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Series GSE218597 Query DataSets for GSE218597
Status Public on Aug 09, 2024
Title Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo [scDam&T-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Summary In this study, we profiled genome-Nuclear Lamina (NL) contacts during the first stages of mouse embryonic development. We discovered a remarkable cell-to-cell variability in NL-contacts at the 2-cell stage, which is particularly strong on the paternal allele. We additionally obtained single-cell profiles for H3K27me3, H3K9me3 and DNA accessibility at this stage, but did not observe the same large-scale variability. The variability in NL-contacts did not appear to affect the transcription of underlying genes. Comparing NL-contact profiles with diverse histone modification profiles showed that large regions of typical NL-contacts are lost and instead are enriched for H3K27me3 during early development. To investigate the relationship between H3K27me3 and NL association, we used a conditional EED KO mouse model, which results in an absence of H3K27me3 during oocyte development and the early embryo. Profiling NL-contacts at the 2-cell stage in this system revealed that regions enriched with H3K27me3 in WT regain NL association in the EED maternal KO. In addition, the loss of H3K27me3 resulted in more similar NL association profiles on the maternal and paternal allele. Together, these results suggest that H3K27me3 antagonizes NL association and that the non-canonical broad H3K27me3 domains present in the early embryo may be responsible for the early-embryo specific loss of NL associations in these regions.
 
Overall design Profiling Nuclear Lamina (NL) contacts, H3K27me3, H3K9me3 and accessibility in mouse preimplantation embryos using scDamID and scDam&T-seq.
 
Contributor(s) Geirreiro I, Rang FJ, Kitazawa Y, Groenveld F, van Beek R, Lochs SJ, Boele E, Peters AH, Kind J
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Submission date Nov 22, 2022
Last update date Aug 10, 2024
Contact name Jop Kind
E-mail(s) j.kind@hubrecht.eu
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (28)
GSM6753079 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3408_index22)
GSM6753080 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3408_index23)
GSM6753081 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3600_index20)
This SubSeries is part of SuperSeries:
GSE218598 Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo
Relations
BioProject PRJNA904384

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

Supplementary file Size Download File type/resource
GSE218597_RAW.tar 283.1 Mb (http)(custom) TAR (of TSV)
GSE218597_bigwig.tar.gz 22.0 Mb (ftp)(http) TAR
GSE218597_bigwig_2.tar.gz 12.4 Mb (ftp)(http) TAR
GSE218597_clustering_of_bins_on_LMNB1_and_H3K27me3.binsize_100000.track.bed.gz 54.7 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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