详细内容（全部8条）

1. GSE322731 对两种蜡螟（Achroia grisella 和 Galleria mellonella）的唇腺和肠道组织进行转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Reginald Young ; Khandaker A Ahmed ; Leon Court ; Rahul Rane ; Tom Walsh ; Gunjan PandeySeries Type : Expression profiling by high throughput sequencingOrganism : Achroia grisellaPlastics are highly stable materials with widespread applications, but their resistance to degradation poses a significant environmental challenge, often resulting in accumulation in landfills or pollution in the form of microplastics. Biodegradation using insect larvae has recently emerged as a promising strategy to address this issue, though the molecular basis of plastic degradation in these organisms remains poorly understood due to limited genomic resources. In this study, we present a complete genome of the lesser wax moth, Achroia grisella, and tissue-specific RNA-Seq data of both the lesser and the greater wax moth, Galleria mellonella, two species known to consume various plastics. Our analyses reveal several highly expressed secretory enzymes in gut and labial tissues. Orthologous comparisons of differentially expressed genes also identified five enzymes (three hexamerins and two monooxygenases) from the lesser wax moth that have been shown or are predicted to have plastic-degrading potential in the greater wax moth. We also identified enzymes that may potentially be involved in polyethylene and polystyrene degradation based on their identities with known bacterial enzymes that have been experimentally validated and are involved in plastic degradation pathways. Together, these genomic and transcriptomic resources provide a foundation for understanding plastic degradation in wax moths and highlight candidate genes for future functional validation.
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2. GSE322730 对两种蜡螟（Achroia grisella 和 Galleria mellonella）的唇腺和肠道组织进行转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Reginald Young ; Khandaker A Ahmed ; Leon Court ; Rahul Rane ; Tom Walsh ; Gunjan PandeySeries Type : Expression profiling by high throughput sequencingOrganism : Galleria mellonellaPlastics are highly stable materials with widespread applications, but their resistance to degradation poses a significant environmental challenge, often resulting in accumulation in landfills or pollution in the form of microplastics. Biodegradation using insect larvae has recently emerged as a promising strategy to address this issue, though the molecular basis of plastic degradation in these organisms remains poorly understood due to limited genomic resources. In this study, we present a complete genome of the lesser wax moth, Achroia grisella, and tissue-specific RNA-Seq data of both the lesser and the greater wax moth, Galleria mellonella, two species known to consume various plastics. Our analyses reveal several highly expressed secretory enzymes in gut and labial tissues. Orthologous comparisons of differentially expressed genes also identified five enzymes (three hexamerins and two monooxygenases) from the lesser wax moth that have been shown or are predicted to have plastic-degrading potential in the greater wax moth. We also identified enzymes that may potentially be involved in polyethylene and polystyrene degradation based on their identities with known bacterial enzymes that have been experimentally validated and are involved in plastic degradation pathways. Together, these genomic and transcriptomic resources provide a foundation for understanding plastic degradation in wax moths and highlight candidate genes for future functional validation.
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3. GSE322550 解析 circZNF827 介导的神经元分化转录调控机制 (RNA-Seq)

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal、RNA-seq
• 📝 描述：Contributors : Ivan A Zaporozhchenko ; Anne K Hollensen ; Christian K DamgaardSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCircular RNAs (circRNAs) originate from backsplicing of numerous genes in animals, but the functions of most circRNAs remain elusive. We previously demonstrated that circZNF827 forms a complex with hnRNPL/K and its host gene-encoded protein ZNF827 that acts in the nucleus to transcriptionally repress the nerve growth factor receptor (NGFR/p75NTR) gene during neuronal differentiation (Hollensen, 2020) [1]. To explore the mechanism of action, and to assess a potential role of the circZNF827-hnRNP complex on additional loci, we scrutinized the genome-wide consequences of circZNF827 and/or hnRNPL knockdown at the transcriptomic and epigenetic level. RNA-sequencing and CUT&RUN confirmed that NGFR and additional loci are transcriptionally repressed by the circZNF827-protein complex, and that these are primarily enriched for H3K27me3 signatures. Only a fraction of the massive transcriptomic changes could be ascribed a direct circZNF827 transcription-regulated phenotype, suggesting that initial key regulatory events elicited by the circZNF827-hnRNP complex likely lead to a secondary response, which further augments neuronal differentiation.
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4. GSE317229 H3糖基化和H3K4me3拮抗串扰的双重机制[RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Yang Xiao ; Yujin Choi ; Richard Koche ; Yael DavidSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer cells undergo profound metabolic reprogramming that elevates the intracellular levels of reactive byproducts such as methylglyoxal (MGO), which can non-enzymatically modify macromolecules in a process known as glycation. Histones are particularly susceptible to glycation, resulting in substantial alterations to chromatin structure and the epigenetic landscape. However, the mechanism by which histone glycation alters epigenetic landscape and impacts specific transcriptional output in vivo has remained unclear due to the lack of high-resolution tools. Here, we utilize adduct-, site-, and target-specific antibodies we developed against histone H3 glycation at arginine 17 (H3R17MG-H1), one of the most abundant histone glycation marks, to perform precise detection and enrichment of this mark. With these, we show that H3 glycation preferentially accumulates in euchromatin and directly crosstalks with a key active transcription-associated mark, H3K4me3, at transcription start sites. Mechanistically, H3 glycation antagonizes global H3K4me3 through dual pathways: by preventing the recruitment of WDR5-containing methyltransferase complexes to glycated H3 and by transcriptionally inducing KDM5 demethylases expression. The combined effects lead to genome-wide depletion of H3K4me3 and reprogramming of cellular transcriptional networks. Our findings reveal a distinct role for histone glycation as a potent modulator of epigenetic landscape and transcriptional output, serving as a direct link between altered metabolism and cell fate.
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5. GSE322813 一种用于高分辨率三维基因组作图的低投入Micro-C方案

