Tissue-Specific Trans Regulation of the Mouse Epigenome.

Christopher L. Baker, The Jackson Laboratory
Michael Walker, The Jackson Laboratory
Seda Arat, The Jackson Laboratory
Guruprasad Ananda, The Jackson Laboratory
Pavlina Petkova, The Jackson Laboratory
Natalie Powers, The Jackson Laboratory
Hui Tian, The Jackson Laboratory
Catrina Spruce, The Jackson Laboratory
Bo Ji, The Jackson Laboratory
Dylan Rausch
Kwangbom Choi, The Jackson Laboratory
Petko M. Petkov, The Jackson Laboratory
Gregory W. Carter, The Jackson Laboratory
Kenneth Paigen, The Jackson Laboratory

This manuscript is dedicated to the memory of Pavlina Petkova, a wonderful scientist, colleague, and wonderful friend. We thank members of the Baker, Paigen, Petkov, and Carter labs for their discussion of the data and manuscript.


The epigenetic landscape varies greatly among cell types. Although a variety of writers, readers, and erasers of epigenetic features are known, we have little information about the underlying regulatory systems controlling the establishment and maintenance of these features. Here, we have explored how natural genetic variation impacts the epigenome in mice. Studying levels of H3K4me3, a histone modification at sites such as promoters, enhancers, and recombination hotspots, we found tissue-specific trans-regulation of H3K4me3 levels in four highly diverse cell types: male germ cells, embryonic stem (ES) cells, hepatocytes and cardiomyocytes. To identify the genetic loci involved, we measured H3K4me3 levels in male germ cells in a mapping population of 59 BXD recombinant inbred lines. We found extensive trans-regulation of H3K4me3 peaks, including six major histone quantitative trait loci (hQTL). These chromatin regulatory loci act dominantly to suppress H3K4me3, which at hotspots reduces the likelihood of subsequent DNA double-strand breaks. QTL locations do not correspond with genes encoding enzymes known to metabolize chromatin features. Instead their locations match clusters of zinc finger genes, making these possible candidates that explain the dominant suppression of H3K4me3. Collectively, these data describe an extensive, set of chromatin regulatory loci that control the epigenetic landscape.