Developmental staging of male murine embryonic gonad by SAGE analysis

Tin-Lap Lee; Yunmin Li; Diana Alba; Queenie P. Vong; Shao-Ming Wu; Vanessa Baxendale; Owen M. Rennert; Yun-Fai Chris Lau; Wai-Yee Chan

doi:10.1016/S1673-8527(08)60109-5

Volume 36 Issue 4

Apr. 2009

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Article Navigation > Journal of Genetics and Genomics > 2009 > 36(4): 215-227

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Developmental staging of male murine embryonic gonad by SAGE analysis

doi: 10.1016/S1673-8527(08)60109-5

a
Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
b
Department of Medicine, VA Medical Center, University of California, San Francisco, CA 94121, USA
c
Department of Pediatrics, Biochemistry, Molecular & Cellular Biology, Georgetown University, Washington, DC 20007, USA

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Corresponding author: E-mail address: chanwy@mail.nih.gov (Wai-Yee Chan)
Received Date: 2009-03-08
Accepted Date: 2009-03-19
Rev Recd Date: 2009-03-18

Available Online: 2009-04-17

Publish Date: 2009-04-20

Abstract

Abstract

Despite the identification of key genes such as Sry integral to embryonic gonadal development, the genomic classification and identification of chromosomal activation of this process is still poorly understood. To better understand the genetic regulation of gonadal development, we performed Serial Analysis of Gene Expression (SAGE) to profile the genes and novel transcripts, and an average of 152,000 tags from male embryonic gonads at E10.5 (embryonic day 10.5), E11.5, E12.5, E13.5, E15.5 and E17.5 were analyzed. A total of 275,583 non-singleton tags that do not map to any annotated sequence were identified in the six gonad libraries, and 47,255 tags were mapped to 24,975 annotated sequences, among which 987 sequences were uncharacterized. Utilizing an unsupervised pattern identification technique, we established molecular staging of male gonadal development. Rather than providing a static descriptive analysis, we developed algorithms to cluster the SAGE data and assign SAGE tags to a corresponding chromosomal position; these data are displayed in chromosome graphic format. A prominent increase in global genomic activity from E10.5 to E17.5 was observed. Important chromosomal regions related to the developmental processes were identified and validated based on established mouse models with developmental disorders. These regions may represent markers for early diagnosis for disorders of male gonad development as well as potential treatment targets.
- SAGE,
- transcriptome,
- male gonads gene tag,
- novel transcripts,
- cluster analysis,
- chromosome,
- transcription hotspot

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References(50)

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