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

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RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 703))

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.

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Acknowledgments

We would like to acknowledge the expert technical help from David Frank and Marcy Kuentzel of the microarray core, Center for Functional Genomics, University at Albany-SUNY and input from the other Tenenbaum Lab members. This work was supported in part by NIH grant U01HG004571 to SAT from the NHGRI.

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Authors and Affiliations

  1. Department of Biomedical Sciences, School of Public Health, Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY, Rensselaer, NY, USA

    Ritu Jain, Tiffany Devine, Ajish D. George, Sridar V. Chittur & Timothy E. Baroni

  2. Department of Cellular and Structural Biology, Children’s Cancer Research Institute, San Antonio, TX, USA

    Luiz O. Penalva

  3. College of Nanoscale Science and Engineering, Nanoscale Constellation, University at Albany-SUNY, Rensselaer, NY, USA

    Scott A. Tenenbaum

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  1. Ritu Jain
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  2. Tiffany Devine
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  3. Ajish D. George
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  4. Sridar V. Chittur
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  5. Timothy E. Baroni
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  6. Luiz O. Penalva
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Correspondence to Scott A. Tenenbaum .

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  1. The Panum Institute, Dept. of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200N, Denmark

    Henrik Nielsen

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Jain, R. et al. (2011). RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. In: Nielsen, H. (eds) RNA. Methods in Molecular Biology, vol 703. Humana Press. https://doi.org/10.1007/978-1-59745-248-9_17

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  • DOI: https://doi.org/10.1007/978-1-59745-248-9_17

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-913-0

  • Online ISBN: 978-1-59745-248-9

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