Molecules and Cells最新文献

{"title":"OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice","authors":"","doi":"10.1016/j.mocell.2024.100093","DOIUrl":"10.1016/j.mocell.2024.100093","url":null,"abstract":"<div><p>Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that <em>OsMYB14</em>, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of <em>OsMYB14 (OsMYB14</em>-ox<em>)</em> in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the <em>osmyb14</em>-knockout (<em>osmyb14-</em>ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the <em>OsMYB14-</em>ox line. Hormone quantitation revealed that inactive GA19 accumulated in <em>OsMYB14</em>-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in <em>OsMYB14</em>-ox and <em>osmyb14</em>-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of <em>OsGA20ox1</em>, encoding GA20 oxidase 1, and <em>OsGH3-2</em>, encoding IAA-amido synthetase, was downregulated in <em>OsMYB14</em>-ox and upregulated in <em>osmyb14</em>-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the <em>OsGA20ox1</em> and <em>GA20ox2</em> genes. These results suggest that <em>OsMYB14</em> may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001183/pdfft?md5=8494307b1e3dd7ac831bb54ad6f58f75&pid=1-s2.0-S1016847824001183-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141616812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking biological mechanisms with integrative functional genomics approaches","authors":"","doi":"10.1016/j.mocell.2024.100092","DOIUrl":"10.1016/j.mocell.2024.100092","url":null,"abstract":"<div><p>Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as <em>Saccharomyces cerevisiae</em>, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001171/pdfft?md5=60d1edbaebce3210f5921cb294e1124e&pid=1-s2.0-S1016847824001171-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting cellular adaptive responses to glutaminolysis perturbation for cancer therapy","authors":"","doi":"10.1016/j.mocell.2024.100096","DOIUrl":"10.1016/j.mocell.2024.100096","url":null,"abstract":"<div><p>Metabolic aberrations, notably deviations in glutamine metabolism, are crucial in the oncogenic process, offering vital resources for the unlimited proliferation and enhanced survival capabilities of cancer cells. The dependency of malignant cells on glutamine metabolism has led to the proposition of targeted therapeutic strategies. However, the capability of cancer cells to initiate adaptive responses undermines the efficacy of these therapeutic interventions. This review meticulously examines the multifaceted adaptive mechanisms that cancer cells deploy to sustain survival and growth following the disruption of glutamine metabolism. Emphasis is placed on the roles of transcription factors, alterations in metabolic pathways, the mechanistic target of rapamycin complex 1 signaling axis, autophagy, macropinocytosis, nucleotide biosynthesis, and the scavenging of ROS. Thus, the delineation and subsequent targeting of these adaptive responses in the context of therapies aimed at glutamine metabolism offer a promising avenue for circumventing drug resistance in cancer treatment.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001213/pdfft?md5=e6c161f29f137350bdf3a5ceccb2d318&pid=1-s2.0-S1016847824001213-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141748634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A practical handbook on single-cell RNA sequencing data quality control and downstream analysis","authors":"","doi":"10.1016/j.mocell.2024.100103","DOIUrl":"10.1016/j.mocell.2024.100103","url":null,"abstract":"<div><p>Advancements in single-cell analysis have facilitated high-resolution observation of the transcriptome in individual cells. However, standards for obtaining high-quality cells and data analysis pipelines remain variable. Here, we provide the groundwork for improving the quality of single-cell analysis by delineating guidelines for selecting high-quality cells and considerations throughout the analysis. This review will streamline researchers' access to single-cell analysis and serve as a valuable guide for analysis.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001286/pdfft?md5=597522eb71b01dbfe0b04c28e76b4444&pid=1-s2.0-S1016847824001286-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brief guide to senescence assays using cultured mammalian cells","authors":"","doi":"10.1016/j.mocell.2024.100102","DOIUrl":"10.1016/j.mocell.2024.100102","url":null,"abstract":"<div><p>Cellular senescence is a crucial biological process associated with organismal aging and many chronic diseases. Here, we present a brief guide to mammalian senescence assays, including the measurement of cell cycle arrest, change in cellular morphology, senescence-associated β-galactosidase (SA-β-gal) staining, and the expression of senescence-associated secretory phenotype (SASP). This work will be useful for biologists with minimum expertise in cellular senescence assays.