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Series GSE102610 Query DataSets for GSE102610
Status Public on Aug 31, 2018
Title DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell-related genes, is globally repressed. The transcription factor MAX represses germ cell-related gene expression in ESCs via PCGF6-polycomb repressive complex (PRC)1, which consists of several epigenetic factors. However, we predicted that MAX represses germ cell-related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell-related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell-related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell-related genes in ESCs.
Overall design L3mbtl2-KD was performed in VV3 ESCs. Total RNA (100 ng) was isolated and purified using an RNeasy micro kit (Qiagen). The quality and quantity of purified total RNA were verified by Agilent 2100 Bioanalyzer (Agilent) and NanoDrop ND-1000 (Thermo Fischer Scientific), respectively. DNA microarray analysis was carried out according to manufacturer’s instruction. In brief, cyanine3-labelled cRNA was obtained from 100 ng of purified total RNA using a Low Input Quick Amp Labeling kit (Agilent). The cRNA was purified, fragmented and then hybridized to an Agilent Whole Mouse Genome Oligo DNA Microarray kit, Ver 2.0 (Agilent) containing over 44,000 probe sets for mouse genes. Following hybridization at 65°C for 17h, the arrays were washed and fluorescence signals were scanned using an Agilent DNA microarray scanner. Agilent Feature Extraction software was used to reduce the array images to the intensity of each probe (TXT files). Each cell type was analyzed in four biological replicates.
Contributor(s) Tatsumi D, Hayashi Y, Endo M, Kobayashi H, Yoshioka T, Kiso K, Kanno S, Nakai Y, Maeda I, Mochizuki K, Tachibana M, Koseki H, Okuda A, Yasui A, Kohno T, Matsui Y
Citation(s) 30403691
Submission date Aug 14, 2017
Last update date Jul 25, 2021
Contact name Yohei Hayashi
Phone +81-22-717-8572
Organization name Tohoku University
Department Institute of Development, Aging and Cancer
Lab Cell Resource Center for Biomedical Research
Street address 4-1 Seiryo-machi, Aobaku
City Sendai
State/province Miyagi
ZIP/Postal code 980-8575
Country Japan
Platforms (1)
GPL11202 Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Probe Name version)
Samples (8)
GSM2741733 ESCs_AllStars_rep1
GSM2741734 ESCs_L3mbtl2_rep1
GSM2741735 ESCs_AllStars_rep2
BioProject PRJNA398205

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
GSE102610_RAW.tar 17.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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