An Integrative Developmental Genomics and Systems Biology Approach to Identify an in Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

Wenqing Jean Lee, Sumantra Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems biology approach offers to complement the reductionist methodology of current developmental biology and provide a more comprehensive and integrated view of the interrelationships of complex regulatory networks that occur during organogenesis. By combining cell type-specific transcriptome analysis and in vivo ChIP-Seq of the Sox trio using mouse embryos, we provide evidence for the direct control of Sox5 and Sox6 by the transcriptional trio in the murine model and by Morpholino knockdown in zebrafish and demonstrate the novel role of Tgfb2, Fbxl18, and Tle3 in formation of Sox5, Sox6, and Sox9 dependent tissues. Concurrently, a complete embryonic gene regulatory network has been generated, identifying a wide repertoire of genes involved and controlled by the Sox trio in the intricate process of normal embryogenesis.

Original languageEnglish
Article number8932583
JournalBioMed Research International
Volume2017
DOIs
Publication statusPublished - 1 Jan 2017

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Developmental Biology
Systems Biology
Organogenesis
Gene Regulatory Networks
Genomics
Embryonic Development
Embryonic Structures
Genes
Morpholinos
Gene Expression Profiling
Zebrafish
Transcription Factors
Tissue

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

An Integrative Developmental Genomics and Systems Biology Approach to Identify an in Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos. / Lee, Wenqing Jean; Chatterjee, Sumantra; Yap, Sook Peng; Lim, Siew Lan; Xing, Xing; Kraus, Petra; Sun, Wenjie; Hu, Xiaoming; Sivakamasundari, V.; Chan, Hsiao Yun; Kolatkar, Prasanna R.; Prabhakar, Shyam; Lufkin, Thomas.

In: BioMed Research International, Vol. 2017, 8932583, 01.01.2017.

Research output: Contribution to journalArticle

Lee, WJ, Chatterjee, S, Yap, SP, Lim, SL, Xing, X, Kraus, P, Sun, W, Hu, X, Sivakamasundari, V, Chan, HY, Kolatkar, PR, Prabhakar, S & Lufkin, T 2017, 'An Integrative Developmental Genomics and Systems Biology Approach to Identify an in Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos', BioMed Research International, vol. 2017, 8932583. https://doi.org/10.1155/2017/8932583
Lee, Wenqing Jean ; Chatterjee, Sumantra ; Yap, Sook Peng ; Lim, Siew Lan ; Xing, Xing ; Kraus, Petra ; Sun, Wenjie ; Hu, Xiaoming ; Sivakamasundari, V. ; Chan, Hsiao Yun ; Kolatkar, Prasanna R. ; Prabhakar, Shyam ; Lufkin, Thomas. / An Integrative Developmental Genomics and Systems Biology Approach to Identify an in Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos. In: BioMed Research International. 2017 ; Vol. 2017.
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