In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.
The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac, and H2BK20ac). Comparison of active chromatin state between somatic, embryonic stem, and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. We found the nuclear receptor Nr5a2 motif to be enriched at a subset of germ cell cis-regulatory regions, and our results implicate Nr5a2 in germ cell biology. Interestingly, in germ cells, the H3K27me3 histone modification occurs more frequently at regions that are enriched for retrotransposons and MHC genes, indicating that these loci are specifically silenced in germ cells. Together, our study provides genome-wide histone modification maps of in vivo germ cells and reveals the molecular chromatin signatures of germ cells.
Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672.
Jia-Hui
JH
Ng
Vibhor
V
Kumar
Masafumi
M
Muratani
Petra
P
Kraus
Jia-Chi
JC
Yeo
Lai-Ping
LP
Yaw
Kun
K
Xue
Thomas
T
Lufkin
Shyam
S
Prabhakar
Huck-Hui
HH
Ng
D000818:Animals; D002843:Chromatin; D002874:Chromosome Mapping; D053595:Embryonic Stem Cells / Q000201:enzymology / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic / Q000235:genetics*; D023281:Genomics; D005854:Germ Cells / Q000201:enzymology / Q000378:metabolism; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D051379:Mice; D011401:Promoter Regions, Genetic; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics / Q000378:metabolism; D018626:Retroelements
D002843:Chromatin; D006657:Histones; C431936:Nr5a2 protein, mouse; D018160:Receptors, Cytoplasmic and Nuclear; D018626:Retroelements; D011495:Histone-Lysine N-Methyltransferase