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Ikeda, S.

Publications and source records attributed to Ikeda, S..

At least 19 recordsLinked to original sources

DHA deficiency drives neural oxidized-lipid stress and microglial activation

Despite the well-established importance of DHA in neural health, the mechanisms by which neural tissues respond to declining DHA availability and how this response contributes to aging remain poorly understood. Here, we show that chronic DHA deficiency triggers a neural-specific compensatory lipid-remodeling program with pathological consequences. DHA loss causes a neural-tissue-selective shift from DHA-containing phospholipids toward arachidonic and adrenic acid-containing omega-6 species, accompanied by an RPE-associated polyunsaturated fatty acid biosynthetic program. This remodeling expands the pool of oxidation-prone lipids, redirects lipid peroxidation toward omega-6-derived products, and increases oxidative damage. Dietary DHA restoration reversed lipid remodeling, oxidative stress, inflammation, and visual dysfunction, establishing DHA deficiency as a causal driver of these phenotypes in mice. We identified an APOE-dependent oxidized-lipid disposal pathway that transfers oxidized lipid cargo from the neural retina to subretinal microglia, limiting its retention within the neural retina and protecting against degeneration. However, with persistent lipid uptake, oxidized phospholipids accumulate in microglial lysosomes, with sustained galectin-3 activation. Galectin-3 deficiency preferentially protected against later-stage degeneration, indicating that prolonged lipid burden converts the initial clearance response into a pathogenic response. Physiologically aged retinas also showed a similar shift toward omega-6 lipid accumulation. These findings define an adaptive-to-maladaptive lipid-remodeling-microglia axis linking declining DHA availability to age-related neural dysfunction.

physiology↗

Cardiomyocyte-derived Wnt5a drives doxorubicin-induced cardiomyopathy by amplifying cellular senescence

Doxorubicin (DOX) is an effective anthracycline chemotherapeutic agent, but its use is limited by cardiotoxicity that can progress to cardiomyopathy and heart failure. Cellular senescence contributes to DOX-induced cardiac injury, yet the upstream signals that initiate and propagate senescence in the injured heart remain unclear. Here, we identify Wnt5a, a non-canonical Wnt ligand, as a mediator of anthracycline cardiomyopathy. WNT5A was increased in serum from cancer patients receiving anthracycline therapy and in a pathologic human cardiomyocyte population in the context of DOX-induced cardiomyopathy. In mouse hearts, DOX induced early cardiomyocyte-enriched Wnt5a expression before overt cardiac dysfunction. Cardiomyocyte-specific Wnt5a deletion attenuated DOX-induced cardiac dysfunction, fibrosis and senescence marker induction, whereas recombinant Wnt5a and cardiomyocyte-targeted Wnt5a overexpression were sufficient to promote cardiomyocyte senescence and cardiac dysfunction. Mechanistically, DOX activated a Wnt5a-Fzd2 feed-forward axis that amplified Wnt5a expression in cardiomyocytes and propagated senescence to neighboring fibroblasts. Genetic disruption of this pathway in cardiomyocytes, fibroblasts or senescent cells reduced DOX-induced cardiomyopathy. Pharmacological inhibition of Wnt5a signaling with secreted frizzled-related protein 5 suppressed DOX-induced cardiac injury without compromising the anticancer efficacy of DOX. These findings identify Wnt5a-Fzd2 signaling as a senescence-amplifying mechanism in anthracycline cardiomyopathy and suggest a therapeutic strategy to mitigate DOX cardiotoxicity.

cell biology↗

TMEM135 deficiency remodels hepatic lipid homeostasis and protein malonylation through a DHA-sensitive lipogenic program buffered by peroxisomal metabolism

