Pub Date : 2024-10-31DOI: 10.1038/s41556-024-01551-3
Fides Zenk
How heterochromatin is established de novo in early embryos is unknown. A study now shows that the sequential recruitment of the key regulator JARID2 recruits PRC2.2 to H2AK119ub and ensures proper H3K27me2/3 deposition. This prevents premature enhancer activation, which is crucial for gene regulation and lineage specification.
{"title":"Building the epigenetic fortress with PRC2.2","authors":"Fides Zenk","doi":"10.1038/s41556-024-01551-3","DOIUrl":"https://doi.org/10.1038/s41556-024-01551-3","url":null,"abstract":"How heterochromatin is established de novo in early embryos is unknown. A study now shows that the sequential recruitment of the key regulator JARID2 recruits PRC2.2 to H2AK119ub and ensures proper H3K27me2/3 deposition. This prevents premature enhancer activation, which is crucial for gene regulation and lineage specification.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"87 1","pages":""},"PeriodicalIF":21.3,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The methyltransferase complex (MTC) deposits N6-adenosine (m6A) onto RNA, whereas the microprocessor produces microRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B tends to form insoluble condensates with poor activity, with its level monitored by the 20S proteasome. Conversely, the microprocessor component SERRATE (SE) forms liquid-like condensates, which in turn promote the solubility and stability of the MTC subunit B, leading to increased MTC activity. Consistently, the hypomorphic lines expressing SE variants, defective in MTC interaction or liquid-like phase behaviour, exhibit reduced m6A levels. Reciprocally, MTC can recruit the microprocessor to the MIRNA loci, prompting co-transcriptional cleavage of primary miRNA substrates. Additionally, primary miRNA substrates carrying m6A modifications at their single-stranded basal regions are enriched by m6A readers, which retain the microprocessor in the nucleoplasm for continuing processing. This reveals an unappreciated mechanism of phase separation in RNA modification and processing through MTC and microprocessor coordination. Zhong et al. find that SERRATE (SE) regulates the m6A methyltransferase complex (MTC) to control m6A deposition, and show cross-regulation between the MTC and the SE-mediated microprocessor governs miRNA production in Arabidopsis.
{"title":"SERRATE drives phase separation behaviours to regulate m6A modification and miRNA biogenesis","authors":"Songxiao Zhong, Xindi Li, Changhao Li, Haiyan Bai, Jingjing Chen, Lu Gan, Jiyun Zhu, Taerin Oh, Xingxing Yan, Jiaying Zhu, Niankui Li, Hisashi Koiwa, Thomas Meek, Xu Peng, Bin Yu, Zhonghui Zhang, Xiuren Zhang","doi":"10.1038/s41556-024-01530-8","DOIUrl":"10.1038/s41556-024-01530-8","url":null,"abstract":"The methyltransferase complex (MTC) deposits N6-adenosine (m6A) onto RNA, whereas the microprocessor produces microRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B tends to form insoluble condensates with poor activity, with its level monitored by the 20S proteasome. Conversely, the microprocessor component SERRATE (SE) forms liquid-like condensates, which in turn promote the solubility and stability of the MTC subunit B, leading to increased MTC activity. Consistently, the hypomorphic lines expressing SE variants, defective in MTC interaction or liquid-like phase behaviour, exhibit reduced m6A levels. Reciprocally, MTC can recruit the microprocessor to the MIRNA loci, prompting co-transcriptional cleavage of primary miRNA substrates. Additionally, primary miRNA substrates carrying m6A modifications at their single-stranded basal regions are enriched by m6A readers, which retain the microprocessor in the nucleoplasm for continuing processing. This reveals an unappreciated mechanism of phase separation in RNA modification and processing through MTC and microprocessor coordination. Zhong et al. find that SERRATE (SE) regulates the m6A methyltransferase complex (MTC) to control m6A deposition, and show cross-regulation between the MTC and the SE-mediated microprocessor governs miRNA production in Arabidopsis.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 12","pages":"2129-2143"},"PeriodicalIF":17.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-24DOI: 10.1038/s41556-024-01532-6
Marina Uroz, Amy E. Stoddard, Bryan P. Sutherland, Olivia Courbot, Roger Oria, Linqing Li, Cara R. Ravasio, Mai T. Ngo, Jinling Yang, Juliann B. Tefft, Jeroen Eyckmans, Xue Han, Alberto Elosegui-Artola, Valerie M. Weaver, Christopher S. Chen
In brain metastasis, cancer cells remain in close contact with the existing vasculature and can use vessels as migratory paths—a process known as vessel co-option. However, the mechanisms regulating this form of migration are poorly understood. Here we use ex vivo brain slices and an organotypic in vitro model for vessel co-option to show that cancer cell invasion along brain vasculature is driven by the difference in stiffness between vessels and the brain parenchyma. Imaging analysis indicated that cells move along the basal surface of vessels by adhering to the basement membrane extracellular matrix. We further show that vessel co-option is enhanced by both the stiffness of brain vasculature, which reinforces focal adhesions through a talin-dependent mechanism, and the softness of the surrounding environment that permits cellular movement. Our work reveals a mechanosensing mechanism that guides cell migration in response to the tissue’s intrinsic mechanical heterogeneity, with implications in cancer invasion and metastasis. Uroz et al. report that the distinct mechanical properties of brain vasculature versus parenchyma drive cancer cell migration through a talin-dependent mechanism, enabling vessel co-option and metastatic invasion in the brain.
