Machine learning sequence prioritization for cell type-specific enhancer design.
Machine learning sequence prioritization for cell type-specific enhancer design.
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DOI：
10.7554/elife.69571
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发表时间：
2022-05-16
期刊：
影响因子：
7.7
通讯作者：
Pfenning, Andreas R.
中科院分区：
文献类型：
--
作者：
Lawler, Alyssa J.;Ramamurthy, Easwaran;Brown, Ashley R.;Shin, Naomi;Kim, Yeonju;Toong, Noelle;Kaplow, Irene M.;Wirthlin, Morgan;Zhang, Xiaoyu;Phan, BaDoi N.;Fox, Grant A.;Wade, Kirsten;He, Jing;Ozturk, Bilge Esin;Byrne, Leah C.;Stauffer, William R.;Fish, Kenneth N.;Pfenning, Andreas R.
关键词：
最近发现大脑中的极端细胞多样性保证了技术的快速发展，以获得异质组织中的特定细胞群。用于新神经元亚型的工程靶向技术的可用方法是低产量的，涉及密集的转基因菌株或病毒筛选。在这里，我们提出了特异性核锚定独立标记（SNAIL），一种改进的基于病毒的细胞标记和核分离异质组织的策略。SNAIL通过利用机器学习和其他计算方法来识别赋予细胞类型特异性基因激活的DNA序列特征，然后制造驱动亲和纯化兼容报告基因的探针。作为概念的证明，我们设计并验证了两种新的SNAIL探针，靶向小白蛋白表达（PV+）神经元。在野生型小鼠中使用SNAIL的核分离足以捕获皮质、纹状体和外部苍白球中PV+神经元的特征性开放染色质特征。SNAIL框架对于多物种细胞探针工程也具有很高的实用性;来自小鼠PV+ SNAIL增强子序列的表达在猕猴皮层的PV+神经元中富集。该技术的扩展在跨物种和疾病模型的细胞类型特异性观察、操作和治疗方面具有广泛的应用。
Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations within heterogeneous tissue. Available approaches for engineering-targeted technologies for new neuron subtypes are low yield, involving intensive transgenic strain or virus screening. Here, we present Specific Nuclear-Anchored Independent Labeling (SNAIL), an improved virus-based strategy for cell labeling and nuclear isolation from heterogeneous tissue. SNAIL works by leveraging machine learning and other computational approaches to identify DNA sequence features that confer cell type-specific gene activation and then make a probe that drives an affinity purification-compatible reporter gene. As a proof of concept, we designed and validated two novel SNAIL probes that target parvalbumin-expressing (PV+) neurons. Nuclear isolation using SNAIL in wild-type mice is sufficient to capture characteristic open chromatin features of PV+ neurons in the cortex, striatum, and external globus pallidus. The SNAIL framework also has high utility for multispecies cell probe engineering; expression from a mouse PV+ SNAIL enhancer sequence was enriched in PV+ neurons of the macaque cortex. Expansion of this technology has broad applications in cell type-specific observation, manipulation, and therapeutics across species and disease models.