Pub Date : 2024-02-08DOI: 10.1038/s41580-024-00708-0
Khalid A. Ibrahim
In this Tools of the Trade article, Khalid Ibrahim (Radenovic and Lashuel labs) describes a tool for the artificial intelligence (AI)-driven detection of cellular aggregates that bypasses the need for fluorescent labelling.
在这篇 "贸易工具"（Tools of the Trade）文章中，Khalid Ibrahim（Radenovic and Lashuel 实验室）介绍了一种人工智能（AI）驱动的细胞聚集体检测工具，该工具无需荧光标记。
{"title":"AI-driven detection and analysis of label-free protein aggregates","authors":"Khalid A. Ibrahim","doi":"10.1038/s41580-024-00708-0","DOIUrl":"10.1038/s41580-024-00708-0","url":null,"abstract":"In this Tools of the Trade article, Khalid Ibrahim (Radenovic and Lashuel labs) describes a tool for the artificial intelligence (AI)-driven detection of cellular aggregates that bypasses the need for fluorescent labelling.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139707364","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 : 2024-02-08DOI: 10.1038/s41580-024-00712-4
Carolina E. Hagberg, Kirsty L. Spalding
{"title":"Publisher Correction: White adipocyte dysfunction and obesity-associated pathologies in humans","authors":"Carolina E. Hagberg, Kirsty L. Spalding","doi":"10.1038/s41580-024-00712-4","DOIUrl":"10.1038/s41580-024-00712-4","url":null,"abstract":"","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41580-024-00712-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139707365","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 : 2024-02-05DOI: 10.1038/s41580-024-00704-4
Lei Yuan
In this Tools of the Trade article, Lei Yuan (from the Cai lab) highlights a new culture system that allows in vitro reconstitution of a dynamic miniature mammary gland.
在这篇 "贸易工具"（Tools of the Trade）文章中，Lei Yuan（来自蔡氏实验室）重点介绍了一种新的培养系统，它可以在体外重建动态微型乳腺。
{"title":"A dynamic culture system that models the intricacy of the mammary gland","authors":"Lei Yuan","doi":"10.1038/s41580-024-00704-4","DOIUrl":"10.1038/s41580-024-00704-4","url":null,"abstract":"In this Tools of the Trade article, Lei Yuan (from the Cai lab) highlights a new culture system that allows in vitro reconstitution of a dynamic miniature mammary gland.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139692431","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 : 2024-02-02DOI: 10.1038/s41580-024-00707-1
Lisa Heinke
Rapid reactivation of gene expression following mitosis-induced silencing is facilitated by a network of redundantly acting nuclear receptors that function as mitotic bookmarks.
有丝分裂诱导基因沉默后，基因表达的快速重新激活得益于作为有丝分裂书签发挥作用的冗余核受体网络。
{"title":"Bookmarking pluripotency genes","authors":"Lisa Heinke","doi":"10.1038/s41580-024-00707-1","DOIUrl":"10.1038/s41580-024-00707-1","url":null,"abstract":"Rapid reactivation of gene expression following mitosis-induced silencing is facilitated by a network of redundantly acting nuclear receptors that function as mitotic bookmarks.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139660018","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 : 2024-02-02DOI: 10.1038/s41580-023-00697-6
Lukas Villiger, Julia Joung, Luke Koblan, Jonathan Weissman, Omar O. Abudayyeh, Jonathan S. Gootenberg
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health. L. Villiger, J. Joung et al. review CRISPR applications for programmable editing of the genome, epigenome and transcriptome. They discuss how CRISPR–Cas systems can be optimized to further improve editing specificity and efficiency and highlight a multitude of applications in basic biological research and for changing clinical practice.
