Biology subjects

Kurimoto, K.

Publications and source records attributed to Kurimoto, K..

3 recordsLinked to original sources

bioRxiv2023

Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

The imprinted ZDBF2 gene is controlled by oocyte-derived DNA methylation, but its epigenetic regulation is quite different from that of other canonically imprinted genes that are dependent on DNA methylation deposited in the gametes. At the ZDBF2 locus, maternal DNA methylation in the imprinted differentially methylated region (DMR) does not persist after implantation. Instead, a transient transcript expressed in the early embryo exclusively from the unmethylated paternal allele of the DMR, known as GPR1-AS in humans and Liz in mice, contributes to establishing secondary DMRs that maintain paternal expression of ZDBF2 in the somatic lineage. While the imprinting of ZDBF2 is evident in humans and mice, whether this process is conserved in other mammals has not been addressed. Here, we show that the first exon of human GPR1-AS overlaps with that of a long terminal repeat (LTR) belonging to the MER21C subfamily of retrotransposons. Although this LTR family appears and is amplified in Boroeutherians, the magnorder of placental mammals that includes the Euarchontoglires and Laurasiatheria superorders, the MER21C insertion into the GPR1-AS orthologous region occurred specifically in the common ancestor of Euarchontoglires, a clade that includes extant primates, rodents, and rabbits. The first exon of mouse Liz does not overlap with an annotated LTR in standard repeat annotation; however, promoter activity assay and multiple sequence alignment suggests that it retains a functionally conserved relationship with the MER21C-overlapping first exon of GPR1-AS. Furthermore, directional RNA sequencing of placental tissues from rabbits and nonhuman primates also revealed GPR1-AS orthologs, with their first exon embedded within the same ancestral LTR. In contrast, allele-specific expression profiling of cow and tammar wallaby, mammals outside the Euarchontoglires group, revealed expression from both alleles in all tissues analyzed. Taken together, these observations suggest that imprinting of ZDBF2 in Euarchontoglires had its genesis in the insertion of a MER21C element in their common ancestor. Our previous studies showed that LTRs reactivated in oocytes contribute to lineage-specific imprinting during mammalian evolution. The data presented here suggest that post-fertilization activation of an ancestral LTR-derived sequence can also contribute to the lineage-specific establishment of imprinted genes.

genomics↗

bioRxiv2022

Histology-associated transcriptomic heterogeneity in ovarian folliculogenesis revealed by quantitative single-cell RNA-sequencing for tissue sections with DRaqL

High-quality single-cell RNA-sequencing (RNA-seq) with spatial resolution remains challenging. Laser capture microdissection (LCM) is a widely used, potent approach to isolate arbitrarily targeted cells from tissue sections for comprehensive transcriptomics. Here, we developed DRaqL (direct RNA recovery and quenching for LCM), an experimental approach for efficient lysis of single cells isolated by LCM from alcohol- and formalin-fixed sections without RNA purification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable to that of profiling from freshly dissociated cells, together with effective exon- exon junction profiling. Furthermore, the combination of DRaqL and protease treatment enabled robust and efficient single-cell transcriptome analysis from tissue sections strongly fixed with formalin. Applying this method to mouse ovarian sections, we revealed a transcriptomic continuum of growing oocytes quantitatively associated with oocyte size, and detected oocyte-specific splice isoforms. In addition, our statistical model revealed heterogeneity of the relationship between the transcriptome of oocytes and their size, resulting in identification of a size-transcriptome relationship anomaly in a subset of oocytes. Finally, we identified genes that were differentially expressed in granulosa cells in association with the histological affiliations of granulosa cells to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ-soma relationship. Thus, we developed a versatile, efficient approach for robust single-cell cDNA amplification from tissue sections and provided an experimental platform conducive to high-quality transcriptomics, thereby revealing histology-associated transcriptomic heterogeneity in folliculogenesis in ovarian tissues.

developmental biology↗

bioRxiv2022

Conservation and divergence of canonical and non-canonical imprinting in murids

BackgroundGenomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behaviour. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we used low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extra-embryonic tissues at allele-specific resolution. ResultsWe identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extra-embryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Meta-analysis of novel imprinted genes revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. ConclusionsIn summary, we provide a comprehensive list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.

genomics↗