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001274/pdfft?md5=a375700595e6fc9ad63d230ed24edd4b&pid=1-s2.0-S1016847824001274-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcellular transmission and molecular heterogeneity of aggregation-prone proteins in neurodegenerative diseases","authors":"","doi":"10.1016/j.mocell.2024.100089","DOIUrl":"10.1016/j.mocell.2024.100089","url":null,"abstract":"<div><p>The accumulation of aggregation-prone proteins in a specific neuronal population is a common feature of neurodegenerative diseases, which is correlated with the development of pathological lesions in diseased brains. The formation and progression of pathological protein aggregates in susceptible neurons induce cellular dysfunction, resulting in progressive degeneration. Moreover, recent evidence supports the notion that the cell-to-cell transmission of pathological protein aggregates may be involved in the onset and progression of many neurodegenerative diseases. Indeed, several studies have identified different pathological aggregate strains. Although how these different aggregate strains form remains unclear, a variety of biomolecular compositions or cross-seeding events promoted by the presence of other protein aggregates in the cellular environment may affect the formation of different strains of pathological aggregates, which in turn can influence complex pathologies in diseased brains. In this review, we summarize the recent results regarding cell-to-cell transmission and the molecular heterogeneity of pathological aggregate strains, raising key questions for future research directions.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001146/pdfft?md5=cd39e1d0f82a47c4f47e0e671f220962&pid=1-s2.0-S1016847824001146-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Guide for generating single-cell–derived knockout clones in mammalian cell lines using the CRISPR/Cas9 system","authors":"Taeyeon Hong ,&nbsp;Seung-Min Bae ,&nbsp;Gwonhwa Song ,&nbsp;Whasun Lim","doi":"10.1016/j.mocell.2024.100087","DOIUrl":"10.1016/j.mocell.2024.100087","url":null,"abstract":"<div><p>Genome editing has developed rapidly in various research fields for targeted genome modifications in many organisms, including cells, plants, viruses, and animals. The clustered regularly interspaced short palindromic repeats-associated protein 9 system stands as a potent tool in gene editing for generating cells and animal models with high precision. The clinical potential of clustered regularly interspaced short palindromic repeats-associated protein 9 has been extensively reported, with applications in genetic disease correction, inhibition of viral replication, and personalized or targeted therapeutics for various cancers. In this study, we provide a guide on single-guide RNA design, cloning single-guide RNA into plasmid vectors, single-cell isolation via transfection, and identification of knockout clones using next-generation sequencing. In addition, by providing the results of insertion into mammalian cell lines through next-generation sequencing, we offer useful information to those conducting research on human and animal cell lines.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001122/pdfft?md5=a6cbd4698f274574f1ca2139da8fca70&pid=1-s2.0-S1016847824001122-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141469559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Board Members/Copyright","authors":"","doi":"10.1016/S1016-8478(24)00124-9","DOIUrl":"10.1016/S1016-8478(24)00124-9","url":null,"abstract":"","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001249/pdfft?md5=1a04d8ba1b4042d12dc610be8c0da2a0&pid=1-s2.0-S1016847824001249-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141729636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering vimentin assembly: Bridging theoretical models and experimental approaches","authors":"Soyeon Jeong ,&nbsp;Nam-Chul Ha","doi":"10.1016/j.mocell.2024.100080","DOIUrl":"10.1016/j.mocell.2024.100080","url":null,"abstract":"<div><p>The intricate assembly process of vimentin intermediate filaments (IFs), key components of the eukaryotic cytoskeleton, has yet to be elucidated. In this work, we investigated the transition from soluble tetrameric vimentin units to mature 11-nm tubular filaments, addressing a significant gap in the understanding of IF assembly. Through a combination of theoretical modeling and analysis of experimental data, we propose a novel assembly sequence, emphasizing the role of helical turns and gap filling by soluble tetramers. Our findings shed light on the unique structural dynamics of vimentin and suggest broader implications for the general principles of IF formation.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001055/pdfft?md5=4ba75d097e6e59434abc56a9612dd8e8&pid=1-s2.0-S1016847824001055-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome editing using CRISPR, CAST, and Fanzor systems","authors":"Beomjong Song ,&nbsp;Sangsu Bae","doi":"10.1016/j.mocell.2024.100086","DOIUrl":"10.1016/j.mocell.2024.100086","url":null,"abstract":"<div><p>Genetic engineering technologies are essential not only for basic science but also for generating animal models for therapeutic applications. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system, derived from adapted prokaryotic immune responses, has led to unprecedented advancements in the field of genome editing because of its ability to precisely target and edit genes in a guide RNA-dependent manner. The discovery of various types of CRISPR-Cas systems, such as CRISPR-associated transposons (CASTs), has resulted in the development of novel genome editing tools. Recently, research has expanded to systems associated with obligate mobile element guided activity (OMEGA) RNAs, including ancestral CRISPR-Cas and eukaryotic Fanzor systems, which are expected to complement the conventional CRISPR-Cas systems. In this review, we briefly introduce the features of various CRISPR-Cas systems and their application in diverse animal models.</p></div>","PeriodicalId":18795,"journal":{"name":"Molecules and Cells","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1016847824001110/pdfft?md5=a29a79cfb9cbbf3d4bc4ebb240126548&pid=1-s2.0-S1016847824001110-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}