TMEM135 has been implicated in lipid metabolism, but its role in regulating hepatic lipid homeostasis remains unclear. Here, we investigated how TMEM135 affects hepatic lipid metabolism using Tmem135 mutant mice with liver-specific Pex5 deletion. The Tmem135 mutation induced a lipogenic state characterized by depletion of docosahexaenoic acid (DHA), activation of SREBP-dependent pathways, and increased monounsaturated fatty acids without causing hepatic steatosis. In contrast, loss of PEX5-dependent peroxisomal function in Tmem135 mutant mice resulted in marked hepatic lipid accumulation, indicating that peroxisomal metabolism buffers the elevated lipogenic state. Fish oil supplementation to Tmem135 mutant mice restored DHA levels and suppressed lipogenesis. Proteomics identified distinct DHA-sensitive metabolic programs, including activation of SREBP-dependent lipogenesis. Quantitative malonyl-proteomics revealed increased malonylation of glycolytic enzymes, accompanied by altered glycolytic output. Together, these findings identify TMEM135 as a central regulator of hepatic lipid metabolism and uncover a coordinated mechanism linking lipid availability, lipogenesis, and post-translational metabolic regulation. HighlightTmem135 mutation induces a lipogenic state with increased lipolysis without hepatic steatosis. PEX5-dependent peroxisomal function buffers lipid accumulation in Tmem135 mutant liver. Fish oil supplementation restores DHA and suppresses SREBP-dependent lipogenesis in Tmem135 mutants. DHA-sensitive protein malonylation targets glycolytic enzymes in Tmem135 mutant liver.

cell biology↗

MARiO: predicting cancer variant pathogenicity by integrating in silico evaluation and patient-level mutational contexts

Comprehensive genomic profiling (CGP) supports precision medicine in cancer care, but accurate assessment of missense variant pathogenicity, especially for variants without established consensus, remains challenging. Various computational tools have been developed for variant functional prediction, but most current tools rely solely on variant-level features and do not capture the clinical context of individual patients. To address this limitation, we developed MARiO (Missense Alteration Risk for Oncogenicity), a machine-learning model that integrates variant-level features and patient-level clinical and genomic contexts to effectively predict the pathogenicity of missense variants in cancer. We collected a total of 10,642 missense variants from 1271 patients, and evaluated candidate features for their association with variant pathogenicity, identifying informative features including in silico functional predictions, population allele frequency, variant allele frequency, and tumor mutational burden. Using these selected features, MARiO was developed with extreme gradient boosting. The model integrates multiple in silico prediction tools and patient-specific genomic contexts while accommodating missing values frequently observed in real-world CGP datasets. MARiO outperformed existing tools, achieving an area under the receiver operating characteristic curve of 0.942. The model demonstrated strong generalizability across multiple external datasets and showed consistency with real-world molecular treatment proposals. MARiO offers a robust and clinically relevant approach for missense variant pathogenicity assessment by integrating variant- and patient-level features and serves as a valuable tool to support clinical decision-making.

bioinformatics↗

Long-read sequencing reveals transposable element-derived chimeric transcripts at zygotic genome activation in mammalian embryos

BackgroundTransposable elements (TEs) are mobile genomic sequences that constitute one-third to one-half of the mammalian genome. Recently, TEs have been recognized for their important roles as cis-regulatory elements. TEs are broadly activated during zygotic genome activation (ZGA) in mammalian embryos, where they function as alternative promoters of host genes and drive the transcription of chimeric transcripts. However, the construction of comprehensive chimeric transcript databases based on short-read sequencing remains limited due to the repetitive and abundant nature of TEs in the genome. Here, we used long-read RNA sequencing to construct a comprehensive dataset of chimeric transcripts expressed in ZGA mouse and bovine embryos. ResultsWe identified 11,996 and 4,755 chimeric transcripts variants derived from 2,695 and 1,200 host genes in mouse and bovine, respectively, exceeding the numbers reported in previous short-read-based studies. Among them, 114 orthologous pairs produced chimeric transcripts in both species. Gene Ontology analysis revealed significant enrichment of terms related to transcriptional regulation and protein modification in mouse, whereas no terms were significantly enriched in bovine. Assessment of the protein-coding potential of the TE-driven transcripts using predicted open reading frames (ORFs) revealed that the proportion of "Protein-coding" transcripts was lower, whereas that of "LncRNA" (long non-coding RNA) was higher compared with all transcripts in both species. Among the ORFs classified as "Protein-coding", comparison with canonical ORFs revealed a tendency for the N terminus to be truncated while the C terminus remained intact in both species. TE-derived promoters used in mouse were enriched for mouse-specific TEs, whereas those in bovine were enriched for older TEs conserved among eutherians. In addition, long-read sequencing detected a greater number and proportion of TEs used as promoters in mouse and bovine than short-read sequencing. Although motif analysis identified KLF5 and OTX2 binding sites upstream of TE-derived promoters in both species, the specific TEs containing these motifs differed between the two species. ConclusionsThis study presents the first long-read sequencing analysis of chimeric transcripts in mammalian embryos in two species. Our approach revealed the functional similarities of chimeric transcripts between species, as well as species-specific differences in their TE compositions.

