E-GEOD-45211 - Chromosome-wide profiling of X-inactivation status and epigenetic regulation in opossum fetal brain and placenta

Status
Released on 23 September 2013, last updated on 3 May 2014
Organism
Monodelphis domestica
Samples (16)
Protocols (2)
Description
Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. The majority (152/176) of X-linked genes exhibited paternally imprinted expression with nearly 100% maternal allele expression, whereas 24 loci (14%) escaped inactivation showing varying levels of biallelic expression. In addition to regulation by the non-coding RSX transcript, strong depletion of H3K27me3 at escaper gene loci indicates that histone states also influence opossum XCI. Notably, the opossum does not show an association between X-linked gene expression and promoter DNA methylation. Our study provides the first comprehensive catalogue of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. Profiling of expression level and allele-specific expression ratios in embryonic day 13 opossum (Monodelphis domestica) fetal brain and extra-embyonic membranes by Illumina RNA-seq
Experiment type
RNA-seq of coding RNA 
Contacts
Andrew Clark <ac347@cornell.edu>, Andrew G Clark, Paul B Samollow, Xu Wang
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-45211.idf.txt
Sample and data relationshipE-GEOD-45211.sdrf.txt
Links