Mapping the mouse Allelome reveals tissue specific regulation of allelic expression Journal Article

Author(s): Andergassen, Daniel; Dotter, Christoph P; Wenzel, Dyniel; Sigl, Verena; Bammer, Philipp C; Muckenhuber, Markus; Mayer, Daniela; Kulinski, Tomasz M; Theussl, Hans-Christian; Penninger, Josef M; Bock, Christoph; Barlow, Denise P; Pauler, Florian M; Hudson, Quanah J
Article Title: Mapping the mouse Allelome reveals tissue specific regulation of allelic expression
Affiliation IST Austria
Abstract: To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.
Journal Title: eLife
Volume: 6
ISSN: 2050-084X
Publisher: eLife Sciences Publications  
Date Published: 2017-08-14
Start Page: Article number: e25125
Copyright Statement: CC BY
DOI: 10.7554/eLife.25125
Notes: This work was partly supported by the Austrian Science Fund (FWF P25185-B22, FWF F4302-B09, FWF W1207-B09). High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna. Rita Casari and Philipp Guenzl helped with tissue collection. We thank Anton Wutz for critical reading of an earlier version of the manuscript. Johannes Tkadletz from the IMP/IMBA Graphics Service and Pieter-Jan Volders helped with figure production.
Open access: yes (OA journal)