Single nucleus analysis of the chromatin landscape in mouse forebrain development
Single nucleus analysis of the chromatin landscape in mouse forebrain development
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DOI：
10.1101/159137
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发表时间：
2017-07
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通讯作者：
S. Preissl;Rongxin Fang;Yuan Zhao;R. Raviram;Yanxiao Zhang;B. Sos;Hui Huang;David U. Gorkin;Veena Afzal;D. Dickel;Samantha Kuan;A. Visel;L. Pennacchio;Kun Zhang;B. Ren
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文献类型：
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作者：
S. Preissl;Rongxin Fang;Yuan Zhao;R. Raviram;Yanxiao Zhang;B. Sos;Hui Huang;David U. Gorkin;Veena Afzal;D. Dickel;Samantha Kuan;A. Visel;L. Pennacchio;Kun Zhang;B. Ren
对初级组织中染色质可及性的全基因组分析已经在人类和小鼠基因组1-4中发现了数百万个候选调控序列。然而，先前研究中使用的生物样本的异质性阻碍了对特定细胞类型中动态染色质景观的准确理解。在这里，我们表明，分析从冰冻组织样本中分离的单个细胞核中的转座酶可及染色质可以解决细胞的异质性，并描绘组成细胞类型的转录调控序列。我们的策略是基于转座酶可达染色蛋白5的组合条形码辅助单细胞分析，并针对快速冷冻原始组织样本的核(SnATAC-SEQ)进行了优化。我们使用这种方法在七个发育阶段和成人中检查了小鼠的前脑。从超过15,000个高质量细胞核的SnATAC-SEQ图谱中，我们识别出20个不同的细胞群，对应于胎儿和成人前脑中主要的神经细胞和非神经细胞类型。我们进一步定义了细胞类型特定的顺式调控序列，并推断出每个细胞群体潜在的主要转录调控因子。我们的结果证明了一种在不同组织样本中识别特定细胞类型的顺式调控序列的通用方法的可行性，并为理解哺乳动物的前脑发育提供了丰富的资源。
Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes1–4. However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin5 and is optimized for nuclei from flash-frozen primary tissue samples (snATAC-seq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specific cis regulatory sequences and infer potential master transcriptional regulators of each cell population. Our results demonstrate the feasibility of a general approach for identifying cell-type-specific cis regulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals.