Transcription Networks in Embryonic Stem Cells

Speaker

Sheng Zhong
Assistant Professor of Bioengineering
University of Illinois

Time

2-3pm, Wednesday, May 21, 2008

Location

Room 610, New Life Science Building, Peking University

Abstract

• Embryonic Stem Cells (ESCs) possess several notable properties that account for their exceptional scientific and medical importance, including development of treatments to degenerative, malignant, or genetic diseases such as diabetes, Parkinson's disease, Alzheimer's and heart failure, as well as injury due to inflammation, infection, and trauma, such as spinal cord injury. Transcriptional control is thought to be a key control mechanism for ESCs to maintain their undifferentiated state. Our group use experimental and computational methods to study the engineering principles built within the transcriptional networks of ESCs.

  In this talk, I present genomic data and computational analysis of the dynamic gene expression during the differentiation of mouse and human ESCs. We developed a novel Markov Chain Monte Carlo approach that achieved better accuracy than peer algorithms for detecting transcription regulatory elements in the mammalian genomes. Chromatin immunoprecipitation (ChIP) experiments confirmed that this method could distinguish functional and non-function transcription factor binding sites within a DNA regulatory region [1]. Hybridizing protein-DNA interaction data and gene expression data, specific interaction forms of collaborating transcription factors were identified [2]. With this theoretical development, a larger computational scheme was implemented to incorporate three types of genomic data and multiple datasets to reconstruct transcription networks [3][4]. The identified networks and experimental data served as empirical knowledge and enabled us to develop novel machine learning methods to dissect essential and non-essential components of transcription networks [5]. In particular, a small module of the transcription network that is essential in mouse ESCs but not essential for human ESCs was experimentally characterized [6].

  [1] Xie, Cai, Cha, Ng & Zhong. (2008), Genome Research, in press.
  [2] Chen, Zhu & Zhong. (2007), BMC Genomics, 9(Suppl 1):S18.
  [3] Lin, He, Ji, Shi, Davis & Zhong. (2006), Nature Biotechnology, 4(12): 6-7.
  [4] Chen & Zhong. (2008), BMC Genomics, in press.
  [5] Lu, He & Zhong. (2007), Nucleic Acids Research, 35: W105-W114
  [6] Jiang, Chan, Loh, Cai, Tong, Lim, Robson, Zhong & Ng. (2008), Nature Cell Biology, 10: 353 – 360

Bio

• Sheng Zhong received BS/BA in Mathematics and Economics from Beijing University, China. He did his Ph.D. research with Professor Wing Wong in Department of Biostatistics at Harvard University, with a Ph.D. minor in Molecular Biology. From 2004 to 2005 he was an exchange student scholar at Department of Statistics and BioX Center at Stanford University. He joined University of Illinois as an Assistant Professor of Bioengineering in 2005. He has since also held affiliate positions in Departments of Statistics, Computer Science, Biophysics and Computational Biology and Institute for Genomic Biology. He became a Faculty Fellow of National Center for Supercomputing Applications in 2007. He received Xerox Award for Faculty Research in 2008.