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Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

National Science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

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