Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis

Paul A. Gray; Hui Fu; Ping Luo; Qing Zhao; Jing Yu; Annette Ferrari; Toyoaki Tenzen; Dong-in Yuk; Eric F. Tsung; Zhaohui Cai; John A. Alberta; Le-ping Cheng; Yang Liu; Jan M. Stenman; M. Todd Valerius; Nathan Billings; Haesun A. Kim; Michael E. Greenberg; Andrew P. McMahon; David H. Rowitch; Charles D. Stiles; Qiufu Ma

doi:10.1126/science.1104935

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Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis

Paul A. Gray1,3,*,†,
Hui Fu2,3,*,
Ping Luo1,3,*,
Qing Zhao4,
Jing Yu5,
Annette Ferrari3,
Toyoaki Tenzen5,
Dong-in Yuk4,
Eric F. Tsung6,‡,
Zhaohui Cai6,
John A. Alberta3,
Le-ping Cheng1,3,
Yang Liu1,3,
Jan M. Stenman5,
M. Todd Valerius5,
Nathan Billings4,
Haesun A. Kim2,3,§,
Michael E. Greenberg1,8,
Andrew P. McMahon5,
David H. Rowitch4,7,
Charles D. Stiles2,3,∥,
Qiufu Ma1,3,∥

¹ Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
² Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.
³ Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.
⁴ Department of Pediatric Oncology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.
⁵ Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
⁶ Informatics Program, Children's Hospital, Boston, MA 02115, USA.
⁷ Division of Newborn Medicine, Children's Hospital, Boston, MA 02115, USA.
⁸ Division of Neuroscience, Children's Hospital, Boston, MA 02115, USA.

↵∥ To whom correspondence should be addressed. E-mail: Qiufu_Ma{at}dfci.harvard.edu (Q.M.); Charles_Stiles{at}dfci.harvard.edu (C.D.S.)

↵* These authors contributed equally to this work.
↵† Present address: Molecular Neurobiology Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
↵‡ Present address: Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
↵§ Present address: Department of Biological Sciences, Rutgers University, 101 Warren Street, Newark, NJ 07102 USA.

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Science 24 Dec 2004:
Vol. 306, Issue 5705, pp. 2255-2257
DOI: 10.1126/science.1104935

Paul A. Gray

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Hui Fu

2 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Ping Luo

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Qing Zhao

4 Department of Pediatric Oncology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Jing Yu

5 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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Annette Ferrari

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Toyoaki Tenzen

5 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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Dong-in Yuk

4 Department of Pediatric Oncology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Eric F. Tsung

6 Informatics Program, Children's Hospital, Boston, MA 02115, USA.

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Zhaohui Cai

6 Informatics Program, Children's Hospital, Boston, MA 02115, USA.

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John A. Alberta

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Le-ping Cheng

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Yang Liu

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Jan M. Stenman

5 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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M. Todd Valerius

5 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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Nathan Billings

4 Department of Pediatric Oncology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Haesun A. Kim

2 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Michael E. Greenberg

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

8 Division of Neuroscience, Children's Hospital, Boston, MA 02115, USA.

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Andrew P. McMahon

5 Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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David H. Rowitch

4 Department of Pediatric Oncology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

7 Division of Newborn Medicine, Children's Hospital, Boston, MA 02115, USA.

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Charles D. Stiles

2 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Qiufu Ma

1 Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.

3 Department of Cancer Biology, Dana-Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA.

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Abstract

In the developing brain, transcription factors (TFs) direct the formation of a diverse array of neurons and glia. We identifed 1445 putative TFs in the mouse genome. We used in situ hybridization to map the expression of over 1000 of these TFs and TF-coregulator genes in the brains of developing mice. We found that 349 of these genes showed restricted expression patterns that were adequate to describe the anatomical organization of the brain. We provide a comprehensive inventory of murine TFs and their expression patterns in a searchable brain atlas database.

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Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression Analysis

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