Cell Reports Methods最新文献_第9页

A compact, versatile drug-induced splicing switch system with minimal background expression. 结构紧凑、用途广泛的药物诱导剪接开关系统，背景表达量极低。

IF 4.3

Cell Reports Methods Pub Date : 2024-09-16 Epub Date: 2024-09-04 DOI: 10.1016/j.crmeth.2024.100842

Yue Chi, Xuan Lu, Shuangpeng Li, Jinling Wang, Jiahui Xi, Xiaoqing Zhou, Chengcheng Tang, Min Chen, Hui Yuan, Shuo Lin, Yingying Xiao, Liangxue Lai, Qingjian Zou

{"title":"A compact, versatile drug-induced splicing switch system with minimal background expression.","authors":"Yue Chi, Xuan Lu, Shuangpeng Li, Jinling Wang, Jiahui Xi, Xiaoqing Zhou, Chengcheng Tang, Min Chen, Hui Yuan, Shuo Lin, Yingying Xiao, Liangxue Lai, Qingjian Zou","doi":"10.1016/j.crmeth.2024.100842","DOIUrl":"10.1016/j.crmeth.2024.100842","url":null,"abstract":"Gene-switch techniques hold promising applications in contemporary genetics research, particularly in disease treatment and genetic engineering. Here, we developed a compact drug-induced splicing system that maintains low background using a human ubiquitin C (hUBC) promoter and optimized drug (LMI070) binding sequences based on the Xon switch system. To ensure precise subcellular localization of the protein of interest (POI), we inserted a 2A self-cleaving peptide between the extra N-terminal peptide and POI. This streamlined and optimized switch system, named miniXon2G, effectively regulated POIs in different subcellular localizations both in vitro and in vivo. Furthermore, miniXon2G could be integrated into endogenous gene loci, resulting in precise, reversible regulation of target genes by both endogenous regulators and drugs. Overall, these findings highlight the performance of miniXon2G in controlling protein expression with great potential for general applicability to diverse biological scenarios requiring precise and delicate regulation.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100842"},"PeriodicalIF":4.3,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11440066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. 由 PTMoreR 支持的哺乳动物跨物种 PTM 图谱和比较磷酸化蛋白质组学。

IF 4.3

Cell Reports Methods Pub Date : 2024-09-16 Epub Date: 2024-09-09 DOI: 10.1016/j.crmeth.2024.100859

Shisheng Wang, Yi Di, Yin Yang, Barbora Salovska, Wenxue Li, Liqiang Hu, Jiahui Yin, Wenguang Shao, Dong Zhou, Jingqiu Cheng, Dan Liu, Hao Yang, Yansheng Liu

{"title":"PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.","authors":"Shisheng Wang, Yi Di, Yin Yang, Barbora Salovska, Wenxue Li, Liqiang Hu, Jiahui Yin, Wenguang Shao, Dong Zhou, Jingqiu Cheng, Dan Liu, Hao Yang, Yansheng Liu","doi":"10.1016/j.crmeth.2024.100859","DOIUrl":"10.1016/j.crmeth.2024.100859","url":null,"abstract":"To support PTM proteomic analysis and annotation in different species, we developed PTMoreR, a user-friendly tool that considers the surrounding amino acid sequences of PTM sites during BLAST, enabling a motif-centric analysis across species. By controlling sequence window similarity, PTMoreR can map phosphoproteomic results between any two species, perform site-level functional enrichment analysis, and generate kinase-substrate networks. We demonstrate that the majority of real P-sites in mice can be inferred from experimentally derived human P-sites with PTMoreR mapping. Furthermore, the compositions of 129 mammalian phosphoproteomes can also be predicted using PTMoreR. The method also identifies cross-species phosphorylation events that occur on proteins with an increased tendency to respond to the environmental factors. Moreover, the classic kinase motifs can be extracted across mammalian species, offering an evolutionary angle for refining current motifs. PTMoreR supports PTM proteomics in non-human species and facilitates quantitative phosphoproteomic analysis.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"4 9","pages":"100859"},"PeriodicalIF":4.3,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11440062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Generation of dual-attribute iTNK cells from hPSCs for cancer immunotherapy. 从 hPSCs 中生成用于癌症免疫疗法的双重属性 iTNK 细胞。

IF 4.3

Cell Reports Methods Pub Date : 2024-09-16 Epub Date: 2024-08-30 DOI: 10.1016/j.crmeth.2024.100843

