Supplementary code repository for: Novel imprinted genes exemplify predominantly H3K27me3-dependent imprinting in mouse blastocysts

Laura Santini^1,*, Florian Halbritter^2,3,*, Fabian Titz-Teixeira⁵, Toru Suzuki⁴, Maki Asami⁴, Xiaoyan Ma⁶, Julia Ramesmayer¹, Andreas Lackner¹, Nick Warr⁷, Florian Pauler⁸, Simon Hippenmeyer⁸, Ernest Laue⁶, Matthias Farlik³, Christoph Bock^3,9, Andreas Beyer⁵, Anthony C. F. Perry^4,# and Martin Leeb^1,#

Abstract:

In mammalian genomes, differentially methylated regions (DMRs) and histone marks including H3K27me3 at imprinted genes are asymmetrically inherited to control parentallybiased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. Seventy-one genes exhibited novel parentof-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental nBiX expression disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 16% of nBiXs were associated with a DMR, whereas most were associated with, and/or dependent on, parentally-biased H3K27me3, indicating a major role for Polycomb-mediated imprinting in blastocysts. nBiX genes were clustered: five clusters contained at least one published imprinted gene, and five novel clusters contained exclusively nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.

Repository structure:

The folder structure is organized as follows:

• metadata/ - sample metadata and config parameters
• src/ - data analysis code
• data/ - additional preprocessed input data

Links:

• WGBS and RNA-seq data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152106
• Paper: https://doi.org/10.1038/s41467-021-23510-4