GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE85185 Query DataSets for GSE85185
Status Public on May 22, 2017
Title YY1 and CTCF Orchestrate a 3D Chromatin Looping Switch during Early Neural Lineage Commitment
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3-D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naïve/primed pluripotency to multipotent primary neural progenitor cells (NPCs). Many pluripotency gene-enhancer interactions are anchored by CTCF and its occupancy is lost in parallel with loop decommissioning during differentiation. Conversely, CTCF binding sites in NPCs are largely pre-existing in pluripotent stem cells. Only a small number of CTCF sites arise de novo in NPCs. We identify another zinc finger protein, Yin Yang 1 (YY1), at the base of looping interactions between NPC-specific genes and enhancers. Putative NPC-specific enhancers exhibit strong YY1 signal when engaged in 3-D contacts and negligible YY1 signal when not in loops. Moreover, siRNA knockdown of YY1 specifically disrupts interactions between key NPC enhancers and their target genes. YY1-mediated interactions between NPC regulatory elements are often nested within constitutive loops anchored by CTCF. Together, our results support a model in which YY1 acts as an architectural protein to connect developmentally regulated looping interactions; the location of YY1-mediated interactions may be demarcated in development by a pre-existing topological framework created by constitutive CTCF-mediated interactions.
Overall design Analysis of CTCF binding and higher-order chromatin architecture in mouse ES cells under 2i/LIF and serum/LIF conditions, and primary NPCs.
ChIP-Seq libraries and Chromosome-Conformation-Capture-Carbon-Copy (5C) libraries.
Contributor(s) Beagan JA, Duong MT, Lachanski CV, Phillips-Cremins JE
Citation(s) 28536180
Submission date Aug 04, 2016
Last update date May 15, 2019
Contact name Jennifer E Phillips-Cremins
Organization name University of Pennsylvania
Department Bioengineering
Street address 415 Curie Blvd
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (16)
GSM2259905 ES_2i_CTCF_ChIPseq_library
GSM2259906 ES_2i_Input_ChIPseq_library
GSM2259907 ES_Serum_CTCF_ChIPseq_library
BioProject PRJNA336482
SRA SRP080920

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
GSE85185_BED_314-ES-NPC-LOCI_mm9.bed.gz 24.2 Kb (ftp)(http) BED
GSE85185_Beagan_et_al_Binned_Bedfile_2_22_17.bed.gz 12.9 Kb (ftp)(http) BED
GSE85185_Beagan_et_al_Classified_Results_2_22_17.txt.gz 289.1 Kb (ftp)(http) TXT
GSE85185_Beagan_et_al_Primer_Bedfile_for_YY1_knockdown.bed.gz 7.5 Kb (ftp)(http) BED
GSE85185_Beagan_et_al_Processed_Data_File_2_22_2017.txt.gz 38.5 Mb (ftp)(http) TXT
GSE85185_Beagan_et_al_YY1_Knockdown_5C_Processed_Data_File_2_22_2017.txt.gz 7.1 Mb (ftp)(http) TXT
GSE85185_Beagan_et_al_YY1_knockdown_Binned_Bedfile_2_22_17.bed.gz 3.1 Kb (ftp)(http) BED
GSE85185_ES-2i-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSE85185_ES-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak.gz 1.3 Mb (ftp)(http) NARROWPEAK
GSE85185_NPC-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak.gz 745.9 Kb (ftp)(http) NARROWPEAK
GSE85185_RAW.tar 18.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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