我们编辑基因组的能力落后于我们对基因组进行测序的能力，但人们对 CRISPR 生物学及其在基因组、表观基因组和转录组工程中的应用的了解不断加深，正在缩小这一差距。在本综述中，我们将讨论基于 CRISPR 的各种系统的最新发展，这些系统可以瞬时或永久地修改基因组和转录组。通过功能元基因组学发现的更多 CRISPR 酶和系统大大拓宽了基于 CRISPR 编辑的适用性。经过改造的 Cas 变体具有碱基编辑、质粒编辑、基因插入和基因调控等多种功能，从而为科学界提供了一系列工具。我们强调了当前 CRISPR 工具的优缺点，考虑了它们的效率、精确性、特异性、对细胞 DNA 修复机制的依赖以及它们在基础生物学和治疗学中的应用。最后，我们讨论了正在进行的临床试验，这些试验说明了 CRISPR 系统对人类健康的潜在影响。
{"title":"CRISPR technologies for genome, epigenome and transcriptome editing","authors":"Lukas Villiger, Julia Joung, Luke Koblan, Jonathan Weissman, Omar O. Abudayyeh, Jonathan S. Gootenberg","doi":"10.1038/s41580-023-00697-6","DOIUrl":"10.1038/s41580-023-00697-6","url":null,"abstract":"Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health. L. Villiger, J. Joung et al. review CRISPR applications for programmable editing of the genome, epigenome and transcriptome. They discuss how CRISPR–Cas systems can be optimized to further improve editing specificity and efficiency and highlight a multitude of applications in basic biological research and for changing clinical practice.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139660806","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 : 2024-01-19DOI: 10.1038/s41580-023-00694-9
Jorge Ferrer, Nadya Dimitrova
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets. This Review discusses the emerging roles of long non-coding RNAs (lncRNAs) in the regulation of transcription, for example by controlling the expression of transcription factors. Some lncRNA loci function in trans, but most function in cis, through their own transcription or through the lncRNA transcripts themselves.
长非编码 RNA（lncRNA）的数量超过了蛋白质编码转录本，但它们的功能在很大程度上仍不为人所知。在这篇综述中，我们将讨论 lncRNA 在基因转录控制中的新作用。一些特征最明显的 lncRNAs 具有重要的转录顺式调控功能，而 DNA 相互作用转录因子无法轻松实现这些功能，如控制 X 染色体失活的 XIST 或指导等位基因特异性抑制的印记 lncRNAs。越来越多的lncRNA转录单元，包括CHASERR、PVT1和HASTER（又称HNF1A-AS1）作为转录稳定元件，对编码转录因子的剂量敏感基因的活性进行微调。遗传实验表明，这类转录稳定因子的缺陷往往会导致严重的表型。其他lncRNA，如lincRNA-p21（又称Trp53cor1）和Maenli（Gm29348）有助于基因转录的局部激活，而不同的lncRNA则影响基因的反式转录。我们讨论了通过激活其转录、转录本伸长和加工或 lncRNA 分子本身激发功能的 lncRNA 的研究结果。我们还讨论了lncRNA参与人类疾病的新证据，以及它们作为治疗靶点的潜力。
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Pub Date : 2024-01-15DOI: 10.1038/s41580-024-00701-7
William M. Bement, Andrew B. Goryachev, Ann L. Miller, George von Dassow
{"title":"Publisher Correction: Patterning of the cell cortex by Rho GTPases","authors":"William M. Bement, Andrew B. Goryachev, Ann L. Miller, George von Dassow","doi":"10.1038/s41580-024-00701-7","DOIUrl":"10.1038/s41580-024-00701-7","url":null,"abstract":"","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41580-024-00701-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472557","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 : 2024-01-09DOI: 10.1038/s41580-024-00699-y
Lisa Heinke
Farmer et al. show that mRNAs encoding abscission proteins are targeted to the midbody during cell division and are locally translated to enable cytokinesis.
{"title":"Translating the midbody for cytokinesis","authors":"Lisa Heinke","doi":"10.1038/s41580-024-00699-y","DOIUrl":"10.1038/s41580-024-00699-y","url":null,"abstract":"Farmer et al. show that mRNAs encoding abscission proteins are targeted to the midbody during cell division and are locally translated to enable cytokinesis.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":null,"pages":null},"PeriodicalIF":112.7,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139400422","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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