Non-destructive epigenetic sequencing with DNA deaminase enzymes

使用 DNA 脱氨酶进行非破坏性表观遗传测序

• 批准号: 10004705
• 负责人: Rahul Manu Kohli
• 金额: $ 60万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10004705
• 关键词: Address; Adoption; Alkylation; Biochemical; Biological; Biology; Biotechnology; Brain; Cell Lineage; Cells; Chemicals; Clinic; Code; Coupled; CpG dinucleotide; Cytosine; Cytosine deaminase; DNA; DNA sequencing; Deaminase; Deamination; Detection; Development; Discrimination; Enzymes; Epigenetic Process; Exhibits; FOXP3 gene; Foundations; Gene Expression; Genetic Fingerprintings; Genetic Transcription; Genome; Genomic DNA; Genomics; Goals; Gold; Heterogeneity; Immune; Immune system; Length; Link; Location; Mediating; Methods; Modification; Mus; Neurons; Pathologic Processes; Pattern; Physiological Processes; Play; Population; Positioning Attribute; Process; Refractory; Regulatory T-Lymphocyte; Reporting; Resolution; Role; Sampling; Shapes; Signal Transduction; Site; Stretching; Technology; Temperature; Third Generation Sequencing; Time; Tissues; Work; base; bisulfite; bisulfite sequencing; epigenetic profiling; epigenome; frontal lobe; frontier; insight; multimodality; novel; nucleobase; oxidation; pluripotency; single cell analysis; single-cell RNA sequencing; tool; transcriptome; tumorigenesis

PROJECT SUMMARY This proposal aims to establish DNA cytosine deaminase enzymes as a non-destructive alternative to bisulfite for base-resolution mapping of cytosine modifications. Epigenetic modifications to the genome play an important role in cellular adaptation and in specialization of various cell lineages derived from the same coding sequence. On DNA, these epigenetic changes include modification of cytosine bases at the 5-postion of the nucleobase. The most common modification is 5-methylcytosine (5mC), followed closely by 5- hydroxymethylcytosine (5hmC), a product of TET enzyme-mediated oxidation of 5mC. Transformations involved in development, pluripotency and oncogenesis entail changes in the genomic patterns of 5mC and 5hmC, making it important to have robust methods to localize these modifications. The methods most commonly used to detect these modifications involve treatment of genomic DNA with bisulfite, as the different cytosine modification states have a different propensity for bisulfite-induced deamination which can be analyzed by sequencing. Chemical deamination, however, can degrade the vast majority of starting DNA. As a result, bisulfite-based approaches constrain our ability to understand the landscapes of cytosine modifications in many small or transient cell populations, or to study how changes are coordinated across long stretches of genomic DNA. In this proposal, we will develop and apply DNA deaminase-based sequencing approaches that address the major shortcomings of bisulfite. Our methods rely upon enzymatic, rather than chemical deamination, using APOBEC3A (A3A), a DNA deaminase from the immune system repurposed for these biotechnological applications. In our biochemical studies, we have established that A3A potently discriminates between different cytosine modification states, and, in foundational work leading up to this proposal, we developed APOBEC- Coupled Epigenetic Sequencing (ACE-Seq) as a non-destructive, base resolution sequencing method for localizing 5hmC. Building on this precedent, we propose to advance two new DNA deaminase-based sequencing approaches that can now localize 5mC and 5hmC together, providing a surrogate for bisulfite, or to directly detect 5mC alone through deamination, which is without precedent. We will apply these methods to address important biological questions that are refractory to bisulfite-based approaches, specifically resolving C, 5mC and 5hmC to decipher epigenetic heterogeneity at the single cell level, revealing how in cis changes across loci are coordinated across long stretches of DNA, and reporting on the ‘ternary code’ of all three modifications in a single read. Our proposal therefore aims to establish DNA deaminases as a non-destructive and more reliable means for sequencing that can displace bisulfite and its associated limitations, and to thereby drive the widespread adoption of DNA deaminases in epigenetic sequencing in the clinic and the lab.

项目总结 这项提议旨在建立dna胞嘧啶脱氨酶作为亚硫酸氢盐的非破坏性替代品。 用于胞嘧啶修饰的碱基分辨率图谱。对基因组的表观遗传修饰起到了 在细胞适应和来自相同编码的不同细胞谱系的特化中的重要作用 序列。在DNA上，这些表观遗传变化包括5位胞嘧啶碱基的修饰 核酸库。最常见的修饰是5-甲基胞嘧啶(5mC)，其次是5-甲基胞嘧啶(5-mC)。 羟甲基胞嘧啶(5hmC)，是Tet酶催化氧化5mC的产物。变换 参与发育、多能性和肿瘤发生需要改变5mC和 5hmC，因此拥有可靠的方法来本地化这些修改非常重要。使用最多的方法 通常用于检测这些修饰涉及用亚硫酸氢盐处理基因组DNA，因为不同的 胞嘧啶修饰状态对亚硫酸氢盐诱导的脱氨有不同的倾向，这可能是 通过测序进行分析。然而，化学脱氨作用可以降解绝大多数起始DNA。作为一名 结果，基于亚硫酸氢盐的方法限制了我们理解胞嘧啶修饰的能力 在许多小的或瞬时的细胞群体中，或者研究变化是如何在很长一段时间内协调的 基因组DNA。 在这项提案中，我们将开发和应用基于DNA脱氨酶的测序方法，以解决 亚硫酸氢盐的主要缺点。我们的方法依赖于酶法，而不是化学脱氨法，使用 APOBEC3A(A3A)，一种来自免疫系统的DNA脱氨酶，被重新用于这些生物技术 申请。在我们的生化研究中，我们已经确定A3A可以有效地区分不同的 胞嘧啶修饰状态，在导致这一提议的基础工作中，我们开发了APOBEC- 联合表观遗传测序(ACE-Seq)作为一种非破坏性的、碱基分辨测序方法 本地化5hmC。在此先例的基础上，我们建议提出两种新的基于DNA脱氨酶的 测序方法现在可以同时定位5mC和5hmC，提供亚硫酸氢盐的替代品，或者 直接通过脱氨基直接检测5mC，这是没有先例的。我们将把这些方法应用于 解决以亚硫酸盐为基础的方法难以解决的重要生物学问题，特别是解决 C、5mC和5hmC在单细胞水平上破译表观遗传异质性，揭示顺式基因如何变化 不同的基因座在很长的DNA片段上是协调的，并报告了所有三个基因的“三元密码” 在一次读取中进行修改。因此，我们的建议旨在建立DNA脱氨酶作为一种非破坏性的 以及更可靠的测序方法，可以取代亚硫酸氢盐及其相关限制，并 从而推动DNA脱氨酶在临床和实验室的表观遗传测序中的广泛采用。