developmental biology↗

Environment-responsive individual cell growth behavior shapes stochastic and deterministic population establishment in ammonia-oxidizing bacteria

Many environmental bacteria do not readily grow under laboratory conditions and population establishment often occurs stochastically. Although the scout hypothesis has been proposed to explain stochastic population establishment in environmental bacteria, how stochastic population establishment is shaped by individual cell growth behaviors in environmental isolates remains unclear. In the present study, we focused on the ammonia-oxidizing bacterium Nitrosomonas sp. PY1 and showed that environmentally responsive individual cell growth behavior, incorporating time-dependent stochastic growth initiation, shapes both deterministic and stochastic population establishment dynamics. Using single-cell observation, we revealed that PY1 altered cell growth behavior in response to surrounding biomass production ({Delta}Vt). These {Delta}Vt-dependent changes in growth behavior were suppressed by the addition of its own cell-free supernatant (CFS), indicating the presence of a growth regulation mechanism via cell-cell communication. Replicate cultures under the same conditions showed that the population establishment of PY1 was stochastic, whereas the model strain Nitrosomonas europaea exhibited synchronized population establishment, consistent with previous reports. This stochasticity in PY1 was also eliminated by the addition of CFS. Finally, a simulation model based on {Delta}Vt-dependent cell growth behavior of PY1 successfully reproduced synchronized population establishment in the presence of CFS. By contrast, the stochastic population establishment observed in the absence of CFS was successfully reproduced by a model incorporating {Delta}Vt-independent growth initiation following a Weibull distribution. Such environmentally responsive changes in population establishment dynamics may contribute to the low isolation success of environmental bacteria and sudden blooms of the rare biosphere.

microbiology↗

Improving Emotion Classification by Combining fNIRS-Derived Hemodynamic Responses with Peripheral Physiological Signals

We investigated whether multimodal sensing that combines functional near-infrared spectroscopy (fNIRS) with peripheral physiological signals can improve subject-independent classification of arousal and valence, the fundamental affective dimensions in Russells circumplex model. We developed Japanese emotion-inducing music-video stimuli (60 seconds each) and recorded subjects central nervous system activity using fNIRS, alongside peripheral physiological measures, specifically electrodermal activity (EDA) and photoplethysmography (PPG), during video viewing. To prioritize reproducibility and methodological transparency, we extracted simple, easily computed features from each modality and performed binary (high vs. low) classification separately for arousal and valence using a support vector machine. The combination of fNIRS and EDA yielded the highest performance, with a macro-averaged F1 score of 0.73 for arousal and 0.64 for valence. These findings underscore the utility of integrating fNIRS with peripheral physiological signals for subject-independent emotion classification.

neuroscience↗

Nardilysin regulates Slc2a2 expression through ISLET1 recruitment to an evolutionarily conserved enhancer in pancreatic β-cells

