Epigenomic mapping approaches for cell-type classification in the brain

用于大脑细胞类型分类的表观基因组图谱方法

• 批准号: 9107493
• 负责人: M MARGARITA BEHRENS
• 金额: $ 91.33万
• 依托单位: SALK INSTITUTE FOR BIOLOGICAL STUDIES
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-26 至 2017-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9107493
• 关键词: Adult; Age-associated memory impairment; Alzheimer' s Disease; Atlases; BRAIN initiative; Base of the Brain; Behavioral; Brain; Brain Mapping; Brain region; Cataloging; Catalogs; Categories; Cells; Censuses; Characteristics; Classification; Cortical Cell Layer; Cytosine; DNA; DNA Methylation; Data; Detection; Development; Epigenetic Process; Equipment and supply inventories; Evaluation; Foundations; Gene Expression; Genome; Genomics; Goals; Human; In Situ; Individual; Label; Learning; Location; Maps; Memory; Methylation; Mitotic; Modification; Molecular; Mus; Neuroglia; Neuronal Plasticity; Neurons; Parvalbumins; Pattern; Physiological; Population; Primary Cell Cultures; Primates; Process; Reading; Research; Resolution; Rodent; Schizophrenia; Slice; Specificity; Structure; Systems Biology; Technology; Testing; base; bisulfite; brain cell; cell type; design; epigenomics; frontal lobe; genome-wide; methylome; nervous system disorder; neurochemistry; novel; public health relevance

 DESCRIPTION (provided by applicant): Understanding the exact cell-type composition in brain regions is fundamental to integrating physiological, behavioral and neurochemical data to systematically understand the brain structure and function. At present, although the major categories of cell-types present in brain have been defined, the different subtypes within these categories, as well as their location and connectivity are far from understood. DNA methylation (mC) is a stable covalent modification that persists in post-mitotic cells throughout their lifetim, defining their cellular identity. It was recently demonstrated that mC patterns in brain are highly dynamic throughout development, and that there are clear differences between the major types of cells i.e., neurons and glia, in the rodent and human cortex. These analyses have been taken a step further and have produced data at the cell-type level that shows that each neuronal type carry specific mC signatures in their genomes that define the population they belong to. These results now open the possibility of producing a catalog of cell-types in brain defined by methylome signatures. This proposal will utilize this cell-type-specific base-resolution methylome data to produce complete maps of cell-types in the rodent brain in situ, and by this means develop a systematic inventory and census of cell types in the brain based on an integrated view of their molecular identity. Based on preliminary results showing clear-cut differences between the methylomes of specific neuronal types, we propose to use cutting edge technology to discover and test specific differentially methylated regions that define, at the molecular level, cell-populations in the frontal cortex of mice. The results obtained will be made publically available, and will serve as foundation to produce a complete genomic census of cell-types in a brain region that can be scaled to the whole brain. If successful, the approach could be ultimately tested in the primate brain. This proposal is thus responsive to RFA MH-14-215 "BRAIN Initiative: Transformative Approaches for Cell-Type Classification in the Brain (U01)".

 描述（由申请人提供）：了解大脑区域中的确切细胞类型组成对于整合生理、行为和神经化学数据以系统地了解大脑结构和功能至关重要。目前，虽然大脑中存在的细胞类型的主要类别已经被定义，但这些类别中的不同亚型以及它们的位置和连接性还远未被理解。DNA甲基化（mC）是一种稳定的共价修饰，在有丝分裂后的细胞中持续存在，定义了它们的细胞身份。最近的研究表明，大脑中的mC模式是高度相关的。 在整个发育过程中是动态的，并且主要类型的细胞之间存在明显差异，即，神经元和神经胶质，在啮齿动物和人类的皮层。这些分析已经更进一步，并在细胞类型水平上产生了数据，表明每种神经元类型在其基因组中携带特定的mC签名，这些签名定义了它们所属的群体。这些结果现在打开了产生由甲基化组签名定义的大脑细胞类型目录的可能性。该提案将利用这种细胞类型特异性碱基分辨率甲基化组数据来原位产生啮齿动物大脑中细胞类型的完整地图，并通过这种方式基于其分子身份的综合观点开发大脑中细胞类型的系统库存和普查。基于初步结果显示特定神经元类型的甲基化之间存在明显差异，我们建议使用尖端技术来发现和测试特定的差异甲基化区域，这些区域在分子水平上定义小鼠额叶皮质中的细胞群体。所获得的结果将在计算机上可用，并将作为基础，以产生一个完整的基因组普查的细胞类型在大脑区域，可以扩展到整个大脑。如果成功的话，这种方法最终可以在灵长类动物的大脑中进行测试。因此，该提案响应RFA MH-14-215“BRAIN Initiative：Transformative Approaches for Cell-Type Classification in the Brain（U 01）"。

项目成果

Epigenomic landscapes of retinal rods and cones.

• DOI: 10.7554/elife.11613
• 发表时间: 2016-03-07
• 期刊: eLife
• 影响因子: 7.7
• 作者: Mo A;Luo C;Davis FP;Mukamel EA;Henry GL;Nery JR;Urich MA;Picard S;Lister R;Eddy SR;Beer MA;Ecker JR;Nathans J
• 通讯作者: Nathans J

Robust single-cell DNA methylome profiling with snmC-seq2.

• DOI: 10.1038/s41467-018-06355-2
• 发表时间: 2018-09-20
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Luo C;Rivkin A;Zhou J;Sandoval JP;Kurihara L;Lucero J;Castanon R;Nery JR;Pinto-Duarte A;Bui B;Fitzpatrick C;O'Connor C;Ruga S;Van Eden ME;Davis DA;Mash DC;Behrens MM;Ecker JR
• 通讯作者: Ecker JR

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

• DOI: 10.1016/j.neuron.2015.05.018
• 发表时间: 2015-06-17
• 期刊: Neuron
• 影响因子: 16.2
• 作者: Mo A;Mukamel EA;Davis FP;Luo C;Henry GL;Picard S;Urich MA;Nery JR;Sejnowski TJ;Lister R;Eddy SR;Ecker JR;Nathans J
• 通讯作者: Nathans J