{"title":"Differential stiffness between brain vasculature and parenchyma promotes metastatic infiltration through vessel co-option","authors":"Marina Uroz, Amy E. Stoddard, Bryan P. Sutherland, Olivia Courbot, Roger Oria, Linqing Li, Cara R. Ravasio, Mai T. Ngo, Jinling Yang, Juliann B. Tefft, Jeroen Eyckmans, Xue Han, Alberto Elosegui-Artola, Valerie M. Weaver, Christopher S. Chen","doi":"10.1038/s41556-024-01532-6","DOIUrl":"10.1038/s41556-024-01532-6","url":null,"abstract":"In brain metastasis, cancer cells remain in close contact with the existing vasculature and can use vessels as migratory paths—a process known as vessel co-option. However, the mechanisms regulating this form of migration are poorly understood. Here we use ex vivo brain slices and an organotypic in vitro model for vessel co-option to show that cancer cell invasion along brain vasculature is driven by the difference in stiffness between vessels and the brain parenchyma. Imaging analysis indicated that cells move along the basal surface of vessels by adhering to the basement membrane extracellular matrix. We further show that vessel co-option is enhanced by both the stiffness of brain vasculature, which reinforces focal adhesions through a talin-dependent mechanism, and the softness of the surrounding environment that permits cellular movement. Our work reveals a mechanosensing mechanism that guides cell migration in response to the tissue’s intrinsic mechanical heterogeneity, with implications in cancer invasion and metastasis. Uroz et al. report that the distinct mechanical properties of brain vasculature versus parenchyma drive cancer cell migration through a talin-dependent mechanism, enabling vessel co-option and metastatic invasion in the brain.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 12","pages":"2144-2153"},"PeriodicalIF":17.3,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-23DOI: 10.1038/s41556-024-01537-1
Jinyang Zhang, Lingling Hou, Lianjun Ma, Zhengyi Cai, Shujun Ye, Yang Liu, Peifeng Ji, Zhenqiang Zuo, Fangqing Zhao
The high diversity and complexity of the eukaryotic transcriptome make it difficult to effectively detect specific transcripts of interest. Current targeted RNA sequencing methods often require complex pre-sequencing enrichment steps, which can compromise the comprehensive characterization of the entire transcriptome. Here we describe programmable full-length isoform transcriptome sequencing (PROFIT-seq), a method that enriches target transcripts while maintaining unbiased quantification of the whole transcriptome. PROFIT-seq employs combinatorial reverse transcription to capture polyadenylated, non-polyadenylated and circular RNAs, coupled with a programmable control system that selectively enriches target transcripts during sequencing. This approach achieves over 3-fold increase in effective data yield and reduces the time required for detecting specific pathogens or key mutations by 75%. We applied PROFIT-seq to study colorectal polyp development, revealing the intricate relationship between host immune responses and bacterial infection. PROFIT-seq offers a powerful tool for accurate and efficient sequencing of target transcripts while preserving overall transcriptome quantification, with broad applications in clinical diagnostics and targeted enrichment scenarios. Zhang, Hou, Ma et al. present PROFIT-seq, a sequencing strategy that involves adaptive sampling of transcriptome libraries to enrich genes of interest and allows unbiased quantification of the whole transcriptome.
