Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice

Abstract

We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed F1 hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 alleles×(2 cell lines×4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)− transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)− transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome.

MoG+: a database of genomic variations across three mouse subspecies for biomedical research

“…Information on the comparative genomic variations was made available in a public database named NIG_MoG (Takada et al 2015 ). The data on single nucleotide polymorphisms (SNPs) in MSM and JF1 has been widely used to identify allele-specific markers for epigenetic and gene expression analyses in commonly used laboratory strains (Yagi et al 2017 , 2019 ; Kondo et al 2019 ).…”

Expression analysis of box C/D snoRNAs with SNPs between C57BL/6 and MSM/Ms strains in male mouse

“…Most genes that is subject to the genomic imprinting control have important roles in regulating the development of individuals and the activities of living organisms [ 27 ]. It has been demonstrated that monoallelic expression of RNAs can be analyzed by using the F1 hybrid mice between B6 and MSM [ 28 ]. In the hybrid F1, there are several genes that show different expression patterns compared to fathers and mothers.…”

“…In the hybrid F1, there are several genes that show different expression patterns compared to fathers and mothers. For example, incompatibility due to strain difference occurs due to factors such as mismatching combinations of transcription regulatory factors [ 28 ]. To analyze the incompatibility, it is important to know the normal expression pattern and the proposed method based on the SNPs are useful for such analyses.…”

Inter-subspecies mouse F1 hybrid embryonic stem cell lines newly established for studies of allelic imbalance in gene expression

“…Genomic imprinting is one of the most intriguing phenomena of gene expression regulation in mammals. To understand its mechanisms, research has used F1 offspring between two genetically distant inbred mouse strains; our group has analyzed genomic imprinting in F1 hybrid mice from a cross between the C57BL/6 (B6) and MSM/Ms (MSM) strains [ 1 , 2 , 3 ]. This experimental system allowed us to discern the maternal and paternal allele expression by using SNPs on each strain’s chromosomes.…”

“…This experimental system allowed us to discern the maternal and paternal allele expression by using SNPs on each strain’s chromosomes. We have also established an in vitro neurogenesis system based on F1-blastocyst-derived embryonic stem (ES) cells [ 2 , 3 ].…”