|
| Status |
Public on Feb 03, 2015 |
| Title |
Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs, and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification.
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| |
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| Overall design |
Examination of chromatin contacts between Oct4 alleles using PE-4Cseq
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| |
|
| Contributor(s) |
Hogan MS, Zepeda Mendoza CJ, Spector DL |
| Citation(s) |
25748933 |
| |
| Submission date |
Feb 02, 2015 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Cinthya J Zepeda-Mendoza |
| E-mail(s) |
[email protected]
|
| Phone |
5163678478
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Lab |
David L. spector
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
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| Platforms (1) |
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| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA274253 |
| SRA |
SRP053044 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65510_OctSox154.9_FourCSeqResults.txt.gz |
76.0 Kb |
(ftp)(http) |
TXT |
| GSE65510_OctSoxOcfWTOct4_FourCSeqResults.txt.gz |
6.8 Kb |
(ftp)(http) |
TXT |
| GSE65510_OctSox_d0_d3_154.9_countmatrix.txt.gz |
62.1 Kb |
(ftp)(http) |
TXT |
| GSE65510_OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt.gz |
19.7 Kb |
(ftp)(http) |
TXT |
| GSE65510_OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt.gz |
26.8 Kb |
(ftp)(http) |
TXT |
| GSE65510_RAW.tar |
708.1 Mb |
(http)(custom) |
TAR (of FA) |
| GSE65510_YY1154.9_FourCSeqResults.txt.gz |
116.2 Kb |
(ftp)(http) |
TXT |
| GSE65510_YY1OcfWTOct4_FourCSeqResults.txt.gz |
7.0 Kb |
(ftp)(http) |
TXT |
| GSE65510_YY1_d0_d3_154.9_countmatrix.txt.gz |
69.3 Kb |
(ftp)(http) |
TXT |
| GSE65510_YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt.gz |
32.0 Kb |
(ftp)(http) |
TXT |
| GSE65510_YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt.gz |
34.7 Kb |
(ftp)(http) |
TXT |
| GSE65510_chr11_hindiii_fragments.txt.gz |
212.9 Kb |
(ftp)(http) |
TXT |
| GSE65510_chr17_hindiii_fragments.txt.gz |
166.7 Kb |
(ftp)(http) |
TXT |
| GSE65510_chr4_hindiii_fragments.txt.gz |
283.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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