Yingfeng Zhang, Yuanyuan He, Chenyi Dai, Zhengyang Zhou, Yudi Miao, Zixin Zhao, Qi Lei, Cheng Li, Chengyan Wang, Hongkui Deng

{"title":"Generation of dual-attribute iTNK cells from hPSCs for cancer immunotherapy.","authors":"Yingfeng Zhang, Yuanyuan He, Chenyi Dai, Zhengyang Zhou, Yudi Miao, Zixin Zhao, Qi Lei, Cheng Li, Chengyan Wang, Hongkui Deng","doi":"10.1016/j.crmeth.2024.100843","DOIUrl":"10.1016/j.crmeth.2024.100843","url":null,"abstract":"Dual-attribute immune cells possess advantageous features of cytotoxic T cells and natural killer (NK) cells and hold promise for advancing immunotherapy. Dual-attribute cell types such as invariant natural killer T cells, induced T-to-NK cells, and cytokine-induced killer cells have demonstrated efficacy and safety in preclinical and clinical studies. However, their limited availability hinders their widespread application. Human pluripotent stem cells (hPSCs) offer an ideal source. Here, we generate dual-attribute induced T-NK (iTNK) cells from hPSCs, expressing markers of both cytotoxic T and NK cells. Single-cell RNA and T cell receptor (TCR) sequencing analyses reveal that iTNK cells expressed signature genes associated with both NK and T cells and displayed a diverse TCR repertoire. iTNK cells release cytotoxic mediators, exert cytotoxicity against diverse tumor cell lines, and inhibit tumor growth in vivo. By harnessing adaptive and innate immune responses, hPSC-derived iTNK cells offer promising strategies for cancer immunotherapy.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100843"},"PeriodicalIF":4.3,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11440056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format. 用化学酶法同时分析糖蛋白上的 N-和 O-聚糖，采用一锅法。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-07 DOI: 10.1016/j.crmeth.2024.100834

Uriel Ortega-Rodriguez, John Q Bettinger, Guozhang Zou, Vincent M Falkowski, Mari Lehtimaki, Alicia M Matthews, Thomas G Biel, Jordan D Pritts, Wells W Wu, Rong-Fong Shen, Cyrus Agarabi, V Ashutosh Rao, Hang Xie, Tongzhong Ju

{"title":"A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format.","authors":"Uriel Ortega-Rodriguez, John Q Bettinger, Guozhang Zou, Vincent M Falkowski, Mari Lehtimaki, Alicia M Matthews, Thomas G Biel, Jordan D Pritts, Wells W Wu, Rong-Fong Shen, Cyrus Agarabi, V Ashutosh Rao, Hang Xie, Tongzhong Ju","doi":"10.1016/j.crmeth.2024.100834","DOIUrl":"10.1016/j.crmeth.2024.100834","url":null,"abstract":"Glycosylation is generally characterized and controlled as a critical quality attribute for therapeutic glycoproteins because glycans can impact protein drug-product efficacy, half-life, stability, and safety. Analytical procedures to characterize N-glycans are relatively well established, but the characterization of O-glycans is challenging due to the complex workflows and lack of enzymatic tools. Here, we present a simplified chemoenzymatic method to simultaneously profile N- and O-glycans from the same sample using a one-pot format by mass spectrometry (MS). N-glycans were first released by PNGase F, followed by O-glycopeptide generation by proteinase K, selective N-glycan reduction, and O-glycan release by β-elimination during permethylation of both N- and O-glycans. Glycan structural assignments and determination of N- to O-glycan ratio was obtained from the one-pot mass spectra. The streamlined, one-pot method is a reliable approach that will facilitate advanced characterizations for quality assessments of therapeutic glycoproteins.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100834"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Generation of densely labeled oligonucleotides for the detection of small genomic elements. 生成用于检测小基因组元素的高密度标记寡核苷酸。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-12 DOI: 10.1016/j.crmeth.2024.100840

Clemens Steinek, Miguel Guirao-Ortiz, Gabriela Stumberger, Annika J Tölke, David Hörl, Thomas Carell, Hartmann Harz, Heinrich Leonhardt

