Abstract

Long noncoding RNAs are emerging as important regulators of cellular functions, but little is known of their role in the human immune system. Here we investigated long intergenic noncoding RNAs (lincRNAs) in 13 subsets of T lymphocytes and B lymphocytes by next-generation sequencing–based RNA sequencing (RNA-seq analysis) and de novo transcriptome reconstruction. We identified over 500 previously unknown lincRNAs and described lincRNA signatures. Expression of linc-MAF-4, a chromatin-associated lincRNA specific to the TH1 subset of helper T cells, was inversely correlated with expression of MAF, a TH2-associated transcription factor. Downregulation of linc-MAF-4 skewed T cell differentiation toward the TH2 phenotype. We identified a long-distance interaction between the genomic regions of the gene encoding linc-MAF-4 and MAF, where linc-MAF-4 associated with the chromatin modifiers LSD1 and EZH2; this suggested that linc-MAF-4 regulated MAF transcription through the recruitment of chromatin modifiers. Our results demonstrate a key role for lincRNA in T lymphocyte differentiation.

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Acknowledgements

We thank C. Cheroni for support in statistical analysis; M. Moro and M.C. Crosti for technical assistance with cell sorting; S. Biffo, D. Gabellini, P. Della Bona and A. Lanzavecchia for discussions and critical revision of the manuscript; B.J. Haas and A. Dobin for help with the integration of genome-guided Trinity with STAR aligner; the Istituto Nazionale Genetica Molecolare Bioinformatics Facility for support; and the Google Summer of Code Project for supporting C. Wheeler in the development of a plug-in used here for the open-source bioinformatics library BioRuby that adds support for the multiple-alignment format (https://github.com/csw/bioruby-maf). Supported by Il Consiglio Nazionale delle Ricerche–Il Ministero dell'Istuzione dell'Universita e della Ricerca (EPIGEN), Fondazione Cariplo (2013-0955), the Associazione Italiana per la Ricerca sul Cancro (IG2013-ID14596), the European Research Council (269022 to S.A.; 617978 to M.P.) and Fondazione Romeo ed Enrica Invernizzi.

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Author notes

    • Valeria Ranzani
    • , Grazisa Rossetti
    • , Ilaria Panzeri
    • , Alberto Arrigoni
    •  & Raoul J P Bonnal

    These authors contributed equally to this work.

Affiliations

  1. Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milano, Italy.

    • Valeria Ranzani
    • , Grazisa Rossetti
    • , Ilaria Panzeri
    • , Alberto Arrigoni
    • , Raoul J P Bonnal
    • , Serena Curti
    • , Paola Gruarin
    • , Elena Provasi
    • , Elisa Sugliano
    • , Raffaele De Francesco
    • , Jens Geginat
    • , Beatrice Bodega
    • , Sergio Abrignani
    •  & Massimiliano Pagani
  2. IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.

    • Maurizio Marconi

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Contributions

V.R., A.A. and R.J.P.B. set up all the bioinformatics pipelines, performed the bioinformatics analyses and contributed to the preparation of the manuscript; G.R. and I.P. designed and performed the main experiments, analyzed the data and contributed to the preparation of the manuscript; S.C., P.G., E.P., E.S. and B.B. performed experiments and analyzed the data; M.M., R.D.F. and J.G. discussed results, provided advice and commented on the manuscript; S.A. and M.P. designed the study, supervised research and wrote the manuscript; and all authors discussed and interpreted the results.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sergio Abrignani or Massimiliano Pagani.

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    Supplementary Table 2

    GSEA gene lists CD4+ TH1 and TH2 specific genes

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DOI

https://doi.org/10.1038/ni.3093

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