GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE67955 Query DataSets for GSE67955
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
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.
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.
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
Organization name University of Minnesota, Minneapolis
Department Minnesota Supercomputing Institute
Street address 117 Pleasant Street SE
City Minneapolis
ZIP/Postal code 55455
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (18)
GSM1659603 MEL_PU.1_D0R1
GSM1659604 MEL_PU.1_D0R2
GSM1659605 MEL_PU.1_D5R1
BioProject PRJNA281363
SRA SRP057256

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap