详细内容（前10条）

1. GSE306390 聚苯乙烯微塑料通过细胞骨架重塑和表观遗传重编程破坏卵巢发育，尤其是在颗粒细胞中 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、epigenetic
• 📝 描述：Contributor : Mengyao LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe emerging environmental health issue posed by micro (nano) plastics (MNPs) has raised significant concerns. Accumulating evidence suggested that MNPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene microplastics (PS-MPs; 100 nm and 5 µm) on ovarian development and function in pubertal female mice. Following 35 days of exposure, we observed size-dependent reproductive toxicity, with 100 nm PS-MPs causing reduced body weight gain and ovarian size, and compromised ovarian structures and functions, including altered follicle and corpora lutea counts, alongside disrupted hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks and signaling flow patterns across seven identified ovarian cell types. Granulosa cells (GCs) were identified as the primary target PS-MPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100 nm PS-MPs were internalized by GCs, leading to cell cycle arrest, necroptosis and hormonal dysfunction. Mechanistically, PS-MPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and reducing histone marks (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-MP-induced epigenetic and transcriptional changes. Overall, this study first revealed PS-MP-mediated reproductive toxicity from a single-cell perspective, identifying granulosa cells as particularly vulnerable targets. It uncovered novel mechanisms involving cytoskeletal disruption and epigenetic reprogramming, while demonstrating size-dependent internalization patterns that directly correlate with reproductive impairment. These findings provide unprecedented insights into the molecular and epigenetic consequences of MNPs in mammalian reproduction, emphasizing the potential health risks of environmental MNPs exposure.
• 🔗 查看原文

2. GSE306389 聚苯乙烯微塑料通过细胞骨架重塑和表观遗传重编程破坏卵巢发育，尤其是在颗粒细胞中 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq、epigenetic
• 📝 描述：Contributor : Mengyao LiuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe emerging environmental health issue posed by micro (nano) plastics (MNPs) has raised significant concerns. Accumulating evidence suggested that MNPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene microplastics (PS-MPs; 100 nm and 5 µm) on ovarian development and function in pubertal female mice. Following 35 days of exposure, we observed size-dependent reproductive toxicity, with 100 nm PS-MPs causing reduced body weight gain and ovarian size, and compromised ovarian structures and functions, including altered follicle and corpora lutea counts, alongside disrupted hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks and signaling flow patterns across seven identified ovarian cell types. Granulosa cells (GCs) were identified as the primary target PS-MPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100 nm PS-MPs were internalized by GCs, leading to cell cycle arrest, necroptosis and hormonal dysfunction. Mechanistically, PS-MPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and reducing histone marks (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-MP-induced epigenetic and transcriptional changes. Overall, this study first revealed PS-MP-mediated reproductive toxicity from a single-cell perspective, identifying granulosa cells as particularly vulnerable targets. It uncovered novel mechanisms involving cytoskeletal disruption and epigenetic reprogramming, while demonstrating size-dependent internalization patterns that directly correlate with reproductive impairment. These findings provide unprecedented insights into the molecular and epigenetic consequences of MNPs in mammalian reproduction, emphasizing the potential health risks of environmental MNPs exposure.
• 🔗 查看原文

3. GSE210344 基因组的三维结构决定了HNF1β介导的基因调控的特异性（ChIP-Seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq、genome
• 📝 描述：Contributors : Lotte Tholen ; Eveline Kahlman ; Peter Krijger ; Branco Heuts ; Amin Allahyar ; Joost Martens ; Wouter de Laat ; Joost Hoenderop ; Jeroen de BaaijSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusCell-type specific gene expression patterns are essential for kidney function. This is governed by binding of polymerases and transcription (co)-factors to regulatory DNA elements that can either be located close to their target genes or at great genomic distances from their target genes. Therefore, the 3D structure of the genome is an essential factor in cell-type specific gene transcription. Here, we generated a chromosome conformation capture (Hi-C) map in a distal convoluted tubule (DCT) cell line with a 5kb resolution. To study the role of the 3D genome in transcriptional regulation in the DCT the Hi-C data was integrated with chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq data of the same cell line. Our analysis uncovered the basis of 3D genome characteristics in the DCT. Similar to other studies, promoter connectivity correlated with gene expression levels of the participating genes. As proof of principle, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that HNF1β controls the expression of housekeeping genes primarily by binding to promoters in close proximity of the transcription start site (TSS) of the gene, while the expression of developmental genes is regulated by both promoters and distal enhancers. Moreover, by employing a CRISPR/Cas9 enhancer mutant, we demonstrated that Caveolin-1 expression is regulated by an HNF1β-bound enhancer ~95kb from the TSS of the gene. In conclusion, we describe the first Hi-C map in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.
• 🔗 查看原文

4. GSE210343 基因组的三维结构决定了 HNF1β 介导的基因调控的特异性 (ATAC-Seq)

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq、genome
• 📝 描述：Contributors : Lotte Tholen ; Eveline Kahlman ; Peter Krijger ; Branco Heuts ; Amin Allahyar ; Joost Martens ; Wouter de Laat ; Joost Hoenderop ; Jeroen de BaaijSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusCell-type specific gene expression patterns are essential for kidney function. This is governed by binding of polymerases and transcription (co)-factors to regulatory DNA elements that can either be located close to their target genes or at great genomic distances from their target genes. Therefore, the 3D structure of the genome is an essential factor in cell-type specific gene transcription. Here, we generated a chromosome conformation capture (Hi-C) map in a distal convoluted tubule (DCT) cell line with a 5kb resolution. To study the role of the 3D genome in transcriptional regulation in the DCT the Hi-C data was integrated with chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq data of the same cell line. Our analysis uncovered the basis of 3D genome characteristics in the DCT. Similar to other studies, promoter connectivity correlated with gene expression levels of the participating genes. As proof of principle, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that HNF1β controls the expression of housekeeping genes primarily by binding to promoters in close proximity of the transcription start site (TSS) of the gene, while the expression of developmental genes is regulated by both promoters and distal enhancers. Moreover, by employing a CRISPR/Cas9 enhancer mutant, we demonstrated that Caveolin-1 expression is regulated by an HNF1β-bound enhancer ~95kb from the TSS of the gene. In conclusion, we describe the first Hi-C map in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.
• 🔗 查看原文

5. GSE296891 Menin通过表观遗传激活晚期出生神经元中的EphA4来调控皮质发生

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic
• 📝 描述：Contributors : Shuzhong Wang ; Kai Zhuang ; Liurong Chen ; Li Zhong ; Yibo Qu ; Jie ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe development of the mammalian cerebral cortex is tightly regulated by epigenetic mechanisms. However, the role of epigenetic modifications in gene regulation and their impact on neocortical function remain poorly understood. Here, we demonstrate that Menin, encoded by the multiple endocrine neoplasia type 1 (Men1) gene, is essential for neurogenesis. Deficiency in Men1 disrupts the formation of the laminated neocortex, particularly in the upper-layer neurons. In Men1-deficient late-born neurons, migration to their final positions is impaired, accompanied by defective neuronal polarization. Mechanistic studies reveal that Menin regulates global chromatin accessibility at transcriptional start sites of genes critical for neuronal development. The loss function of Menin primarily reduces H3K4me3 deposition at promoter regions. Notably, complementation with EphA4 in late-born neurons mitigates polarization defects in the context of Men1 deficiency. These findings support the importance of Menin in corticogenesis, providing insight into the formation of the cerebral cortex.
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6. GSE296806 Menin 通过表观遗传激活晚期出生神经元中的 EphA4 来协调皮质发生 [snRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic
• 📝 描述：Contributors : Shuzhong Wang ; Kai Zhuang ; Liurong Chen ; Li Zhong ; Yibo Qu ; Jie ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe development of the mammalian cerebral cortex is tightly regulated by epigenetic mechanisms. However, the role of epigenetic modifications in gene regulation and their impact on neocortical function remain poorly understood. Here, we demonstrate that Menin, encoded by the multiple endocrine neoplasia type 1 (Men1) gene, is essential for neurogenesis. Deficiency in Men1 disrupts the formation of the laminated neocortex, particularly in the upper-layer neurons. In Men1-deficient late-born neurons, migration to their final positions is impaired, accompanied by defective neuronal polarization. Mechanistic studies reveal that Menin regulates global chromatin accessibility at transcriptional start sites of genes critical for neuronal development. The loss function of Menin primarily reduces H3K4me3 deposition at promoter regions. Notably, complementation with EphA4 in late-born neurons mitigates polarization defects in the context of Men1 deficiency. These findings support the importance of Menin in corticogenesis, providing insight into the formation of the cerebral cortex.
• 🔗 查看原文

7. GSE296598 Menin通过表观遗传激活晚期出生神经元中的EphA4来调控皮质发生

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic
• 📝 描述：Contributors : Shuzhong Wang ; Kai Zhuang ; Liurong Chen ; Li Zhong ; Yibo Qu ; Jie ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe development of the mammalian cerebral cortex is tightly regulated by epigenetic mechanisms. However, the role of epigenetic modifications in gene regulation and their impact on neocortical function remain poorly understood. Here, we demonstrate that Menin, encoded by the multiple endocrine neoplasia type 1 (Men1) gene, is essential for neurogenesis. Deficiency in Men1 disrupts the formation of the laminated neocortex, particularly in the upper-layer neurons. In Men1-deficient late-born neurons, migration to their final positions is impaired, accompanied by defective neuronal polarization. Mechanistic studies reveal that Menin regulates global chromatin accessibility at transcriptional start sites of genes critical for neuronal development. The loss function of Menin primarily reduces H3K4me3 deposition at promoter regions. Notably, complementation with EphA4 in late-born neurons mitigates polarization defects in the context of Men1 deficiency. These findings support the importance of Menin in corticogenesis, providing insight into the formation of the cerebral cortex.
• 🔗 查看原文

