Tissue-Specific Trans Regulation of the Mouse Epigenome.
Document Type
Article
Publication Date
3-2019
Keywords
JMG
JAX Source
Genetics 2019 Mar; 211(3):831-845
Volume
211
Issue
3
First Page
831
Last Page
845
ISSN
1943-2631
PMID
30593494
DOI
https://doi.org/10.1534/genetics.118.301697
Grant
CA034196,GM101736,GM099640, Jackson Laboratory Start-up Funds
Abstract
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 affects 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 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 (QTL). 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.
Recommended Citation
Baker CL,
Walker M,
Arat S,
Ananda G,
Petkova P,
Powers N,
Tian H,
Spruce C,
Ji B,
Rausch D,
Choi K,
Petkov PM,
Carter GW,
Paigen K.
Tissue-Specific Trans Regulation of the Mouse Epigenome. Genetics 2019 Mar; 211(3):831-845
Comments
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.