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：Contributors : Fengnian Shan ; Chongren Pei ; Sijian Xia ; Fei LingSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusStandard Micro-C protocols typically require millions of cells, which limits their application to rare cell populations. Here, we present an optimized low-input Micro-C workflow that requires only 100,000 cells. By comparing 30 G of sequencing data from 100,000 cells with that from 5 million G1E-ER4 cells, we demonstrate that all key architectural features—compartments, TADs, and chromatin loops—are reliably detected. Applying this method to investigate acute CTCF degradation, we observed the loss of loops and TAD boundaries in CTCF-degraded samples, consistent with previous reports. Our optimized protocol enables nucleosome-resolution 3D genome mapping for sample-limited studies.
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6. GSE322765 通过高通量筛选 (HTS) 鉴定针对孤立性纤维瘤 (SFT) 的 BET 抑制剂 (BETi)

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor
• 📝 描述：Contributors : Jose L Mondaza-Hernandez ; Yi Li ; Jesus L MartiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSolitary Fibrous Tumor (SFT) is a rare mesenchymal tumor driven by the NAB2-STAT6 fusion oncogene. To investigate transcriptional changes induced by BET inhibition in SFT models, we performed bulk RNA sequencing of INT-SFT and IEC139 cell lines treated with the BET inhibitors Mivebresib (ABBV-075) or BMS-986158 (50 nM for 24 h). Total RNA was extracted and libraries were sequenced on the Illumina NovaSeq X platform. Gene-level expression was quantified using Salmon against the GRCh38 reference genome with GENCODE annotation. Differential expression and pathway enrichment analyses were performed to characterize transcriptional programs associated with BET inhibitor treatment.
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7. GSE322552 解析 circZNF827 介导的神经元分化转录调控机制 (CUT&RUN)

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal
• 📝 描述：Contributors : Ivan A Zaporozhchenko ; Anne K Hollensen ; Christian K DamgaardSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCircular RNAs (circRNAs) originate from backsplicing of numerous genes in animals, but the functions of most circRNAs remain elusive. We previously demonstrated that circZNF827 forms a complex with hnRNPL/K and its host gene-encoded protein ZNF827 that acts in the nucleus to transcriptionally repress the nerve growth factor receptor (NGFR/p75NTR) gene during neuronal differentiation (Hollensen, 2020) [1]. To explore the mechanism of action, and to assess a potential role of the circZNF827-hnRNP complex on additional loci, we scrutinized the genome-wide consequences of circZNF827 and/or hnRNPL knockdown at the transcriptomic and epigenetic level. RNA-sequencing and CUT&RUN confirmed that NGFR and additional loci are transcriptionally repressed by the circZNF827-protein complex, and that these are primarily enriched for H3K27me3 signatures. Only a fraction of the massive transcriptomic changes could be ascribed a direct circZNF827 transcription-regulated phenotype, suggesting that initial key regulatory events elicited by the circZNF827-hnRNP complex likely lead to a secondary response, which further augments neuronal differentiation.
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8. GSE319953 肠道干细胞和咽侧体中 Pumilio 的外周调控影响果蝇的睡眠潜伏期

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:intestin(e|al)
• 📝 描述：Contributors : Josué A Rodríguez-Cordero ; Marialena Dorta-Avilés ; Imilce A Rodriguez-Fernandez ; Alfredo Ghezzi ; José E Lizardi-Ortiz ; José L Agosto-RiveraSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterWhile central circuits governing sleep are well-studied, the contribution of signaling from peripheral tissues remains a critical yet less understood aspect of sleep regulation. The highly conserved RNA-binding protein Pumilio (Pum) is a post-transcriptional regulator expressed in multiple tissues that influence systemic physiology, but its role in modulating basal sleep has not been established. Although Pumilio’s function in central neurons has been linked to sleep homeostasis following deprivation, whether it regulates sleep through peripheral mechanisms remains unknown. Here, we use conditional genetic tools in the fruit fly Drosophila melanogaster to demonstrate that genetic manipulation of Pumilio targeting the intestinal stem cells (ISCs) and the endocrine corpus allatum (CA) regulates the transition to sleep. Reducing Pumilio function in either the ISCs or the CA independently and significantly accelerates nighttime sleep onset, while overexpression produces the opposite effect. This behavioral change is accompanied by widespread transcriptional alterations in the head, characterized by a robust upregulation of genes involved in cellular stress responses. Our findings reveal a previously unrecognized gut-endocrine-brain signaling axis and identify peripheral post-transcriptional regulation as a key input to the central control of sleep behavior.
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详细内容（全部1条）

1. 研究发现，减少蛋白质摄入可能减缓肝癌的生长。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A Rutgers-led study found that eating less protein may help slow liver cancer in people with impaired liver function. When damaged livers can’t properly clear toxic ammonia from protein metabolism, the excess ammonia can feed tumor growth. In mice, reducing dietary protein lowered ammonia levels, slowed tumor growth, and significantly improved survival.
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