Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene

Kory C Douglas,Xu Wang,Andrew G Clark,Abigail Wolff,John L Vandeberg,Paul B Samollow,Madhuri Jasti

doi:10.1186/1471-2164-15-89

Kory C Douglas, Xu Wang + Show 5 more

Open Access

https://doi.org/10.1186/1471-2164-15-89

Copy DOI

Abstract

BackgroundImprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications.ResultsWe identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters.ConclusionsIn generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines.

Highlights

Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages
In metatherian (a.k.a. marsupial) mammals, genomic imprinting has been examined primarily in the tammar wallaby (Macropus eugenii: Australasian family Macropodidae), gray short-tailed opossum (Monodelphis domestica: American family Didelphidae), and Virginia opossum (Didelphis virginiana: Didelphidae), wherein only 19 genes, each already known to be imprinted in human and/or mouse, have been scrutinized in one or another of these species with regard to parent-of-origin-specific allele expression
Chromatin immunoprecipitation (ChIP)-seq analysis The genomic distributions of four histone modifications were analyzed in opossum fibroblasts by ChIP-seq, using antibodies against H3K4me3, H3K9me3, H3K27me3, and H3K9Ac

Summary

Introduction

Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. In metatherian (a.k.a. marsupial) mammals, genomic imprinting has been examined primarily in the tammar wallaby (Macropus eugenii: Australasian family Macropodidae), gray short-tailed opossum (Monodelphis domestica: American family Didelphidae), and Virginia opossum (Didelphis virginiana: Didelphidae), wherein only 19 genes, each already known to be imprinted in human and/or mouse, have been scrutinized in one or another of these species with regard to parent-of-origin-specific allele expression. Eight of these 19 loci have been shown to be imprinted in at least one of these marsupial species; nine show biallelic expression; and two have no marsupial homolog [11,12,13,14]. The remaining six marsupial imprinted genes are individually imprinted, associated with no known clusters, and mechanisms that regulate their expression remain unknown

Methods

Results

Discussion

Conclusion