A multi-omics atlas of the human retina at single-cell resolution.
A multi-omics atlas of the human retina at single-cell resolution.
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DOI：
10.1016/j.xgen.2023.100298
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发表时间：
2023-06-14
期刊：
影响因子：
--
通讯作者：
Chen R
中科院分区：
文献类型：
--
作者：
Liang Q;Cheng X;Wang J;Owen L;Shakoor A;Lillvis JL;Zhang C;Farkas M;Kim IK;Li Y;DeAngelis M;Chen R
人类视网膜中的细胞种类是高度异质性的，它们的丰度变化了几个数量级。在这里，我们生成并整合了成人视网膜的多组学单细胞图谱，包括超过250,000个单核RNA-seq细胞核和137,000个单核ATAC-seq细胞核。人、猴、鼠和鸡的视网膜图谱的跨物种比较揭示了相对保守型和非保守型。有趣的是，与啮齿动物和鸡的视网膜相比，灵长类动物视网膜的整体细胞异质性降低。通过整合分析，我们确定了35,000对远端顺式元件-基因对，构建了超过200个TF的转录因子（TF）靶调控，并将TF划分为不同的协同活性模块。我们还揭示了不同细胞类型中顺式元件-基因关系的异质性，甚至来自同一类。综上所述，我们提出了一个全面的单细胞多组学人类视网膜图谱，作为一种资源，可以在单个细胞类型分辨率下进行系统的分子表征。跨物种分析揭示了不同细胞类型间的不同保护水平通过整合分析鉴定出的顺式和反式调控元件在不同细胞类型中同一基因调控元件的异质性Liang等人报道了成人视网膜中近40万个细胞核和69个细胞类型的综合多组学单细胞图谱。他们通过综合分析确定特定于细胞类别和细胞类型的调控元件。该数据集能够在单个细胞类型水平上对人类视网膜进行分子表征。
Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution. Targeted enrichment of rare cell types in the human retina Cross-species analysis reveals different conservation levels among cell types Cis- and trans-regulatory elements identified through integrative analysis Heterogeneity in regulatory elements for the same gene in different cell types Liang et al. report a comprehensive multi-omics single-cell atlas with nearly 400,000 nuclei and 69 cell types in adult human retina. They identify regulatory elements that are specific to cell classes and cell types through integrative analysis. The dataset enables molecular characterization of the human retina at individual cell-type level.
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影响因子：
33.6
作者：
Do MT;Yau KW
通讯作者：
Yau KW
影响因子：
64.5
作者：
Cowan CS;Renner M;De Gennaro M;Gross-Scherf B;Goldblum D;Hou Y;Munz M;Rodrigues TM;Krol J;Szikra T;Cuttat R;Waldt A;Papasaikas P;Diggelmann R;Patino-Alvarez CP;Galliker P;Spirig SE;Pavlinic D;Gerber-Hollbach N;Schuierer S;Srdanovic A;Balogh M;Panero R;Kusnyerik A;Szabo A;Stadler MB;Orgül S;Picelli S;Hasler PW;Hierlemann A;Scholl HPN;Roma G;Nigsch F;Roska B
通讯作者：
Roska B
单细胞染色质可及性揭示了调节变化的原理。
影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
通讯作者：
Greenleaf WJ
影响因子：
8.8
作者：
Lyu P;Hoang T;Santiago CP;Thomas ED;Timms AE;Appel H;Gimmen M;Le N;Jiang L;Kim DW;Chen S;Espinoza DF;Telger AE;Weir K;Clark BS;Cherry TJ;Qian J;Blackshaw S
通讯作者：
Blackshaw S
影响因子：
9.3
作者：
McGinnis, Christopher S.;Murrow, Lyndsay M.;Gartner, Zev J.
通讯作者：
Gartner, Zev J.