{"title":"Real-time and programmable transcriptome sequencing with PROFIT-seq","authors":"Jinyang Zhang, Lingling Hou, Lianjun Ma, Zhengyi Cai, Shujun Ye, Yang Liu, Peifeng Ji, Zhenqiang Zuo, Fangqing Zhao","doi":"10.1038/s41556-024-01537-1","DOIUrl":"10.1038/s41556-024-01537-1","url":null,"abstract":"The high diversity and complexity of the eukaryotic transcriptome make it difficult to effectively detect specific transcripts of interest. Current targeted RNA sequencing methods often require complex pre-sequencing enrichment steps, which can compromise the comprehensive characterization of the entire transcriptome. Here we describe programmable full-length isoform transcriptome sequencing (PROFIT-seq), a method that enriches target transcripts while maintaining unbiased quantification of the whole transcriptome. PROFIT-seq employs combinatorial reverse transcription to capture polyadenylated, non-polyadenylated and circular RNAs, coupled with a programmable control system that selectively enriches target transcripts during sequencing. This approach achieves over 3-fold increase in effective data yield and reduces the time required for detecting specific pathogens or key mutations by 75%. We applied PROFIT-seq to study colorectal polyp development, revealing the intricate relationship between host immune responses and bacterial infection. PROFIT-seq offers a powerful tool for accurate and efficient sequencing of target transcripts while preserving overall transcriptome quantification, with broad applications in clinical diagnostics and targeted enrichment scenarios. Zhang, Hou, Ma et al. present PROFIT-seq, a sequencing strategy that involves adaptive sampling of transcriptome libraries to enrich genes of interest and allows unbiased quantification of the whole transcriptome.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 12","pages":"2183-2194"},"PeriodicalIF":17.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41556-024-01537-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142487090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-21DOI: 10.1038/s41556-024-01527-3
Patrizia Romani, Giada Benedetti, Martina Cusan, Mattia Arboit, Carmine Cirillo, Xi Wu, Georgia Rouni, Vassiliki Kostourou, Mariaceleste Aragona, Costanza Giampietro, Paolo Grumati, Graziano Martello, Sirio Dupont
Tissue-scale architecture and mechanical properties instruct cell behaviour under physiological and diseased conditions, but our understanding of the underlying mechanisms remains fragmentary. Here we show that extracellular matrix stiffness, spatial confinements and applied forces, including stretching of mouse skin, regulate mitochondrial dynamics. Actomyosin tension promotes the phosphorylation of mitochondrial elongation factor 1 (MIEF1), limiting the recruitment of dynamin-related protein 1 (DRP1) at mitochondria, as well as peri-mitochondrial F-actin formation and mitochondrial fission. Strikingly, mitochondrial fission is also a general mechanotransduction mechanism. Indeed, we found that DRP1- and MIEF1/2-dependent fission is required and sufficient to regulate three transcription factors of broad relevance—YAP/TAZ, SREBP1/2 and NRF2—to control cell proliferation, lipogenesis, antioxidant metabolism, chemotherapy resistance and adipocyte differentiation in response to mechanical cues. This extends to the mouse liver, where DRP1 regulates hepatocyte proliferation and identity—hallmark YAP-dependent phenotypes. We propose that mitochondria fulfil a unifying signalling function by which the mechanical tissue microenvironment coordinates complementary cell functions. Romani et al. show that matrix stiffness, confinement and applied forces impact mitochondrial dynamics and DRP1- and MIEF1-dependent mitochondrial fission regulates transcription factors in response to mechanical cues.
{"title":"Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces","authors":"Patrizia Romani, Giada Benedetti, Martina Cusan, Mattia Arboit, Carmine Cirillo, Xi Wu, Georgia Rouni, Vassiliki Kostourou, Mariaceleste Aragona, Costanza Giampietro, Paolo Grumati, Graziano Martello, Sirio Dupont","doi":"10.1038/s41556-024-01527-3","DOIUrl":"10.1038/s41556-024-01527-3","url":null,"abstract":"Tissue-scale architecture and mechanical properties instruct cell behaviour under physiological and diseased conditions, but our understanding of the underlying mechanisms remains fragmentary. Here we show that extracellular matrix stiffness, spatial confinements and applied forces, including stretching of mouse skin, regulate mitochondrial dynamics. Actomyosin tension promotes the phosphorylation of mitochondrial elongation factor 1 (MIEF1), limiting the recruitment of dynamin-related protein 1 (DRP1) at mitochondria, as well as peri-mitochondrial F-actin formation and mitochondrial fission. Strikingly, mitochondrial fission is also a general mechanotransduction mechanism. Indeed, we found that DRP1- and MIEF1/2-dependent fission is required and sufficient to regulate three transcription factors of broad relevance—YAP/TAZ, SREBP1/2 and NRF2—to control cell proliferation, lipogenesis, antioxidant metabolism, chemotherapy resistance and adipocyte differentiation in response to mechanical cues. This extends to the mouse liver, where DRP1 regulates hepatocyte proliferation and identity—hallmark YAP-dependent phenotypes. We propose that mitochondria fulfil a unifying signalling function by which the mechanical tissue microenvironment coordinates complementary cell functions. Romani et al. show that matrix stiffness, confinement and applied forces impact mitochondrial dynamics and DRP1- and MIEF1-dependent mitochondrial fission regulates transcription factors in response to mechanical cues.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 12","pages":"2046-2060"},"PeriodicalIF":17.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41556-024-01527-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16DOI: 10.1038/s41556-024-01524-6
Christopher Thomas, Tabea Lilian Marx, Sarah Mae Penir, Melina Schuh
During ovulation, an egg is released from an ovarian follicle, ready for fertilization. Ovulation occurs inside the body, impeding direct studies of its progression. Therefore, the exact mechanisms that control ovulation have remained unclear. Here we devised live imaging methods to study the entire process of ovulation in isolated mouse ovarian follicles. We show that ovulation proceeds through three distinct phases, follicle expansion (I), contraction (II) and rupture (III), culminating in the release of the egg. Follicle expansion is driven by hyaluronic acid secretion and an osmotic gradient-directed fluid influx into the follicle. Then, smooth muscle cells in the outer follicle drive follicle contraction. Follicle rupture begins with stigma formation, followed by the exit of follicular fluid and cumulus cells and the rapid release of the egg. These results establish a mechanistic framework for ovulation, a process of fundamental importance for reproduction. Thomas, Marx et al. devise a live imaging approach to spatiotemporally dissect mouse ovulation ex vivo.
