Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

Georges St Laurent, Yuri Vyatkin, Denis Antonets, Maxim Ri, Yao Qi, Olga Saik, Dmitry Shtokalo, Michiel J L De Hoon, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Erik Arner, Alistair R R Forrest, Estelle Nicolas, Timothy A. McCaffrey, Piero Carninci, Yoshihide Hayashizaki, Claes R Wahlestedt, Philipp Kapranov

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16 Scopus citations

Abstract

Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlincRNAs genes likely function in cis to activate nearby genes. This effect while most pronounced in closely spaced vlincRNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlincRNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs.

Original languageEnglish (US)
Pages (from-to)3233-3252
Number of pages20
JournalNucleic Acids Research
Volume44
Issue number7
DOIs
StatePublished - Mar 21 2016

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ASJC Scopus subject areas

  • Genetics

Cite this

Laurent, G. S., Vyatkin, Y., Antonets, D., Ri, M., Qi, Y., Saik, O., Shtokalo, D., De Hoon, M. J. L., Kawaji, H., Itoh, M., Lassmann, T., Arner, E., Forrest, A. R. R., Nicolas, E., McCaffrey, T. A., Carninci, P., Hayashizaki, Y., Wahlestedt, C. R., & Kapranov, P. (2016). Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. Nucleic Acids Research, 44(7), 3233-3252. https://doi.org/10.1093/nar/gkw162