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Using RNase sequence specificity to refine the identification of RNA-protein binding regions

Authors
  • Wang, Xin1, 2, 3
  • Wang, Guohua1, 2, 4
  • Shen, Changyu1
  • Li, Lang1
  • Wang, Xinguo5
  • Mooney, Sean D2, 6
  • Edenberg, Howard J6, 7, 8
  • Sanford, Jeremy R7
  • Liu, Yunlong1, 2, 8
  • 1 Indiana University School of Medicine, Division of Biostatistics Department of Medicine, Indianapolis, IN, 46202, USA , Indianapolis
  • 2 Indiana University School of Medicine, Center for Computational Biology and Bioinformatics, Indianapolis, IN, 46202, USA , Indianapolis
  • 3 Harbin Engineering University, College of Automation, Harbin, Heilongjiang, 150001, China , Harbin
  • 4 Harbin Institute of Technology, School of Computer Science and Technology, Harbin, Heilongjiang, 150001, China , Harbin
  • 5 Indiana University, The Center for Genomics and Bioinformatics, Bloomington, IN, 47405, USA , Bloomington
  • 6 Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN, 46202, USA , Indianapolis
  • 7 Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, Indianapolis, IN, 46202, USA , Indianapolis
  • 8 Indiana University School of Medicine, Center for Medical Genomics, Indianapolis, IN, 46202, USA , Indianapolis
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Mar 20, 2008
Volume
9
Issue
Suppl 1
Identifiers
DOI: 10.1186/1471-2164-9-S1-S17
Source
Springer Nature
Keywords
License
Yellow

Abstract

Massively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical assays, such as cross-linking immunoprecipitation (CLIP), provides a genome-wide method to detect the sites at which proteins bind DNA or RNA. In a CLIP-pyrosequencing experiment, the resolutions of the detected protein binding regions are partially determined by the length of the detected RNA fragments (CLIP amplicons) after trimming by RNase digestion. The lengths of these fragments usually range from 50-70 nucleotides. Many genomic regions are marked by multiple RNA fragments. In this paper, we report an empirical approach to refine the localization of protein binding regions by using the distribution pattern of the detected RNA fragments and the sequence specificity of RNase digestion. We present two regions to which multiple amplicons map as examples to demonstrate this approach.

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