GLUT2 (Slc2a2) is a key glucose transporter in pancreatic {beta}-cells, and its reduced expression is closely linked to defective glucose-stimulated insulin secretion (GSIS) and diabetes. We previously reported that pancreatic {beta}-cell-specific nardilysin (NRDC)-deficient mice (BetaKO) exhibit severe diabetic phenotype with defective GSIS and reduced Slc2a2 expression in islets. However, because BetaKO mice also showed reduced MafA, a key upstream regulator of Slc2a2, along with an increased -cell/{beta}-cell ratio and other secondary changes that could influence GLUT2 levels, the mechanism by which NRDC regulates Slc2a2 transcription remained unclear. Here, we demonstrate that NRDC controls Slc2a2 expression in a {beta}-cell autonomous and MafA-independent manner. By integrating publicly available ATAC-seq and ChIP-seq datasets, we identified four active enhancer regions around the murine Slc2a2 locus, two of which are evolutionarily conserved in human islets. Luciferase assays revealed that NRDC selectively controls the activity of a conserved enhancer located 39k bp downstream of the Slc2a2 transcriptional start site. Chromatin immunoprecipitation (ChIP) and re-ChIP assays further revealed that NRDC binds to this enhancer and is required for efficient recruitment of ISLET1, a transcription factor upstream of Slc2a2. These findings indicate that NRDC directly regulates Slc2a2 in addition to MafA, highlighting multifaceted roles of NRDC in pancreatic {beta}-cell gene regulation.

cell biology↗

Osteochondrogenic Transdifferentiation of Vascular Smooth Muscle Cells and Microenvironmental Dynamics in Medial Arterial Calcification

BackgroundVascular calcification, particularly medial arterial calcification (MAC), considerably affects cardiovascular mortality. Current treatments are limited because of the unclear molecular mechanisms of MAC. This study aimed to establish an MAC mouse model using O-ring-induced transverse aortic constriction (OTAC) and to identify critical genes, pathways, and cellular interactions involved in MAC formation by combining lineage tracing technology and single-cell RNsA sequencing (scRNA-seq). MethodsWe developed an OTAC mouse model to mimic MAC. Adult C57BL/6J male mice underwent OTAC, and subsequent analyses were performed at various intervals. Histological and immunohistochemical evaluations were conducted to observe changes in vascular smooth muscle cells (VSMCs). Lineage tracing was used to confirm the origin of osteochondrogenic cells in the tunica media. Additionally, scRNA-seq was performed to capture the dynamic changes in VSMCs and other cell types involved in MAC development. ResultsOsteochondrogenic cells and the subsequent MAC in OTAC mice were observed using histological evaluations. Immunohistochemistry showed time-dependent decreases in -SMA expression and increases in SOX9 and RUNX2 expression in VSMCs. Lineage tracing using Myh11CreERT2;ROSA26-EGFP mice confirmed that osteochondrogenic cells originated from contractile VSMCs. scRNA-seq confirmed osteochondrogenic transdifferentiation of VSMCs and highlighted dynamic changes in surrounding cells involved in calcification-related and inflammatory processes. ConclusionThe OTAC method enabled a comprehensive understanding of the microenvironmental dynamics during MAC progression at the single-cell level. This powerful model provides a robust platform for future therapeutic intervention research. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/684711v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@c64634org.highwire.dtl.DTLVardef@12b0b9aorg.highwire.dtl.DTLVardef@106c5b4org.highwire.dtl.DTLVardef@19dd4f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Transgenic Bax gene efficiently induces lethality in mouse early embryos

Apoptosis is an essential physiological process involved in embryonic development, immune responses, and tissue homeostasis. Despite many studies on pro-apoptotic genes, few reports have directly compared the lethality-inducing potential between them under identical conditions. In this study, we evaluated the lethality-inducing potential of three representative pro-apoptotic genes, Bax, Casp3, and Casp9, in mouse early embryos under defined conditions using the doxycycline (Dox)-inducible tetracycline-regulated gene expression system (Tet-On system) in combination with the PiggyBac transposon system. All genes were transcriptionally induced by Dox, and Bax showed the strongest lethal effect, followed by Casp9, while Casp3 did not show any effect. Notably, Bax expression severely impaired blastocyst formation and led to the intense accumulation of the DNA damage marker {gamma}H2AX. These findings suggest that introducing upstream apoptotic regulators leads to the more efficient and widespread activation of the apoptotic cascade. Additionally, an unexpected Dox-dependent increase in the expression of reverse tetracycline-controlled transactivator, which is typically driven by a constitutive promoter, was observed, raising the possibility of unanticipated regulatory mechanisms within the Tet-On system. Overall, this study is expected to contribute to a deeper understanding of apoptotic mechanisms and future advancements in regenerative medicine, reproductive engineering, and cancer research.

