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Volume 703 of the series Methods in Molecular Biology pp 247-263

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RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling

  • Ritu JainAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY
  • , Tiffany DevineAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY
  • , Ajish D. GeorgeAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY
  • , Sridar V. ChitturAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY
  • , Timothy E. BaroniAffiliated withDepartment of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY
  • , Luiz O. PenalvaAffiliated withDepartment of Cellular and Structural Biology, Children’s Cancer Research Institute
  • , Scott A. TenenbaumAffiliated withCollege of Nanoscale Science and Engineering, Nanoscale Constellation, University at Albany-SUNY Email author 

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Abstract

Post-transcriptional regulation of gene expression plays an important role in complex cellular processes. Just like transcription factors regulate gene expression through combinatorial binding to multiple, physically dispersed cis elements, mRNA binding proteins can regulate the translation of functionally related gene products by coordinately binding to subsets of mRNAs. The networks of mRNA binding proteins that facilitate this fine-tuning of gene expression are poorly understood. By combining genomic technologies with standard molecular biology tools, we have helped pioneer the development of high-throughput technologies for the global analysis of subsets of mRNAs bound to RNA-binding proteins. This technique is termed RIP-Chip and stands for RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. This approach is also referred to as “ribonomic profiling” and has revealed valuable information about the workings of mRNP networks in the cell and the regulation of gene expression. In this chapter, we describe the latest advances that we have made in the RIP-CHIP technology.

Key words

Post-transcriptional gene regulation Ribonomics RIP-Chip RNA-binding Protein (RBP) Immunoprecipitation (IP) microarray microarray expression profiling array systems biology