A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

被引：476

作者：

Diez-Roux, Graciana ^{[1
]}

Banfi, Sandro ^{[1
]}

Sultan, Marc ^{[2
]}

Geffers, Lars ^{[3
]}

Anand, Santosh ^{[1
]}

Rozado, David ^{[2
]}

Magen, Alon ^{[2
]}

Canidio, Elena ^{[4
]}

Pagani, Massimiliano ^{[4
]}

Peluso, Ivana ^{[1
]}

Lin-Marq, Nathalie ^{[5
]}

Koch, Muriel ^{[6
]}

Bilio, Marchesa ^{[1
]}

Cantiello, Immacolata ^{[1
]}

Verde, Roberta ^{[1
]}

De Masi, Cristian ^{[1
]}

Bianchi, Salvatore A. ^{[1
]}

Cicchini, Juliette ^{[5
]}

Perroud, Elodie ^{[5
]}

Mehmeti, Shprese ^{[5
]}

Dagand, Emilie ^{[2
]}

Schrinner, Sabine ^{[2
]}

Nuernberger, Asja ^{[2
]}

Schmidt, Katja ^{[2
]}

Metz, Katja ^{[2
]}

Zwingmann, Christina ^{[2
]}

Brieske, Norbert ^{[2
]}

Springer, Cindy ^{[2
]}

Hernandez, Ana Martinez ^{[3
]}

Herzog, Sarah ^{[3
]}

Grabbe, Frauke ^{[3
]}

Sieverding, Cornelia ^{[3
]}

Fischer, Barbara ^{[3
]}

Schrader, Kathrin ^{[3
]}

Brockmeyer, Maren ^{[3
]}

Dettmer, Sarah ^{[3
]}

Helbig, Christin ^{[3
]}

Alunni, Violaine ^{[6
]}

Battaini, Marie-Annick ^{[6
]}

Mura, Carole ^{[6
]}

Henrichsen, Charlotte N. ^{[7
]}

Garcia-Lopez, Raquel ^{[8
]}

Echevarria, Diego ^{[8
]}

Puelles, Eduardo ^{[8
]}

Garcia-Calero, Elena ^{[8
]}

Kruse, Stefan ^{[9
]}

Uhr, Markus ^{[3
]}

Kauck, Christine ^{[3
]}

Feng, Guangjie ^{[10
]}

Milyaev, Nestor ^{[10
]}

机构：

[1] Telethon Inst Genet & Med, Naples, Italy

[2] Max Planck Inst Mol Genet, Berlin, Germany

[3] Max Planck Inst Biophys Chem, Genes & Behav Dept, D-37077 Gottingen, Germany

[4] Primm, Milan, Italy

[5] Univ Geneva, Sch Med, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland

[6] Inst Clin Souris, Illkirch Graffenstaden, France

[7] Univ Lausanne, Ctr Integrat Genom, Lausanne, Switzerland

[8] Univ Miguel Hernandez, Inst Neurociencias, Expt Embryol Lab, Alacant, Spain

[9] ORGARAT, Essen, Germany

[10] Western Gen Hosp, Human Genet Unit, MRC, Edinburgh EH4 2XU, Midlothian, Scotland

[11] RZPD Deutsch Ressourcenzentrum Genomforsch, Berlin, Germany

[12] Univ Strasbourg, Inst Genet & Biol Mol & Cellulaire, Fac Med, INSERM,U964,CNRS,UMR 7104, Illkirch Graffenstaden, France

[13] Univ Hosp Geneva, Geneva, Switzerland

[14] Univ Naples Federico II, Dept Pediat, Naples, Italy

[15] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[16] Texas Childrens Hosp, Jan & Dan Duncan Neurol Res Inst, Houston, TX 77030 USA

来源：

PLOS BIOLOGY | 2011年 / 9卷 / 01期

基金：

瑞士国家科学基金会;

关键词：

GENE-EXPRESSION PATTERNS; PROSOMERIC MODEL; NERVOUS-SYSTEM; DATABASE; FOREBRAIN; MECHANISMS; KIDNEY; BRAIN; VIEW; WNT;

D O I：

10.1371/journal.pbio.1000582

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function. It is, therefore, crucial to determine on a genome-wide level, the spatio-temporal gene expression profiles at cellular resolution. This information is provided by colorimetric RNA in situ hybridization that can elucidate expression of genes in their native context and does so at cellular resolution. We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.

引用

页数：13

共 40 条

[1] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[2] Atlas of Gene Expression in the Developing Kidney at Microanatomic Resolution [J].

Brunskill, Eric W. ;

Aronow, Bruce J. ;

Georgas, Kylie ;

Rumballe, Bree ;

Valerius, M. Todd ;

Aronow, Jeremy ;

Kaimal, Vivek ;

Jegga, Anil G. ;

Grimmond, Sean ;

McMahon, Andrew P. ;

Patterson, Larry T. ;

Little, Melissa H. ;

Potter, S. Steven .

DEVELOPMENTAL CELL, 2008, 15 (05) :781-791

[3] A transcriptome atlas of the mouse brain at cellular resolution [J].

Carson, JP ;

Thaller, C ;

Eichele, G .

CURRENT OPINION IN NEUROBIOLOGY, 2002, 12 (05) :562-565

[4] Circulation and chemotaxis of fetal hematopoietic stem cells [J].

Christensen, JL ;

Wright, DE ;

Wagers, AJ ;

Weissman, IL .

PLOS BIOLOGY, 2004, 2 (03) :368-377

[5] EMAGE: a spatial database of gene expression patterns during mouse embryo development [J].

Christiansen, Jeffrey H. ;

Yang, Yiya ;

Venkataraman, Shanmugasundaram ;

Richardson, Lorna ;

Stevenson, Peter ;

Burton, Nicholas ;

Baldock, Richard A. ;

Davidson, Duncan R. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D637-D641

[6] Glutamate uptake [J].

Danbolt, NC .

PROGRESS IN NEUROBIOLOGY, 2001, 65 (01) :1-105

[7] Transcriptional mechanisms controlling motor neuron diversity and connectivity [J].

di Sanguinetto, Simon A. Dalla Torre ;

Dasen, Jeremy S. ;

Arber, Silvia .

CURRENT OPINION IN NEUROBIOLOGY, 2008, 18 (01) :36-43

[8] SEGMENTAL ORGANIZATION OF EMBRYONIC DIENCEPHALON [J].

FIGDOR, MC ;

STERN, CD .

NATURE, 1993, 363 (6430) :630-634

[9] Early mammillary pouch specification in the course of prechordal ventralization of the forebrain tegmentum [J].

Garcia-Calero, Elena ;

Fernandez-Garre, Pedro ;

Martinez, Salvador ;

Puelles, Luis .

DEVELOPMENTAL BIOLOGY, 2008, 320 (02) :366-377

[10]

Gitton Y, 2002, NATURE, V420, P586, DOI 10.1038/nature01178

← 1 2 3 4 →