8. GSE341768 3日龄和5日龄野生型斑马鱼肠上皮细胞的转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:intestin(e|al)
• 📝 描述：Contributors : Daniel Levic ; Michel Bagnat ; Carina BlockSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioFor this experiment, we analyzed gene expression changes and intron splicing events in the WT zebrafish intestine at two developmental stages (3 dpf and 5 dpf). To perform this analysis, we collected > 125 M paired end reads from total RNA isolated from purified cldn15la+ intestinal epithelial cells at each time point.
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9. GSE305839 聚苯乙烯微塑料通过细胞骨架重塑和表观遗传重编程干扰卵巢发育，尤其是在颗粒细胞中。

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic
• 📝 描述：Contributor : Mengyao LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe emerging environmental health issue posed by micro (nano) plastics (MNPs) has raised significant concerns. Accumulating evidence suggested that MNPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene microplastics (PS-MPs; 100 nm and 5 µm) on ovarian development and function in pubertal female mice. Following 35 days of exposure, we observed size-dependent reproductive toxicity, with 100 nm PS-MPs causing reduced body weight gain and ovarian size, and compromised ovarian structures and functions, including altered follicle and corpora lutea counts, alongside disrupted hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks and signaling flow patterns across seven identified ovarian cell types. Granulosa cells (GCs) were identified as the primary target PS-MPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100 nm PS-MPs were internalized by GCs, leading to cell cycle arrest, necroptosis and hormonal dysfunction. Mechanistically, PS-MPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and reducing histone marks (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-MP-induced epigenetic and transcriptional changes. Overall, this study first revealed PS-MP-mediated reproductive toxicity from a single-cell perspective, identifying granulosa cells as particularly vulnerable targets. It uncovered novel mechanisms involving cytoskeletal disruption and epigenetic reprogramming, while demonstrating size-dependent internalization patterns that directly correlate with reproductive impairment. These findings provide unprecedented insights into the molecular and epigenetic consequences of MNPs in mammalian reproduction, emphasizing the potential health risks of environmental MNPs exposure.
• 🔗 查看原文

10. GSE210345 远曲小管基因调控的三维结构（RNA-Seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Lotte Tholen ; Eveline Kahlman ; Peter Krijger ; Branco Heuts ; Amin Allahyar ; Joost Martens ; Wouter de Laat ; Joost Hoenderop ; Jeroen de BaaijSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCell-type specific gene expression patterns are essential for kidney function. This is governed by binding of polymerases and transcription (co)-factors to regulatory DNA elements that can either be located close to their target genes or at great genomic distances from their target genes. Therefore, the 3D structure of the genome is an essential factor in cell-type specific gene transcription. Here, we generated a chromosome conformation capture (Hi-C) map in a distal convoluted tubule (DCT) cell line with a 5kb resolution. To study the role of the 3D genome in transcriptional regulation in the DCT the Hi-C data was integrated with chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq data of the same cell line. Our analysis uncovered the basis of 3D genome characteristics in the DCT. Similar to other studies, promoter connectivity correlated with gene expression levels of the participating genes. As proof of principle, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that HNF1β controls the expression of housekeeping genes primarily by binding to promoters in close proximity of the transcription start site (TSS) of the gene, while the expression of developmental genes is regulated by both promoters and distal enhancers. Moreover, by employing a CRISPR/Cas9 enhancer mutant, we demonstrated that Caveolin-1 expression is regulated by an HNF1β-bound enhancer ~95kb from the TSS of the gene. In conclusion, we describe the first Hi-C map in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.
• 🔗 查看原文

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详细内容（全部4条）

1. 人工智能可以判断你的大脑衰老速度是否比你自身衰老速度快。

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：A person’s sleeping brain may reveal warning signs of dementia long before memory problems begin. Researchers used machine learning to analyze EEG recordings from about 7,000 adults and found that an older-than-expected “brain age” was tied to a sharply higher dementia risk. Every additional 10 years of brain aging raised that risk by nearly 40%.
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2. 科学家发现肥胖如何加剧阿尔茨海默病

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Researchers have uncovered a possible biological pathway connecting obesity to Alzheimer’s disease. Obesity appears to raise levels of certain fat molecules that can travel to the brain, disrupt its immune defenses, and promote harmful amyloid buildup. Correcting this fat imbalance improved memory and brain function in Alzheimer’s models.
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3. 血液癌症的基因预警信号可能在数年前就已出现。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Blood cancers that eventually worsen may carry detectable genetic warning signs years before patients develop serious symptoms. The findings could lead to earlier intervention while also helping doctors distinguish true cancer from harmless age-related blood changes.
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4. 一条奇特的量子规则限制了电阻率。

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance
• 📝 描述：Physicists have uncovered a surprising limit to electrical resistance caused by particles colliding. Using ultracold potassium atoms trapped in a grid of light, researchers created a highly controlled stand-in for electrons moving through a solid. As collisions became more frequent and intense, resistance initially rose, but eventually hit a ceiling and stopped increasing.
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• GSE309314 卵磷脂胆固醇酰基转移酶 Lcat 通过脂肪酸代谢重编程促进斑马鱼幼体肝脏脂肪变性
• GSE303342 统一网络系统方法揭示了 T 滤泡辅助细胞分化的核心程序 [RNA-Seq]
• GSE303341 统一网络系统方法揭示了 T 滤泡辅助细胞分化的核心程序 [ATAC-seq]