Biology subjects

Ishizu, H.

Publications and source records attributed to Ishizu, H..

5 recordsLinked to original sources

bioRxiv2025

REFEE Shapes ZGA Through Post-Transcriptional Regulation of Repetitive RNAs in Mouse Embryos

During early mammalian embryonic development, repetitive elements such as transposons and duplicated genes are transcriptionally active and play key roles in embryogenesis. MERVL, an endogenous retrovirus, is essential for shaping the early transcriptome, particularly during the transition from totipotency to pluripotency. However, the function of many repetitive elements remains poorly understood. Here, we add a new repetitive player, REFEE, that regulates repetitive RNAs and contributes to totipotency regulation through post-transcriptional mechanisms. REFEE was initially identified as a paralogue of Alyref, a nucleocytoplasmic RNA exporter, transiently expressed during the 2-cell stage of mouse embryogenesis. REFEE preferentially binds and stabilizes MERVL RNA, promoting its export. REFEE knockdown embryos fail to complete zygotic genome activation (ZGA), accompanied by a significant reduction in MERVL RNA levels. REFEE primarily influences transcript levels of ZGA genes, upregulating or downregulating them in a manner correlated with their genomic proximity to MERVL. Proteomic analysis further revealed that REFEE knockdown also decreases protein levels of its RNA targets, indicating an additional layer of post-transcriptional regulation beyond RNA stability. Our findings identify REFEE as an essential post-transcriptional regulator of early embryonic development and highlight the functional interplay between repetitive elements in shaping the zygotic transcriptome.

developmental biology↗

bioRxiv2024

ADMA-histones define genomic loading of Rhino at the initial step of piRNA cluster formation

In Drosophila germ cells, piRNAs arise from dual-strand piRNA clusters, which are marked by a repressive histone mark H3K9me3, but are transcribed from internal sites in a manner dependent on the HP1 homolog Rhino. Rhino binds to H3K9me3 on these clusters, yet the mechanism controlling its binding to clusters remains unclear. Here, we used cultured ovarian somatic cells (OSCs), which lack endogenous Rhino and its stabilizer Kipferl, whose absence renders the dual-strand clusters inert, and found that exogenous Rhino tends to bind to the ends of dual-strand clusters with asymmetric dimethylarginine histones (ADMA-histones). Depletion of the arginine methyltransferases responsible for ADMA modifications, such as DART4, affected the genomic localization of Rhino in both OSCs and ovaries. We also identified primitive, cluster-like genomic regions, termed DART4 piSL, where Rhino propagates in an DART4-dependent but unstable manner. Our study proposes that ADMA-histones play a crucial role in the initial genome loading of Rhino and may establish the potential sites of its propagation, which are subsequently stabilized to support piRNA production.

molecular biology↗

bioRxiv2022

Transcription of Murine Endogenous Retrovirus MERVL Is Required for Progression of Development in Early Preimplantation Embryos

Zygotic genome activation (ZGA) is a critical post-fertilization step that promotes totipotency and allows different cell fates to emerge in the developing embryo. MERVL, murine endogenous retrovirus-L, is transiently upregulated at the 2-cell stage around the time of ZGA. Although MERVL expression is widely used as a marker of totipotency, the role of this retrotransposon in mouse embryogenesis remains elusive. Here, we develop a method for consistent knockdown of interspersed copies of MERVL and show that MERVL RNA, but not encoded retroviral proteins and their long terminal repeat (LTR) promoter, is essential for accurate regulation of the host transcriptome and chromatin state during preimplantation development. MERVL knockdown (KD) results in embryonic lethality due to defects in differentiation and genomic stability. Furthermore, transcriptome and epigenome analysis revealed that MERVL-KD embryos retained an accessible chromatin state at, and aberrant expression of, a subset of 2-cell specific genes at mid-preimplantation stages. Taken together, our results suggest a model in which an endogenous retrovirus plays a critical role in regulating host cell fate potential.

developmental biology↗

bioRxiv2022

Obox4 secures zygotic genome activation upon loss of Dux

Once fertilized, mouse zygotes rapidly proceed to zygotic genome activation (ZGA), during which long terminal repeats (LTRs) of murine endogenous retroviruses with leucine tRNA primer (MERVL) are activated by a conserved homeodomain-containing transcription factor, DUX. However, Dux-knockout embryos produce fertile mice, suggesting that ZGA is redundantly driven by an unknown factor(s). Here we present multiple lines of evidence that the multicopy homeobox gene, Obox4, encodes a transcription factor that is highly expressed in mouse 2-cell embryos and redundantly drives ZGA. Genome-wide profiling revealed that OBOX4 specifically binds and activates MERVL LTRs as well as a subset of murine endogenous retroviruses with lysine tRNA primer (MERVK) LTRs. Depletion of Obox4 is tolerated by embryogenesis, whereas concomitant Obox4/Dux depletion markedly compromises embryonic development. Our study identified OBOX4 as a transcription factor that provides genetic redundancy to pre-implantation development.

genetics↗

bioRxiv2019

Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing

The PIWI-interacting RNA (piRNA) pathway preserves genomic integrity by repressing transposable elements (TEs) in animal germ cells. Among PIWI-clade proteins in Drosophila, Piwi transcriptionally silences its targets through interactions with cofactors, including Panoramix (Panx) and forms heterochromatin characterized by H3K9me3 and H1. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms complexes with Piwi, Panx, and p15. Panx-Nxf2-p15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. In addition, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Nxf2-Panx-p15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway.\n\nHighlightsO_LINxf2 plays an essential role in the Piwi-piRNA pathway\nC_LIO_LIFormation of Piwi-Panx-Nxf2-p15 (PPNP) complexes stabilizes both Panx and Nxf2\nC_LIO_LIThe PPNP complex triggers transcriptional silencing before heterochromatin formation\nC_LIO_LINxf2 directly binds to target transcripts in a Piwi-dependent manner\nC_LI

molecular biology↗