Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model

• Main Authors: Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng
• Format: Article
• Language: English
• Published: Elsevier 2015-12-01
• Series: Data in Brief
• Subjects: RNA-seq; ChIP-seq; X inactivation; Transcription factor; Gene expression; Allele-specific
• Online Access: http://www.sciencedirect.com/science/article/pii/S2352340915002814

X chromosome inactivation (XCI) is a female-specific mechanism that serves to balance gene dosage between the sexes whereby one X chromosome in females is inactivated during early development. Despite this silencing, a small portion of genes escape inactivation and remain expressed from the inactive X (Xi). Little is known about the distribution of escape from XCI in different tissues in vivo and about the mechanisms that control tissue-specific differences. Using a new binomial model in conjunction with a mouse model with identifiable alleles and skewed X inactivation we are able to survey genes that escape XCI in vivo. We show that escape from X inactivation can be a common feature of some genes, whereas others escape in a tissue specific manner. Furthermore, we characterize the chromatin environment of escape genes and show that expression from the Xi correlates with factors associated with open chromatin and that CTCF co-localizes with escape genes. Here, we provide a detailed description of the experimental design and data analysis pipeline we used to assay allele-specific expression and epigenetic characteristics of genes escaping X inactivation. The data is publicly available through the GEO database under ascension numbers GSM1014171, GSE44255, and GSE59779. Interpretation and discussion of these data are included in a previously published study (Berletch et al., 2015) [1].