Regulatory network of microRNAs in RAW 264.7 macrophage cells

Author

Garmire, Lana X. ; Shen, Zhouxin ; Briggs, Steve ; Yeo, Gene ; Subramaniam, Shankar ; Glass, Christopher

Author_Institution

Bioeng. Dept., UC-San Diego, La Jolla, CA, USA

fYear

2010

fDate

Aug. 31 2010-Sept. 4 2010

Firstpage

6198

Lastpage

6201

Abstract

microRNAs (miRNA) play important roles in regulating immunity. Here we utilize the systems biology approach to predict the regulatory network of miRNAs among the most down-regulated genes by the lipopolysaccharides (LPS) treatment in the macrophage RAW267.4 cell line. We combine the proteome and transcriptome data sets to define 200 target genes that are significantly down-regulated by the LPS treatment. We perform the profiling of over 300 miRNAs with the RNA-Seq method. Using the complementary binding rule between the seed sequences of profiled miRNAs and the 3´UTRs of target genes, we predict genes involved in mobility, metabolism, and oxidative phosphorylation as the top targets of miRNA negative regulation.

Keywords

biochemistry; cellular biophysics; genetics; genomics; macromolecules; proteins; proteomics; RNA-Seq method; complementary binding rule; lipopolysaccharides; macrophage RAW267.4 cell line; metabolism; miRNA negative regulation; oxidative phosphorylation; proteome data set; regulatory network; seed sequences; transcriptome data set; Bioinformatics; Diseases; Genomics; Immune system; Probes; Proteins; RNA; Animals; Down-Regulation; Gene Expression Profiling; Gene Regulatory Networks; Lipopolysaccharides; Macrophages; Mice; MicroRNAs; Proteome; RNA, Messenger;

fLanguage

English

Publisher

ieee

Conference_Titel

Engineering in Medicine and Biology Society (EMBC), 2010 Annual International Conference of the IEEE

Conference_Location

Buenos Aires

ISSN

1557-170X

Print_ISBN

978-1-4244-4123-5

Type

conf

DOI

10.1109/IEMBS.2010.5627742

Filename

5627742