The Drosophila embryo at single-cell transcriptome resolution

被引：248

作者：

Karaiskos, Nikos ^{[1
]}

Wahle, Philipp ^{[2
]}

Alles, Jonathan ^{[1
]}

Boltengagen, Anastasiya ^{[1
]}

Ayoub, Salah ^{[1
]}

Kipar, Claudia ^{[2
]}

Kocks, Christine ^{[1
]}

Rajewsky, Nikolaus ^{[1
]}

Zinzen, Robert P. ^{[2
]}

机构：

[1] Helmholtz Assoc MDC, Berlin Max Delbruck Ctr Mol Med, Syst Biol Gene Regulatory Elements, D-13125 Berlin, Germany

[2] MDC, Syst Biol Neural Tissue Differentiat, BIMSB, D-13125 Berlin, Germany

来源：

SCIENCE | 2017年 / 358卷 / 6360期

关键词：

GENOME-WIDE EXPRESSION; GENE-EXPRESSION; RNA-SEQ; MELANOGASTER; REVEALS; FATE; EVOLUTION; COMPLEX; TISSUE; YORKIE;

D O I：

10.1126/science.aan3235

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produced a virtual embryo with about 8000 expressed genes per cell. Our interactive Drosophila Virtual Expression eXplorer (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.

引用

页码：194 / 199

页数：6

共 47 条

[11] A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm [J].

Fowlkes, Charless C. ;

Luengo Hendriks, Cris L. ;

Keraenen, Soile V. E. ;

Weber, Gunther H. ;

Ruebel, Oliver ;

Huang, Min-Yu ;

Chatoor, Sohail ;

DePace, Angela H. ;

Simirenko, Lisa ;

Henriquez, Clara ;

Beaton, Amy ;

Weiszmann, Richard ;

Celniker, Susan ;

Hamann, Bernd ;

Knowles, David W. ;

Biggin, Mark D. ;

Eisen, Michael B. ;

Malik, Jitendra .

CELL, 2008, 133 (02) :364-374

[12] Linking RNA biology to lncRNAs [J].

Goff, Loyal A. ;

Rinn, John L. .

GENOME RESEARCH, 2015, 25 (10) :1456-1465

[13] FlyBase at 25: looking to the future [J].

Gramates, L. Sian ;

Marygold, Steven J. ;

dos Santos, Gilberto ;

Urbano, Jose-Maria ;

Antonazzo, Giulia ;

Matthews, Beverley B. ;

Rey, Alix J. ;

Tabone, Christopher J. ;

Crosby, Madeline A. ;

Emmert, David B. ;

Falls, Kathleen ;

Goodman, Joshua L. ;

Hu, Yanhui ;

Ponting, Laura ;

Schroeder, Andrew J. ;

Strelets, Victor B. ;

Thurmond, Jim ;

Zhou, Pinglei .

NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D663-D671

[14] The developmental transcriptome of Drosophila melanogaster [J].

Graveley, Brenton R. ;

Brooks, Angela N. ;

Carlson, JosephW. ;

Duff, Michael O. ;

Landolin, Jane M. ;

Yang, Li ;

Artieri, Carlo G. ;

van Baren, Marijke J. ;

Boley, Nathan ;

Booth, Benjamin W. ;

Brown, James B. ;

Cherbas, Lucy ;

Davis, Carrie A. ;

Dobin, Alex ;

Li, Renhua ;

Lin, Wei ;

Malone, John H. ;

Mattiuzzo, Nicolas R. ;

Miller, David ;

Sturgill, David ;

Tuch, Brian B. ;

Zaleski, Chris ;

Zhang, Dayu ;

Blanchette, Marco ;

Dudoit, Sandrine ;

Eads, Brian ;

Green, Richard E. ;

Hammonds, Ann ;

Jiang, Lichun ;

Kapranov, Phil ;

Langton, Laura ;

Perrimon, Norbert ;

Sandler, Jeremy E. ;

Wan, Kenneth H. ;

Willingham, Aarron ;

Zhang, Yu ;

Zou, Yi ;

Andrews, Justen ;

Bickel, Peter J. ;

Brenner, Steven E. ;

Brent, Michael R. ;

Cherbas, Peter ;

Gingeras, Thomas R. ;

Hoskins, Roger A. ;

Kaufman, Thomas C. ;

Oliver, Brian ;

Celniker, Susan E. .

NATURE, 2011, 471 (7339) :473-479

[15] Single-cell messenger RNA sequencing reveals rare intestinal cell types [J].

Grun, Dominic ;

Lyubimova, Anna ;

Kester, Lennart ;

Wiebrands, Kay ;

Basak, Onur ;

Sasaki, Nobuo ;

Clevers, Hans ;

van Oudenaarden, Alexander .

NATURE, 2015, 525 (7568) :251-+

[16] Designing Cell-Type-Specific Genome-wide Experiments [J].

Handley, Ava ;

Schauer, Tamas ;

Ladurner, Andreas G. ;

Margulies, Carla E. .

MOLECULAR CELL, 2015, 58 (04) :621-631

[17]

HARTENSTEIN V, 1985, ROUX ARCH DEV BIOL, V194, P181

[18]

Hartenstein V., 1993, ATLAS DROSOPHILA DEV, V1

[19] The Hippo signaling pathway coordinately regulates cell proliferation and apoptosis by inactivating Yorkie, the Drosophila homolog of YAP [J].

Huang, JB ;

Wu, S ;

Barrera, J ;

Matthews, K ;

Pan, DJ .

CELL, 2005, 122 (03) :421-434

[20] Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types [J].

Jaitin, Diego Adhemar ;

Kenigsberg, Ephraim ;

Keren-Shaul, Hadas ;

Elefant, Naama ;

Paul, Franziska ;

Zaretsky, Irina ;

Mildner, Alexander ;

Cohen, Nadav ;

Jung, Steffen ;

Tanay, Amos ;

Amit, Ido .

SCIENCE, 2014, 343 (6172) :776-779

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