin interaction graphs (CIGs) during DMSO-induced hemoglobin activation. We found that the change of interactions in CIGs is positively correlated to the change of a corresponding genes’ expression as measured by RNA-seq. DNase footprints and ChIP-seq data indicate that these long-range interactions are controlled through distinct combinations of transcription factors before and after differentiation, with Ctcf or cohesin only mediating half of these interactions, and Gata1 and/or Yy1 interactions accounting for an additional 40% of detected interactions. Strikingly, while Ctcf and Gata1–mediated interactions were enriched in genes involved in erythrocyte differentiation and mitochondrial regulation, Yy1-mediated interactions were enriched for genes involved in RNA processing, translation, and histone remodeling. We further found that about two-thirds of MEL DNA elements with long-range interactions as well 35% of these interactions are conserved in human K562 cells and show similar combinations of factor occupancy. Taken together, our study identifies that a large set of long-range interactions between active enhancers and promoters involving RNA Pol II are mediated by factors other than cohesin and Ctcf in both human and mouse.
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| Overall design |
PU.1 ChIP-Seq, RNA-Seq, DNase-Seq, ChIA-PET
The 'MEL_foot_1kb_DHS_cohesin_pol2_peak_blacklistfiltered.bed contains the locations and names of the 1kb vertices used to characterize and quantitate the long-range interaction edges between vertices from the ChIA-PET data.
It was generated from the hotspot bed file of MEL DNase-seq data. After incorporating anti-pol2 and cohesin ChIP-seq peaks from ENCODE consortium, the merged DNase-seq hotspots and ChIP-seq peaks were expanded to 1kb in order to make the 1kb vertices.
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| Contributor(s) |
Zeng W, Ramirez R, Jansen C, Macchietto M, Jiang S, Conesa A, Mortazavi A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Marissa Macchietto |
| E-mail(s) |
mmacchie@umn.edu
|
| Organization name |
University of Minnesota, Minneapolis
|
| Department |
Minnesota Supercomputing Institute
|
| Street address |
117 Pleasant Street SE
|
| City |
Minneapolis |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (18)
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| Relations |
| BioProject |
PRJNA281363 |
| SRA |
SRP057256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67955_MEL_1kb_vertices.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_3kb_vertices.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0D5_consolidated_DHS.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0R1_DHS.bed.gz |
2.1 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0R2_DHS.bed.gz |
2.8 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0_1kb_edge_list.txt.gz |
48.3 Kb |
(ftp)(http) |
TXT |
| GSE67955_MEL_D0_1kb_vertices_with_connection_edge.bed.gz |
68.9 Kb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0_3kb_edge_list.txt.gz |
137.7 Kb |
(ftp)(http) |
TXT |
| GSE67955_MEL_D0_3kb_vertices_with_connection_edge.bed.gz |
152.3 Kb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0_DNase_footprints_p_minus20.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D0_R1R2_intersected_DHS.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5R1_DHS.bed.gz |
6.7 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5R2_DHS.bed.gz |
5.5 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5_1kb_edge_list.txt.gz |
46.8 Kb |
(ftp)(http) |
TXT |
| GSE67955_MEL_D5_1kb_vertices_with_connection_edge.bed.gz |
70.6 Kb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5_3kb_edge_list.txt.gz |
103.0 Kb |
(ftp)(http) |
TXT |
| GSE67955_MEL_D5_3kb_vertices_with_connection_edge.bed.gz |
127.9 Kb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5_DNase_footprints_p_minus20.bed.gz |
2.7 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_D5_R1R2_intersected_DHS.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE67955_MEL_RNA_seq_merged_fpkm.txt.gz |
543.7 Kb |
(ftp)(http) |
TXT |
| GSE67955_MEL_foot_1kb_DHS_cohesin_pol2_peak_blacklistfiltered.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE67955_RAW.tar |
2.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
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