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


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Article Info

DATE

2014-01-31

AUTHORS

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

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. More... »

PAGES

89

References to SciGraph publications

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    40 schema:description 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.
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    47 CpG islands
    48 DNA methylation
    49 H3K4me3
    50 H3K9ac
    51 H3K9me3
    52 Monodelphis domestica
    53 ResultsWe
    54 ab initio search
    55 allele-specific expression
    56 concept
    57 developmental stages
    58 differential DNA methylation
    59 discovery strategies
    60 domestica
    61 epigenetic mechanisms
    62 eutherian mammals
    63 eutherians
    64 expression
    65 fibroblasts
    66 findings
    67 first gene
    68 force
    69 genes
    70 histone modification profiles
    71 histone modifications
    72 histone modifications H3K4me3
    73 imprinted genes
    74 imprinted loci
    75 initio search
    76 interspecific variation
    77 islands
    78 lines
    79 loci
    80 mammals
    81 marsupial genes
    82 marsupials
    83 mechanism
    84 metatherian mammals
    85 metatherians
    86 methylation
    87 modification
    88 modification profiles
    89 multiple epigenetic mechanisms
    90 novel imprinted gene
    91 number
    92 opossum
    93 outcomes
    94 practicality
    95 profile
    96 profiling
    97 promoter
    98 regulation
    99 search
    100 selective forces
    101 set
    102 significant interspecific variation
    103 small number
    104 stage
    105 state profiling
    106 strategies
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    110 therian mammals
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