Nature Reviews Molecular Cell Biology最新文献_第5页

Good neighbours transfer nucleotides 好邻居会转移核苷酸

IF 81.3 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-24 DOI: 10.1038/s41580-025-00872-x

Lisa Heinke

引用次数: 0

Key challenges and recommendations for defining organelle membrane contact sites 定义细胞器膜接触部位的主要挑战和建议。

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-23 DOI: 10.1038/s41580-025-00864-x

Tito Calì, Emmanuelle M. Bayer, Emily R. Eden, György Hajnóczky, Benoit Kornmann, Laura Lackner, Jen Liou, Karin Reinisch, Hyun-Woo Rhee, Rosario Rizzuto, Luca Scorrano, Marisa Brini

{"title":"Key challenges and recommendations for defining organelle membrane contact sites","authors":"Tito Calì, Emmanuelle M. Bayer, Emily R. Eden, György Hajnóczky, Benoit Kornmann, Laura Lackner, Jen Liou, Karin Reinisch, Hyun-Woo Rhee, Rosario Rizzuto, Luca Scorrano, Marisa Brini","doi":"10.1038/s41580-025-00864-x","DOIUrl":"10.1038/s41580-025-00864-x","url":null,"abstract":"Intracellular membrane contact sites (MCSs) between organelles have crucial roles in cellular signalling and homeostasis. These sites, which are often disrupted in pathological conditions, enable the exchange of ions, lipids and metabolites between membrane-bound compartments, helping cells adapt to varying physiological conditions. Specific tether proteins and complexes stabilize these interactions and mediate responses to different intracellular or extracellular stimuli. The study of MCSs has progressed in recent years, owing to the development of new methods such as genetically encoded reporter constructs, advanced imaging techniques, including super-resolution microscopy and electron tomography, and proteomic approaches based on mass spectrometry. These tools have enabled unprecedented visualization and quantification of organelle interactions, as well as identification of the molecular players involved. This Expert Recommendation aims to define and map the ‘organelle contactome’, describing key proteins involved in contact site formation and the roles of MCSs in cellular function. We also explore contact site dynamics and detail advantages and disadvantages of the methodologies for studying them. Importantly, we consolidate open questions in contact site research and discuss challenges and limitations of the current experimental approaches. Membrane contact sites between organelles facilitate the exchange of ions, lipids and metabolites. This Expert Recommendation highlights recent advances in defining the organelle contactome and discusses challenges and future directions in membrane contact site research.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 10","pages":"776-796"},"PeriodicalIF":90.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41580-025-00864-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144370324","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}

引用次数: 0

Decoding the interactions and functions of non-coding RNA with artificial intelligence 用人工智能解码非编码RNA的相互作用和功能

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-19 DOI: 10.1038/s41580-025-00857-w

Vincent Jung, Cédric Vincent-Cuaz, Charlotte Tumescheit, Lisa Fournier, Marousa Darsinou, Zhi Ming Xu, Ali Saadat, Yiran Wang, Petros Tsantoulis, Olivier Michielin, Jacques Fellay, Rickie Patani, Andres Ramos, Pascal Frossard, Janna Hastings, Antonella Riccio, Lonneke van der Plas, Raphaëlle Luisier

{"title":"Decoding the interactions and functions of non-coding RNA with artificial intelligence","authors":"Vincent Jung, Cédric Vincent-Cuaz, Charlotte Tumescheit, Lisa Fournier, Marousa Darsinou, Zhi Ming Xu, Ali Saadat, Yiran Wang, Petros Tsantoulis, Olivier Michielin, Jacques Fellay, Rickie Patani, Andres Ramos, Pascal Frossard, Janna Hastings, Antonella Riccio, Lonneke van der Plas, Raphaëlle Luisier","doi":"10.1038/s41580-025-00857-w","DOIUrl":"10.1038/s41580-025-00857-w","url":null,"abstract":"In addition to encoding proteins, mRNAs have context-specific regulatory roles that contribute to many cellular processes. However, uncovering new mRNA functions is constrained by limitations of traditional biochemical and computational methods. In this Roadmap, we highlight how artificial intelligence can transform our understanding of RNA biology by fostering collaborations between RNA biologists and computational scientists to drive innovation in this fundamental field of research. We discuss how non-coding regions of the mRNA, including introns and 5′ and 3′ untranslated regions, regulate the metabolism and interactomes of mRNA, and the current challenges in characterizing these regions. We further discuss large language models, which can be used to learn biologically meaningful RNA sequence representations. We also provide a detailed roadmap for integrating large language models with graph neural networks to harness publicly available sequencing and knowledge data. Adopting this roadmap will allow us to predict RNA interactions with diverse molecules and the modelling of context-specific mRNA interactomes. Studying RNA function is constrained by limitations of traditional methods. This Roadmap discusses how artificial intelligence (AI) can enhance the study of how non-coding regions of mRNA regulate its function, and suggests how to use AI to harness publicly available data towards that goal.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 10","pages":"797-818"},"PeriodicalIF":90.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144319501","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}

引用次数: 0

How machine learning can help us understand what we have grown in the dish 机器学习如何帮助我们理解我们在培养皿中生长的东西

IF 81.3 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-10 DOI: 10.1038/s41580-025-00868-7

Roser Vento-Tormo

引用次数: 0

Collective migration modes in development, tissue repair and cancer 发育、组织修复和癌症中的集体迁移模式

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-05 DOI: 10.1038/s41580-025-00858-9