{"title":"Ex vivo imaging reveals the spatiotemporal control of ovulation","authors":"Christopher Thomas, Tabea Lilian Marx, Sarah Mae Penir, Melina Schuh","doi":"10.1038/s41556-024-01524-6","DOIUrl":"10.1038/s41556-024-01524-6","url":null,"abstract":"During ovulation, an egg is released from an ovarian follicle, ready for fertilization. Ovulation occurs inside the body, impeding direct studies of its progression. Therefore, the exact mechanisms that control ovulation have remained unclear. Here we devised live imaging methods to study the entire process of ovulation in isolated mouse ovarian follicles. We show that ovulation proceeds through three distinct phases, follicle expansion (I), contraction (II) and rupture (III), culminating in the release of the egg. Follicle expansion is driven by hyaluronic acid secretion and an osmotic gradient-directed fluid influx into the follicle. Then, smooth muscle cells in the outer follicle drive follicle contraction. Follicle rupture begins with stigma formation, followed by the exit of follicular fluid and cumulus cells and the rapid release of the egg. These results establish a mechanistic framework for ovulation, a process of fundamental importance for reproduction. Thomas, Marx et al. devise a live imaging approach to spatiotemporally dissect mouse ovulation ex vivo.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 11","pages":"1997-2008"},"PeriodicalIF":17.3,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41556-024-01524-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16DOI: 10.1038/s41556-024-01538-0
Douglas R. Green
After being activated, T lymphocytes must consume fuel for energy and biomaterials to sustain rapid proliferation and differentiation. As a consequence, waste is generated that must be managed. A new study now explores how activated CD8+ effector T cells handle ammonia, and how this impacts the survival and function of these cells.
T 淋巴细胞被激活后，必须消耗燃料作为能量和生物材料，以维持快速增殖和分化。因此，产生的废物必须加以管理。现在，一项新研究探讨了活化的 CD8+ 效应 T 细胞如何处理氨，以及这对这些细胞的存活和功能有何影响。
{"title":"Waste management and cell death in T cells","authors":"Douglas R. Green","doi":"10.1038/s41556-024-01538-0","DOIUrl":"10.1038/s41556-024-01538-0","url":null,"abstract":"After being activated, T lymphocytes must consume fuel for energy and biomaterials to sustain rapid proliferation and differentiation. As a consequence, waste is generated that must be managed. A new study now explores how activated CD8+ effector T cells handle ammonia, and how this impacts the survival and function of these cells.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 11","pages":"1826-1827"},"PeriodicalIF":17.3,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-16DOI: 10.1038/s41556-024-01528-2
Thomas Brand
Modelling definitive haematopoiesis in organoids has been challenging. A study now develops blood-generating heart-forming organoids that display heart muscle, vascular endothelium formation and definitive haematopoiesis. This organoid represents an in vitro model of human embryonic circulatory system development.
{"title":"Now it’s getting bloody in cardiac organoids","authors":"Thomas Brand","doi":"10.1038/s41556-024-01528-2","DOIUrl":"10.1038/s41556-024-01528-2","url":null,"abstract":"Modelling definitive haematopoiesis in organoids has been challenging. A study now develops blood-generating heart-forming organoids that display heart muscle, vascular endothelium formation and definitive haematopoiesis. This organoid represents an in vitro model of human embryonic circulatory system development.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"26 11","pages":"1830-1831"},"PeriodicalIF":17.3,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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