PARALLEL ANALYSIS OF TRANSCRIPTION AND PROTEIN-DNAINTERACTIONS IN SINGLE CNS CELLS

单 CNS 细胞转录和蛋白质-DNA 相互作用的并行分析

• 批准号: 10044139
• 负责人: JOSEPH D DOUGHERTY
• 金额: $ 9.32万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10044139
• 关键词: Anatomy; Binding; Binding Proteins; Brain; Cells; Chromatin; Chromatin Remodeling Factor; Classification; Communities; Complex; DNA Binding; DNA-Protein Interaction; Data; Data Analyses; Development; Disease; Gene Expression; Gene Expression Regulation; Genetic Transcription; Goals; Health; Location; Maps; Measures; Messenger RNA; Methods; Modeling; Molecular; Mus; Neurobiology; Organ; Physiological; Plasmids; Population Heterogeneity; Proteins; RNA; Reagent; Resources; Technology; Viral; base; cell type; cost; data visualization; genome-wide; mRNA Expression; new technology; tool; transcription factor; user friendly software

PROJECT SUMMARY The brain is the most complex organ in the body, consisting of hundreds of molecularly, physiologically, and anatomically distinct cells. Recently, methods have been developed that can cost-effectively measure mRNA abundance in tens of thousands of single cells, and this has led to a revolution in the identification and classification of new types of cells in the brain. But these methods only measure one aspect of gene regulation – mRNA levels. To fully understand the transcriptional networks that function in the brain, it will be important to also map the genome-wide binding locations of transcription factors and chromatin modifiers in the myriad of different cell types present in the brain. We propose to develop a method to simultaneously map transcription factor binding and measure mRNA abundance from single cells in the brain. To do so, we will adapt our transposon based methods for measuring the binding of DNA interacting proteins to existing single cell profiling methods. This technology, single-cell Calling Cards, builds on our previously developed transposon Calling Card method, but significantly extends the method allowing use in populations of heterogeneous cells, without a priori definition of cell type. We propose here to develop new mouse lines compatible with the wide range of existing resources in mouse, as well as viral and plasmid reagents applicable across model species, and distribute these to the community. Finally, since the tools we will develop generate new types of data, we will develop a user- friendly software for data visualization and analysis of TFs or chromatin modifying proteins binding data across multiple cell types. Robust resources for analysis are crucial if these technologies are to find broad use in the community. Our primary goal is to enable the parallel analysis of transcription factor binding and mRNA expression levels from tens of thousands of single cells in the brain. !

项目总结 大脑是人体中最复杂的器官，由数以百计的分子、生理和 解剖上截然不同的细胞。最近，已经开发出了能够经济有效地测量mRNA的方法 在数以万计的单个细胞中大量存在，这导致了鉴定和 大脑中新类型细胞的分类。但是这些方法只测量基因调控的一个方面。 -信使核糖核酸水平。为了充分了解大脑中起作用的转录网络，重要的是 还绘制了转录因子和染色质修饰物在无数 大脑中存在不同类型的细胞。我们建议开发一种同时绘制转录图谱的方法 因子结合和测量大脑单个细胞的信使核糖核酸丰度。要做到这一点，我们将调整我们的 基于转座子的检测DNA相互作用蛋白与现有单细胞图谱结合的方法 方法：研究方法。这项技术，单细胞电话卡，建立在我们之前开发的转座子电话卡的基础上 方法，但大大扩展了该方法，允许在没有先验的情况下在异种细胞群中使用 单元类型的定义。我们建议在这里开发与现有广泛的鼠标系列兼容的新鼠标系列 小鼠中的资源，以及适用于模式物种的病毒和质粒试剂，并分发这些 对社区的影响。最后，由于我们将开发的工具会生成新类型的数据，因此我们将开发一个用户- 友好的软件，用于对TF或染色质修饰蛋白结合数据进行数据可视化和分析 多种单元格类型。如果这些技术要在 社区。我们的主要目标是实现转录因子结合和mrna的并行分析。 大脑中数以万计的单个细胞的表达水平。 好了！

项目成果

Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome.

• DOI: 10.1016/j.celrep.2018.10.043
• 发表时间: 2018-11-06
• 期刊: Cell reports
• 影响因子: 8.8
• 作者: Cheng C;Deng PY;Ikeuchi Y;Yuede C;Li D;Rensing N;Huang J;Baldridge D;Maloney SE;Dougherty JD;Constantino J;Jahani-Asl A;Wong M;Wozniak DF;Wang T;Klyachko VA;Bonni A
• 通讯作者: Bonni A

A Suite of New Strain Construction Vectors for Gene Expression Knockdown in Budding Yeast.

• DOI: 10.1021/acssynbio.2c00547
• 发表时间: 2023-02-17
• 期刊: ACS SYNTHETIC BIOLOGY
• 影响因子: 4.7
• 作者: Shively, Christian A.;Dong, Fengping;Mitra, Robi D.
• 通讯作者: Mitra, Robi D.

Loss of CELF6 RNA binding protein impairs cocaine conditioned place preference and contextual fear conditioning.

CELF6 RNA 结合蛋白的缺失会损害可卡因条件性位置偏好和情境恐惧条件反射。

• DOI: 10.1111/gbb.12593
• 发表时间: 2019
• 期刊: Genes, brain, and behavior
• 作者: Maloney,SusanE;Rieger,MichaelA;Al-Hasani,Ream;Bruchas,MichaelR;Wozniak,DavidF;Dougherty,JosephD
• 通讯作者: Dougherty,JosephD

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.

• DOI: 10.1093/molbev/msaa194
• 发表时间: 2020-07
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Di Chen;Marzia A. Cremona;Zongtai Qi;R. Mitra;Francesca Chiaromonte;K. Makova

Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.

• DOI: 10.1093/nar/gkad320
• 发表时间: 2023-06-09
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Recio, Pamela S.;Mitra, Nikhil J.;Shively, Christian A.;Song, David;Jaramillo, Grace;Lewis, Kristine Shady;Chen, Xuhua;Mitra, Robi D.
• 通讯作者: Mitra, Robi D.