bioengineering↗

Mitochondrial fusion controls the development of specialized mitochondrial structure and metabolism in rod photoreceptor cells

Mitochondria are dynamic organelles that undergo continuous morphological changes, yet exhibit unique, cell-type-specific structures. In rod photoreceptor cells of the retina, these structures include elongated mitochondria in the inner segments and a distinct, large, circular mitochondrion in each presynaptic terminal. The mechanisms underlying the establishment and maintenance of these specialized mitochondrial morphologies, along with their functional significance, are not well understood. Here, we investigate the roles of mitochondrial fusion proteins mitofusin 1 (MFN1) and mitofusin 2 (MFN2) in shaping these structures and maintaining photoreceptor cell health. Rod photoreceptor cell-specific ablation of MFN1 and MFN2 resulted in mitochondrial fragmentation by one month of age, suggesting that mitochondrial fusion is essential for the development of photoreceptor cell-specific mitochondrial structures. Notably, the layer structures of the retina examined by light microscopy appeared unaffected at this age. Following this time period, significant photoreceptor cell degeneration occurred by three months of age. Furthermore, we showed that impaired mitochondrial fusion perturbed the balance of proteins involved in glycolysis, oxidative phosphorylation (OXPHOS), and {beta}-oxidation, highlighting the critical role of mitochondrial fusion in ensuring the proper levels of proteins necessary for optimal energy metabolism. Additionally, we identified upregulation of cellular stress pathways such as endoplasmic reticulum (ER) stress and unfolded protein response (UPR), which arise in response to energy deprivation, and cytoprotective biosynthetic pathways mediated by CCAAT/enhancer-binding protein gamma (C/EBP{gamma}) and mammalian target of rapamycin complex 1 (mTORC1) signaling. In summary, our findings indicate that mitochondrial fusion through MFN1 and MFN2 is vital for the development of unique mitochondrial structures and proper energy production, underscoring the fundamental importance of mitochondrial dynamics in photoreceptor cell function and survival. Significance StatementsRod photoreceptor cells exhibit unique mitochondrial morphologies and high energy requirements. In this report, we examined how these unique mitochondrial structures are established and their biological significance. We identified that mitochondrial fusion is essential for the development of characteristic mitochondrial morphologies in rod photoreceptor cells. Furthermore, we demonstrated that impaired mitochondrial fusion disrupts the equilibrium of proteins associated with OXPHOS, glycolysis, and {beta}-oxidation, ultimately leading to an imbalance in cellular energy homeostasis. Our findings also revealed activation of cellular stress pathways, including ER stress and the UPR, which are likely triggered by energy depletion. Additionally, we identified activation of cytoprotective biosynthetic pathways that are engaged to preserve cellular homeostasis and function.

molecular biology↗

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

BioSample is a comprehensive repository of experimental sample metadata, playing a crucial role in providing a comprehensive archive and enabling experiment searches regardless of type. However, the difficulty in comprehensively defining the rules for describing metadata and limited user awareness of best practices for metadata have resulted in substantial variability depending on the submitter. This inconsistency poses significant challenges to the findability and reusability of the data. Given the vast scale of BioSample, which hosts over 40 million records, manual curation is impractical. Rule-based automatic ontology mapping methods have been proposed to address this issue, but their effectiveness is limited by the heterogeneity of BioSample metadata. Recently, large language models (LLMs) have gained attention in natural language processing and have been expected as promising tools for automating metadata curation. In this study, we evaluated the performance of LLMs in extracting cell line names from BioSample descriptions using a gold-standard dataset derived from ChIP-Atlas, a secondary database of epigenomics experiment data, which manually curates samples. Our results demonstrated that LLM-assisted methods outperformed traditional approaches, achieving higher accuracy and coverage. We further extended this approach to extraction of information about experimentally manipulated genes from metadata where manual curation had not yet been applied in ChIP-Atlas. This also yielded successful results for the usage of the database, which facilitates more precise filtering of data and prevents misinterpretation caused by inclusion of unintended data. These findings underscore the potential of LLMs to improve the findability and reusability of experimental data in general, significantly reducing user workload and enabling more effective scientific data management.

bioinformatics↗

Endogenous retrovirus-driven Pcgf5 plays critical roles in zygotic genome activation and noncanonical imprinting

MERVL (murine endogenous retrovirus with leucine tRNA primer) is expressed during zygotic genome activation (ZGA) in mammalian embryos. Here, we show that the Polycomb group ring finger 5 (Pcgf5), a key component of Polycomb repressive complex 1 (PRC1), forms a chimeric transcript with MT2C_Mm, one of the long terminal repeat sequences of MERVL. Knockdown of Pcgf5 reduced developmental rates and decreased H3K27me3 and H2AK119ub1 modification during embryogenesis. In addition, not only genes expressed during ZGA but also imprinting genes were upregulated in Pcgf5 knockdown embryos. Moreover, Pcgf5 was involved in the addition of the H3K27me3 modification to the maternal Xist region. This is the first report of a MERVL-regulated transcript regulating Xist expression in mouse preimplantation embryos. Our results suggest that analysis of chimeric transcripts with MERVL will provide insight into the relationship between ZGA and noncanonical imprinting.

developmental biology↗

Cell cycle length regulates heterochromatin reprogramming during early development in non-mammalian vertebrates

Heterochromatin marks such as H3K9me3 undergoes global erasure and re-establishment after fertilization, and the proper reprogramming of H3K9me3 is essential for early development. Despite the widely conserved dynamics of heterochromatin reprogramming in invertebrates and non-mammalian vertebrates, previous studies have shown that the underlying mechanisms may differ between species. In this study, we investigated the molecular mechanism of H3K9me3 dynamics in medaka (Japanese killifish, Oryzias latipes) as a non-mammalian vertebrate model, and found that rapid cell cycle during the cleavage stages causes DNA replication-dependent passive erasure of H3K9me3. We also found that cell cycle slowing, toward the mid-blastula transition, permits increasing nuclear accumulation of H3K9me3 histone methyltransferase Setdb1, leading to the onset of H3K9me3 re-accumulation. We further demonstrated that cell cycle length in early development regulates H3K9me3 reprogramming in zebrafish and Xenopus laevis as well. Together with the previous studies in invertebrates, we propose that the cell cycle length-dependent mechanism for both global erasure and re-accumulation of H3K9me3 is widely conserved among rapid-cleavage species of non-mammalian vertebrates and invertebrates such as Drosophila, C. elegans and teleost fish.

developmental biology↗

NSUN5 is essential for proper Hippo signaling in mouse preimplantation development