Kevin J. Cheung, Sally Horne-Badovinac

{"title":"Collective migration modes in development, tissue repair and cancer","authors":"Kevin J. Cheung, Sally Horne-Badovinac","doi":"10.1038/s41580-025-00858-9","DOIUrl":"10.1038/s41580-025-00858-9","url":null,"abstract":"Migrating cells have key functions in shaping tissues during development, repairing tissues after development and supporting cancer invasion and metastasis. In all these contexts, cells often maintain contact with their neighbours and move as a group, in a process termed collective migration. In this Review, we describe the elegant mechanisms used by collectively migrating cells in vivo to coordinate their movements and obtain directional information. We start by highlighting the diverse physiological roles that migrating collectives have within the body and then focus on dominant paradigms for the organization of migrating collectives including the roles of leader and follower cells, local cell–cell adhesion and signalling, and external guidance cues. By comparing collective migrations occurring during development and cancer, we bring into focus shared principles for collective cell movement and distinct strategies used by cancer cells for their own dispersal. Throughout, we pay particular attention to how migrating collectives display emergent properties not exhibited by individually migrating cells and how these properties provide the robustness needed for efficient cell movement. Collective cell migration has major roles in animal development, tissue repair and cancer metastasis. This Review explores how migrating collectives are organized in development versus cancer, focusing on cell adhesion, signalling and guidance cues.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 10","pages":"741-758"},"PeriodicalIF":90.2,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144228678","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}

引用次数: 0

Nucleosomes as blueprints of genome architecture 核小体是基因组结构的蓝图

IF 81.3 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-06-04 DOI: 10.1038/s41580-025-00866-9

Eytan Zlotorynski

引用次数: 0

Uncovering mRNA sequences that control translation initiation 揭示控制翻译起始的mRNA序列

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00862-z

Kyrillos S. Abdallah

引用次数: 0

Structure, regulation and assembly of the photosynthetic electron transport chain 光合作用电子传递链的结构、调节和组装

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00847-y

Matthew P. Johnson

{"title":"Structure, regulation and assembly of the photosynthetic electron transport chain","authors":"Matthew P. Johnson","doi":"10.1038/s41580-025-00847-y","DOIUrl":"10.1038/s41580-025-00847-y","url":null,"abstract":"The electron transfer chain of chloroplast thylakoid membranes uses solar energy to split water into electrons and protons, creating energetic gradients that drive the formation of photosynthetic fuel in the form of NADPH and ATP. These metabolites are then used to power the fixation of carbon dioxide into biomass through the Calvin–Benson–Bassham cycle in the chloroplast stroma. Recent advances in molecular genetics, structural biology and spectroscopy have provided an unprecedented understanding of the molecular events involved in photosynthetic electron transfer from photon capture to ATP production. Specifically, we have gained insights into the assembly of the photosynthetic complexes into larger supercomplexes, thylakoid membrane organization and the mechanisms underpinning efficient light harvesting, photoprotection and oxygen evolution. In this Review, I focus on the angiosperm plant thylakoid system, outlining our current knowledge on the structure, function, regulation and assembly of each component of the photosynthetic chain. I explain how solar energy is harvested and converted into chemical energy by the photosynthetic electron transfer chain, how its components are integrated into a complex membrane macrostructure and how this organization contributes to regulation and photoprotection. The electron transfer chain in chloroplast thylakoid membranes uses solar energy to produce NADPH and ATP, which power carbon fixation into biomass. This Review discusses the structure and function of the core photosynthesis complexes and provides recent insights into their regulation and assembly.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 9","pages":"667-690"},"PeriodicalIF":90.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144113689","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}

引用次数: 0

Enabling RNA-compatible synthetic receptors through RNA editing 通过RNA编辑实现RNA兼容的合成受体

IF 81.3 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00863-y

Xiaowei Zhang, Luis S. Mille-Fragoso

引用次数: 0

Functions and therapeutic applications of pseudouridylation 假尿嘧啶化的功能和治疗应用

IF 90.2 1区生物学

Nature Reviews Molecular Cell Biology Pub Date : 2025-05-20 DOI: 10.1038/s41580-025-00852-1

Nan Luo, Qiang Huang, Meiling Zhang, Chengqi Yi

{"title":"Functions and therapeutic applications of pseudouridylation","authors":"Nan Luo, Qiang Huang, Meiling Zhang, Chengqi Yi","doi":"10.1038/s41580-025-00852-1","DOIUrl":"10.1038/s41580-025-00852-1","url":null,"abstract":"The success of using pseudouridine (Ψ) and its methylation derivative in mRNA vaccines against SARS-CoV-2 has sparked a renewed interest in this RNA modification, known as the ‘fifth nucleotide’ of RNA. In this Review, we discuss the emerging functions of pseudouridylation in gene regulation, focusing on how pseudouridine in mRNA, tRNA and ribosomal RNA (rRNA) regulates translation. We also discuss the effects of pseudouridylation on RNA secondary structure, pre-mRNA splicing, and in vitro mRNA stability. In addition to nuclear-genome-encoded RNAs, pseudouridine is also present in mitochondria-encoded rRNA, mRNA and tRNA, where it has different distributions and functions compared with their nuclear counterparts. We then discuss the therapeutic potential of programmable pseudouridylation and mRNA vaccine optimization through pseudouridylation. Lastly, we briefly describe the latest quantitative pseudouridine detection methods. We posit that pseudouridine is a highly promising modification that merits further epitranscriptomics investigation and therapeutic application. Pseudouridine is a long-discovered RNA modification that has lately attracted much renewed interest. This Review discusses the emerging functions of pseudouridine in gene regulation and mitochondrial function, and its therapeutic potential following the successful use of pseudouridylation in SARS-CoV-2 mRNA vaccines.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 9","pages":"691-705"},"PeriodicalIF":90.2,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097188","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}

引用次数: 0