{"title":"Generation of densely labeled oligonucleotides for the detection of small genomic elements.","authors":"Clemens Steinek, Miguel Guirao-Ortiz, Gabriela Stumberger, Annika J Tölke, David Hörl, Thomas Carell, Hartmann Harz, Heinrich Leonhardt","doi":"10.1016/j.crmeth.2024.100840","DOIUrl":"10.1016/j.crmeth.2024.100840","url":null,"abstract":"The genome contains numerous regulatory elements that may undergo complex interactions and contribute to the establishment, maintenance, and change of cellular identity. Three-dimensional genome organization can be explored with fluorescence in situ hybridization (FISH) at the single-cell level, but the detection of small genomic loci remains challenging. Here, we provide a rapid and simple protocol for the generation of bright FISH probes suited for the detection of small genomic elements. We systematically optimized probe design and synthesis, screened polymerases for their ability to incorporate dye-labeled nucleotides, and streamlined purification conditions to yield nanoscopy-compatible oligonucleotides with dyes in variable arrays (NOVA probes). With these probes, we detect genomic loci ranging from genome-wide repetitive regions down to non-repetitive loci below the kilobase scale. In conclusion, we introduce a simple workflow to generate densely labeled oligonucleotide pools that facilitate detection and nanoscopic measurements of small genomic elements in single cells.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100840"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SkinCom, a synthetic skin microbial community, enables reproducible investigations of the human skin microbiome. SkinCom 是一种合成皮肤微生物群落，能够对人类皮肤微生物群进行可重复的研究。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-06 DOI: 10.1016/j.crmeth.2024.100832

Asama Lekbua, Deepan Thiruppathy, Joanna Coker, Yuhan Weng, Fatemeh Askarian, Armin Kousha, Clarisse Marotz, Amber Hauw, Victor Nizet, Karsten Zengler

{"title":"SkinCom, a synthetic skin microbial community, enables reproducible investigations of the human skin microbiome.","authors":"Asama Lekbua, Deepan Thiruppathy, Joanna Coker, Yuhan Weng, Fatemeh Askarian, Armin Kousha, Clarisse Marotz, Amber Hauw, Victor Nizet, Karsten Zengler","doi":"10.1016/j.crmeth.2024.100832","DOIUrl":"10.1016/j.crmeth.2024.100832","url":null,"abstract":"Existing models of the human skin have aided our understanding of skin health and disease. However, they currently lack a microbial component, despite microbes' demonstrated connections to various skin diseases. Here, we present a robust, standardized model of the skin microbial community (SkinCom) to support in vitro and in vivo investigations. Our methods lead to the formation of an accurate, reproducible, and diverse community of aerobic and anaerobic bacteria. Subsequent testing of SkinCom on the dorsal skin of mice allowed for DNA and RNA recovery from both the applied SkinCom and the dorsal skin, highlighting its practicality for in vivo studies and -omics analyses. Furthermore, 66% of the responses to common cosmetic chemicals in vitro were in agreement with a human trial. Therefore, SkinCom represents a valuable, standardized tool for investigating microbe-metabolite interactions and facilitates the experimental design of in vivo studies targeting host-microbe relationships.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100832"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. Multiomics2Targets 可从使用转录组学、蛋白质组学和磷酸蛋白组学分析的癌症队列中识别靶点。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI: 10.1016/j.crmeth.2024.100839

Eden Z Deng, Giacomo B Marino, Daniel J B Clarke, Ido Diamant, Adam C Resnick, Weiping Ma, Pei Wang, Avi Ma'ayan

{"title":"Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.","authors":"Eden Z Deng, Giacomo B Marino, Daniel J B Clarke, Ido Diamant, Adam C Resnick, Weiping Ma, Pei Wang, Avi Ma'ayan","doi":"10.1016/j.crmeth.2024.100839","DOIUrl":"10.1016/j.crmeth.2024.100839","url":null,"abstract":"The availability of data from profiling of cancer patients with multiomics is rapidly increasing. However, integrative analysis of such data for personalized target identification is not trivial. Multiomics2Targets is a platform that enables users to upload transcriptomics, proteomics, and phosphoproteomics data matrices collected from the same cohort of cancer patients. After uploading the data, Multiomics2Targets produces a report that resembles a research publication. The uploaded matrices are processed, analyzed, and visualized using the tools Enrichr, KEA3, ChEA3, Expression2Kinases, and TargetRanger to identify and prioritize proteins, genes, and transcripts as potential targets. Figures and tables, as well as descriptions of the methods and results, are automatically generated. Reports include an abstract, introduction, methods, results, discussion, conclusions, and references and are exportable as citable PDFs and Jupyter Notebooks. Multiomics2Targets is applied to analyze version 3 of the Clinical Proteomic Tumor Analysis Consortium (CPTAC3) pan-cancer cohort, identifying potential targets for each CPTAC3 cancer subtype. Multiomics2Targets is available from https://multiomics2targets.maayanlab.cloud/.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100839"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Defining spatial nonuniformities of all ipRGC types using an improved Opn4^cre recombinase mouse line. 利用改良的 Opn4cre 重组酶小鼠品系确定所有 ipRGC 类型的空间不均匀性。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI: 10.1016/j.crmeth.2024.100837