AbstractNOL1/NOP2/Sun domain family, member 5 (NSUN5) is an enzyme belonging to the 5-methylcytosine (m5C) writer family that modifies rRNA and mRNA. By re-analyzing published RNA-sequencing data, we found that Nsun5 expression was increased at the 2-cell stage during mouse preimplantation development. It has been reported that m5C regulates the stability of rRNA and mRNA. Therefore, NSUN5 may affect the expression of genes required for the development and differentiation of early mouse embryos via its role in modifying RNA. The Hippo signaling pathway has been identified as a critical regulator of the segregation of inner cell mass and trophectoderm lineages during mouse embryogenesis. According to these findings, we hypothesized that NSUN5 controls cell differentiation by regulating the expression of components of the Hippo signaling pathway in mouse early embryos. Using Nsun5-specific small interfering RNAs, we efficiently knocked down Nsun5 expression in mouse preimplantation embryos, resulting in impairments in early development, including reduced blastocyst formation, smaller size, and impaired hatching from the zona pellucida. Nsun5 depletion also led to decreased cell numbers, suggesting impaired cell proliferation. Furthermore, Nsun5 knockdown embryos exhibited reduced yes-associated protein 1 (YAP1) nuclear translocation during the morula stage, potentially affecting cell differentiation. The imbalance in pluripotent and trophectoderm lineages was evident with a significant reduction in the ratio of CDX2-positive cells to OCT4-positive cells. Nsun5 depletion impacted the Hippo signaling pathway, increasing the expression of the key genes Lats1 and Lats2 during the morula stage. Our findings underscore the essential role of Nsun5 in early embryonic development by affecting cell proliferation, YAP1 nuclear translocation, and the Hippo pathway. Understanding the roles of Nsun5 in mouse early embryos will provide insights into complex regulatory networks in development, with implications for reproductive medicine and fertility research.

developmental biology↗

Diagnostic histone modification analysis of individual preimplantation embryos

BackgroundWe previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). ResultsWOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. ConclusionsThese results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.

genomics↗

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf-production methods

In ruminants, overgrowth of offspring produced by in vitro fertilization (IVF) is a common problem. Abnormal epigenetic modifications caused by environmental factors during the early embryonic period are suspected as an etiology of overgrowth. In this study, we investigated the genome-wide histone H3K4me3 profiles of bovine placentae that play a pivotal role in fetal development and compared their characteristics between artificial insemination (AI)- and IVF-derived samples. Cotyledons were harvested from the placentae obtained at parturition of 5 AI- and 13 IVF-derived calves, and chromatin immunoprecipitation sequencing was performed for H3K4me3. We confirmed no significant maternal tissue contamination in the samples we used. The revealed H3K4me3 profiles reflected the general characteristics of the H3K4me3 modification, which is abundantly distributed in the promoter region of active genes. By extracting common modifications from multiple samples, the genes involved in placenta-specific biological processes could be enriched. Comparison with the H3K4me3 modifications of blastocyst samples was also effective for enriching the placenta-specific features. Principal component analysis suggested the presence of differential H3K4me3 modifications in AI- and IVF-derived samples. The genes contributing to the difference were related to the developmental biological processes. Imprinted genes such as BEGAIN, ZNF215, and DLX5 were among the extracted genes. Principal component and discriminant analyses using only male samples categorized the samples into three groups based on fetal weight and calf-production methods. To our knowledge, this is the first study to profile the genome-wide histone modifications of bovine fetal placentae and reveal their differential characteristics between different calf-production methods.

genomics↗

MYC is essential for induction of major ZGA and subsequent preimplantation development

In mouse preimplantation development, zygotic genome activation (ZGA), which synthesizes new transcripts from the embryos, begins in the S phase of the one-cell stage, with major ZGA occurring especially at the late two-cell stage. Myc is a transcription factor expressed in parallel with ZGA, but its direct association with the major ZGA has not been clarified. In this study, we found that developmental arrest occurs at the two-cell stage when mouse embryos were treated with antisense oligos targeting Myc or inhibitors specific for MYC from the one-cell stage. In order to identify when MYC inhibition affected development, we applied time-limited inhibitor treatment, and found that inhibition of MYC at the two-cell, four-cell, and morula stages had no effect on preimplantation development, whereas treatment with the inhibitor at the early two-cell stage arrested development at the two-cell stage. Furthermore, transcriptome analysis revealed that when MYC function was inhibited, genes expressed in the major ZGA phase were suppressed. These results suggest that Myc is essential for the induction of major ZGA and its subsequent development. Revealing the function of Myc in preimplantation development is expected to contribute to advances in assisted reproductive technology.

developmental biology↗