The recently finished human genome sequences provide a framework of the entire genetic information. However the functional contents carried within the genome are not completely defined. Current technologies are inefficient to complete this task. Our goal is to develop a new sequencing strategy to define the full transcript units and the cis-regulatory elements in the human genome. The concept of this strategy is to extract short 5' and 3' tags of full length transcript into a ditag structure for efficient sequencing. This ditag sequencing strategy has the potential to accurately and efficiently map all full-length transcripts in the genome. When coupled with the chromatin immunoprecipitation (CHIP) technology, this approach can also help to localize genome-wide cis-regulatory elements of transcription factors.
The specific aims i n this proposal are to: ? 1) Develop a robust ditag sequencing strategy to map all transcript units in the human genome. We have developed a set of prototype methods that extract and map the 5' and 3' tag of transcript sequences to the genome. We will further refine the methodologies of ditag stratagy to become a robust platform for complete transcriptome characterization and genome annotation. ? 2) Expand the capacity of ditag sequencing for genome-wide localization of transcription factor binding sites. The concept of ditag sequencing is directly applicable for analyzing any DNA fragments. We will develop an open system to analyze ChIP enriched DNA fragments for global localization of transcription factor binding sites. ? 3) Validate the ditag sequencing approach in a conditional p53 system. We seek to identify all genes that are responsive to p53, and to ascertain through GIS-ChIP cloning and through our novel GIS analysis strategy all possible cis-regulatory fragments. ? ?

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZHG1-HGR-P (O2))
Program Officer
Feingold, Elise A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Genome Institute of Singapore
Zip Code
Zhang, Yubo; Wong, Chee-Hong; Birnbaum, Ramon Y et al. (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504:306-310
Goh, Yufen; Fullwood, Melissa J; Poh, Huay Mei et al. (2012) Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation. J Vis Exp :
Handoko, Lusy; Xu, Han; Li, Guoliang et al. (2011) CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43:630-8
Laurent, Louise; Wong, Eleanor; Li, Guoliang et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20:320-31
Li, Guoliang; Fullwood, Melissa J; Xu, Han et al. (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22
Schnetz, Michael P; Handoko, Lusy; Akhtar-Zaidi, Batool et al. (2010) CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet 6:e1001023
Ghisletti, Serena; Barozzi, Iros; Mietton, Flore et al. (2010) Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32:317-28
Fullwood, Melissa J; Han, Yuyuan; Wei, Chia-Lin et al. (2010) Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol Chapter 21:Unit 21.15.1-25
Fullwood, Melissa J; Wei, Chia-Lin; Liu, Edison T et al. (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19:521-32
Rosario, Karyna; Nilsson, Christina; Lim, Yan Wei et al. (2009) Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11:2806-20

Showing the most recent 10 out of 23 publications