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A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages

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4 Author(s)
Garmire, L.X. ; Dept. of Bioeng., Univ. of California at San Diego, La Jolla, CA, USA ; Subramaniam, S. ; Garmire, D. ; Glass, C.K.

We present a global clustering approach to identify putative intergenic non-coding RNAs based on the RNA polymerase II and Histone 3 lysine 4 trimethylation signatures. Both of these signatures are processed from the digital sequencing tags produced by chromatin immunoprecipitation, a high-throughput massively parallel sequencing (ChIP-Seq) technology. Our method compares favorably to the comparison method. We characterize the intergenic non-coding RNAs to have conservative promoters. We predict that these nc-RNAs are related to metabolic process without lipopolysaccharides (LPS) treatment, but shift towards developmental and immune-related functions with LPS treatment. We demonstrate that more intergenic nc-RNAs respond positively to LPS treatment, rather than negatively. Using QPCR, we experimentally validate 8 out of 11 nc-RNA regions respond to LPS treatment as predicted by the computational method.

Published in:

BioInformatics and BioEngineering (BIBE), 2010 IEEE International Conference on

Date of Conference:

May 31 2010-June 3 2010