STAMP technology to enable single-cell and isoform-sensitive detection of RBP sites
STAMP 技术可实现 RBP 位点的单细胞和亚型敏感检测
基本信息
- 批准号:10277360
- 负责人:
- 金额:$ 99.54万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-09-01 至 2025-05-31
- 项目状态:未结题
- 来源:
- 关键词:AdoptionAmino AcidsAntibodiesBindingBinding ProteinsBinding SitesBiologicalBirthCellsCollectionCommunitiesCoupledDataData SetDetectionDiseaseElementsGene ExpressionGenetic TranslationGenomicsGoalsGrantHumanImmunoprecipitationLabelLibrariesLife Cycle StagesLocalesMeasurementMeasuresMediatingMessenger RNAMetabolismMethodologyMethodsModificationMolecularMonitorMorphologic artifactsNational Human Genome Research InstituteNatureNoiseProtein IsoformsProtein SubunitsProtocols documentationRNARNA ProcessingRNA analysisRNA-Binding ProteinsReagentRegulatory ElementReproducibilityResearchResolutionResourcesRibosomal ProteinsRibosomesRoleSamplingSignal TransductionSiteSpecificityStructureSurveysTechnologyTestingThird Generation SequencingTimeTranscriptTranslationsUntranslated RNAWorkanalytical toolapoB mRNA editing catalytic subunitbasecell typecomputer frameworkcrosslinkdesigndetection limitflexibilitygenomic RNAimprovedinsightnanoporenew technologynovelparalogous geneprogramsresponseribosome profilingsingle cell analysissingle moleculetechnological innovationtechnology developmenttranscriptometranscriptome sequencing
项目摘要
PROJECT SUMMARY
RNA-binding proteins (RBPs) interact with RNA molecules from synthesis to decay to control their metabolism,
subcellular localization, stability and translation. Methods for transcriptome-wide detection of RBP-RNA
interactions provide insights into how RBPs regulate gene expression programs and how RNA processing is
disrupted in disease state. Despite their association with disease and although the importance of regulating gene
expression is well appreciated, only a small fraction of the over 2,000 RBPs identified thus far have known RNA
targets and molecular roles. Commonly, immunoprecipitation-based technologies coupled to high throughput
(Illumina) sequencing, such as RNA immunoprecipitation (RIP) and Crosslinking Immunoprecipitation (CLIP),
and ribosome profiling are used to identify RBP targets and binding sites across the transcriptome. However,
these experimental protocols are labor-intensive, require large amounts of input material, are not adaptable to
high-throughput workflows. To overcome these limitations, we develop a novel technology, reagent resource,
experimental protocols and a computational framework, that we collectively term STAMP (Surveying Targets By
APOBEC-Mediated Profiling), for detecting RBP-RNA targets and translation at the single-cell and single-
molecule level. In preliminary data we demonstrate, for the first time in the field, discovery of RBP-RNA sites and
translation states at single-cell resolution. We anticipate that STAMP can be used reliably to identify RNA targets,
binding sites and even extract motifs from a few cells to a single cell, thus effectively increasing limits of detection
over current methods by several orders of magnitude. Combined with simultaneous RNA-seq analyses, STAMP
will enable the combined identification of RBP binding sites and global measurement of gene expression, a long-
standing goal for the gene expression, genomics and RNA communities. As a corollary, even without single cell
analyses, STAMP can accept ultra-low input material which enables rare cell-types to be collected and analyzed
for RBP-interactomes. By applying STAMP to ribosomal proteins, we extend this approach for single-cell
detection of ribosome association while simultaneously measuring gene expression. Our conceptual and
technological innovations will, for the first time, enable translation efficiency and RBP-interactomes to be
measured at single-cell level and at scale, opening up new paradigms of biological questions.
项目总结
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
Eugene Wei-Ming Yeo其他文献
Eugene Wei-Ming Yeo的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('Eugene Wei-Ming Yeo', 18)}}的其他基金
STAMP technology to enable single-cell and isoform-sensitive detection of RBP sites
STAMP 技术可实现 RBP 位点的单细胞和亚型敏感检测
- 批准号:
10475206 - 财政年份:2021
- 资助金额:
$ 99.54万 - 项目类别:
STAMP technology to enable single-cell and isoform-sensitive detection of RBP sites
STAMP 技术可实现 RBP 位点的单细胞和亚型敏感检测
- 批准号:
10632150 - 财政年份:2021
- 资助金额:
$ 99.54万 - 项目类别:
Single-Cell Transcriptomic and Epigenetics Core
单细胞转录组学和表观遗传学核心
- 批准号:
10214453 - 财政年份:2018
- 资助金额:
$ 99.54万 - 项目类别:
Single-Cell Transcriptomic and Epigenetics Core
单细胞转录组学和表观遗传学核心
- 批准号:
10453788 - 财政年份:2018
- 资助金额:
$ 99.54万 - 项目类别:
Collaboration on preclinical autism cellular assays, biosignatures, and network analyses (Copacabana)
临床前自闭症细胞检测、生物特征和网络分析方面的合作(Copacabana)
- 批准号:
8935692 - 财政年份:2015
- 资助金额:
$ 99.54万 - 项目类别:
相似海外基金
Double Incorporation of Non-Canonical Amino Acids in an Animal and its Application for Precise and Independent Optical Control of Two Target Genes
动物体内非规范氨基酸的双重掺入及其在两个靶基因精确独立光学控制中的应用
- 批准号:
BB/Y006380/1 - 财政年份:2024
- 资助金额:
$ 99.54万 - 项目类别:
Research Grant
Quantifying L-amino acids in Ryugu to constrain the source of L-amino acids in life on Earth
量化 Ryugu 中的 L-氨基酸以限制地球生命中 L-氨基酸的来源
- 批准号:
24K17112 - 财政年份:2024
- 资助金额:
$ 99.54万 - 项目类别:
Grant-in-Aid for Early-Career Scientists
Collaborative Research: RUI: Elucidating Design Rules for non-NRPS Incorporation of Amino Acids on Polyketide Scaffolds
合作研究:RUI:阐明聚酮化合物支架上非 NRPS 氨基酸掺入的设计规则
- 批准号:
2300890 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Continuing Grant
Basic research toward therapeutic strategies for stress-induced chronic pain with non-natural amino acids
非天然氨基酸治疗应激性慢性疼痛策略的基础研究
- 批准号:
23K06918 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Molecular mechanisms how arrestins that modulate localization of glucose transporters are phosphorylated in response to amino acids
调节葡萄糖转运蛋白定位的抑制蛋白如何响应氨基酸而被磷酸化的分子机制
- 批准号:
23K05758 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Molecular recognition and enantioselective reaction of amino acids
氨基酸的分子识别和对映选择性反应
- 批准号:
23K04668 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Grant-in-Aid for Scientific Research (C)
Design and Synthesis of Fluorescent Amino Acids: Novel Tools for Biological Imaging
荧光氨基酸的设计与合成:生物成像的新工具
- 批准号:
2888395 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Studentship
Structurally engineered N-acyl amino acids for the treatment of NASH
用于治疗 NASH 的结构工程 N-酰基氨基酸
- 批准号:
10761044 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Lifestyle, branched-chain amino acids, and cardiovascular risk factors: a randomized trial
生活方式、支链氨基酸和心血管危险因素:一项随机试验
- 批准号:
10728925 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:
Single-molecule protein sequencing by barcoding of N-terminal amino acids
通过 N 端氨基酸条形码进行单分子蛋白质测序
- 批准号:
10757309 - 财政年份:2023
- 资助金额:
$ 99.54万 - 项目类别:














{{item.name}}会员