Brannen Dyer, Sue O Yu, R Lane Brown, Richard A Lang, Shane P D'Souza

{"title":"Defining spatial nonuniformities of all ipRGC types using an improved Opn4cre recombinase mouse line.","authors":"Brannen Dyer, Sue O Yu, R Lane Brown, Richard A Lang, Shane P D'Souza","doi":"10.1016/j.crmeth.2024.100837","DOIUrl":"10.1016/j.crmeth.2024.100837","url":null,"abstract":"Intrinsically photosensitive retinal ganglion cells (ipRGCs) play a crucial role in several physiological light responses. In this study, we generate an improved Opn4cre knockin allele (Opn4cre(DSO)), which faithfully reproduces endogenous Opn4 expression and improves compatibility with widely used reporters. We evaluated the efficacy and sensitivity of Opn4cre(DSO) for labeling in retina and brain and provide an in-depth comparison with the extensively utilized Opn4cre(Saha) line. Through this characterization, Opn4cre(DSO) demonstrated higher specificity in labeling ipRGCs with minimal recombination escape. Leveraging a combination of electrophysiological, molecular, and morphological analyses, we confirmed its sensitivity in detecting all ipRGC types (M1-M6) and defined their unique topographical distribution across the retina. In the brain, the Opn4cre(DSO) line labels ipRGC projections with minimal labeling of cell bodies. Overall, the Opn4cre(DSO) mouse line represents an improved tool for studying ipRGC function and distribution, offering a means to selectively target these cells to study light-regulated behaviors and physiology.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100837"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a 3-dimensional organotypic model with characteristics of peripheral sensory nerves. 开发具有外周感觉神经特征的三维器官模型。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-07 DOI: 10.1016/j.crmeth.2024.100835

Madoka Koyanagi, Ryosuke Ogido, Akari Moriya, Mamiko Saigo, Satoshi Ihida, Tomoko Teranishi, Jiro Kawada, Tatsuya Katsuno, Kazuo Matsubara, Tomohiro Terada, Akira Yamashita, Satoshi Imai

{"title":"Development of a 3-dimensional organotypic model with characteristics of peripheral sensory nerves.","authors":"Madoka Koyanagi, Ryosuke Ogido, Akari Moriya, Mamiko Saigo, Satoshi Ihida, Tomoko Teranishi, Jiro Kawada, Tatsuya Katsuno, Kazuo Matsubara, Tomohiro Terada, Akira Yamashita, Satoshi Imai","doi":"10.1016/j.crmeth.2024.100835","DOIUrl":"10.1016/j.crmeth.2024.100835","url":null,"abstract":"We developed a rat dorsal root ganglion (DRG)-derived sensory nerve organotypic model by culturing DRG explants on an organoid culture device. With this method, a large number of organotypic cultures can be produced simultaneously with high reproducibility simply by seeding DRG explants derived from rat embryos. Unlike previous DRG explant models, this organotypic model consists of a ganglion and an axon bundle with myelinated A fibers, unmyelinated C fibers, and stereo-myelin-forming nodes of Ranvier. The model also exhibits Ca2+ signaling in cell bodies in response to application of chemical stimuli to nerve terminals. Further, axonal transection increases the activating transcription factor 3 mRNA level in ganglia. Axons and myelin are shown to regenerate 14 days following transection. Our sensory organotypic model enables analysis of neuronal excitability in response to pain stimuli and tracking of morphological changes in the axon bundle over weeks.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100835"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. 通过嵌合 RNA 测序分析体内小非编码 RNA 与靶 RNA 相互作用的全基因组和细胞类型选择性概况。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI: 10.1016/j.crmeth.2024.100836

Xinbei Li, William T Mills, Daniel S Jin, Mollie K Meffert

{"title":"Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing.","authors":"Xinbei Li, William T Mills, Daniel S Jin, Mollie K Meffert","doi":"10.1016/j.crmeth.2024.100836","DOIUrl":"10.1016/j.crmeth.2024.100836","url":null,"abstract":"Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100836"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0