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SRX9302836: GSM4832680: WT-H3K27me3-rep2; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 26M spots, 7.8G bases, 3.4Gb downloads

Submitted by: NCBI (GEO)
Study: Role of CxxC-finger Protein 1 in the Establishment of Epigenetic Landscapes in Mouse Oocytes
show Abstracthide Abstract
During oogenesis, oocytes gain competence to accomplish meiotic maturation and prepare for embryonic development following fertilization. Trimethylated histone H3 on lysine-4 (H3K4me3) mediates a wide range of nuclear events during these processes. Oocyte-specific knockout of CxxC-finger protein 1 (CXXC1, also known as CFP1), the chromatin-binding subunit of SETD1 methyltransferase, impairs the H3K4me3 accumulation during murine oogenesis and caused changes in chromatin configurations. This study investigated the changes of genomic H3K4me3 landscapes in oocytes after Cxxc1 knockout, as well as the influences of H3K4me3 changes on other epigenetic marks including DNA methylation, H3K27me3, H2AK119ub1, and H3K36me3. Chromatin immunoprecipitation and sequencing results indicated that H3K4me3 is globally decreased after abolishing Cxxc1, including both the promoter region and the gene body. The results also demonstrate that CXXC1 and another histone H3 methyltransferase MLL2 have nonoverlapping roles in mediating H3K4 trimethylation during oogenesis. In addition, Cxxc1 deletion caused a significant decrease of DNA methylation level in oocytes, and affected H3K27me3 and H2AK119ub1 distributions in the maternal genome, particularly at the regions that have high DNA methylation levels. The changes of epigenetic networks caused by Cxxc1 deletion correlated with transcription changes of the genes in the corresponding genomic regions. Taken together, this study provided mechanistic explanations underlying the phenotypes and molecular defects in Cxxc1 deleted oocytes, and highlighted a role of CXXC1 in orchestrating multiple factors to build up the appropriate epigenetic states of maternal genome during oocyte maturation. Overall design: WT and Cxxc1 null oocytes are collected to performed high-throughput sequencing.
Sample: WT-H3K27me3-rep2
SAMN16475162 • SRS7526587 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: STAR ChIP-seq was performed according to a protocol described previously (Zhang et al., 2016). Briefly, samples were directly lysed and fragmented by micrococcal nuclease (MNase) at 37 °C for 5 min before being incubated with the primary antibody overnight with rotation at 4 °C. The next day, 100 μg Dynabeads Protein A (Thermo Fisher Scientific) was added to each sample and incubated for 2–3 h with rotation at 4 °C. The beads were washed five times with 150 μl radioimmunoprecipitation assay buffer (RIPA) and once with 150 μl lithium chloride buffer. For each sample, beads were resuspended with 27 μl deionized H2O and 1 μl 10× Ex-Taq buffer (Takara, RR006B); 1 μl proteinase K (catalog no. 10910000; Roche) was added to each sample and incubated at 55 °C for 90 min to elute DNA from the beads. After incubation at 80 °C for 40 min to inactivate the proteinase K, the sample was subjected to TELP (tailing, extension, ligation and PCR) library preparation without DNA purification.
Experiment attributes:
GEO Accession: GSM4832680
Links:
Runs: 1 run, 26M spots, 7.8G bases, 3.4Gb
Run# of Spots# of BasesSizePublished
SRR1283530226,017,4267.8G3.4Gb2021-02-04

ID:
12152379

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