Abstract
Although intergenic long noncoding RNAs (lincRNAs) have been linked to gene regulation in various tissues, little is known about lincRNA transcriptomes in the T cell lineages. Here we identified 1,524 lincRNA clusters in 42 T cell samples, from early T cell progenitors to terminally differentiated helper T cell subsets. Our analysis revealed highly dynamic and cell-specific expression patterns for lincRNAs during T cell differentiation. These lincRNAs were located in genomic regions enriched for genes that encode proteins with immunoregulatory functions. Many were bound and regulated by the key transcription factors T-bet, GATA-3, STAT4 and STAT6. We found that the lincRNA LincR-Ccr2-5′AS, together with GATA-3, was an essential component of a regulatory circuit in gene expression specific to the TH2 subset of helper T cells and was important for the migration of TH2 cells.
Similar content being viewed by others
Accession codes
References
Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25, 1915–1927 (2011).
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).
Rinn, J.L. & Chang, H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).
Spizzo, R., Almeida, M.I., Colombatti, A. & Calin, G.A. Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene 31, 4577–4587 (2012).
Payer, B. & Lee, J.T. X chromosome dosage compensation: how mammals keep the balance. Annu. Rev. Genet. 42, 733–772 (2008).
Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007).
Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667–11672 (2009).
Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).
Orom, U.A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).
Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358–369 (2011).
Hansen, T.B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).
Zhu, J., Yamane, H. & Paul, W.E. Differentiation of effector CD4 T cell populations. Annu. Rev. Immunol. 28, 445–489 (2010).
Vigneau, S., Rohrlich, P.S., Brahic, M. & Bureau, J.F. Tmevpg1, a candidate gene for the control of Theiler's virus persistence, could be implicated in the regulation of γ interferon. J. Virol. 77, 5632–5638 (2003).
Collier, S.P., Collins, P.L., Williams, C.L., Boothby, M.R. & Aune, T.M. Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J. Immunol. 189, 2084–2088 (2012).
Gomez, J.A. et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell 152, 743–754 (2013).
Pang, K.C. et al. Genome-wide identification of long noncoding RNAs in CD8+ T cells. J. Immunol. 182, 7738–7748 (2009).
Pagani, M. et al. Role of microRNAs and long-non-coding RNAs in CD4+ T-cell differentiation. Immunol. Rev. 253, 82–96 (2013).
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).
Pruitt, K.D., Tatusova, T., Brown, G.R. & Maglott, D.R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130–D135 (2012).
Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48–D55 (2013).
Meyer, L.R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64–D69 (2013).
Bu, D. et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 40, D210–D215 (2012).
Kong, L. et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345–W349 (2007).
Sigova, A.A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. USA 110, 2876–2881 (2013).
Vahedi, G. et al. STATs shape the active enhancer landscape of T cell populations. Cell 151, 981–993 (2012).
Wei, L. et al. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity 32, 840–851 (2010).
Szabo, S.J. et al. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100, 655–669 (2000).
Zheng, W. & Flavell, R.A. The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 89, 587–596 (1997).
Zhu, J. et al. The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses. Immunity 37, 660–673 (2012).
Yagi, R., Zhu, J. & Paul, W.E. An updated view on transcription factor GATA3-mediated regulation of Th1 and Th2 cell differentiation. Int. Immunol. 23, 415–420 (2011).
Wei, G. et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35, 299–311 (2011).
Mathew, A., Medoff, B.D., Carafone, A.D. & Luster, A.D. Cutting edge: Th2 cell trafficking into the allergic lung is dependent on chemoattractant receptor signaling. J. Immunol. 169, 651–655 (2002).
Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409–419 (2010).
Loewer, S. et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat. Genet. 42, 1113–1117 (2010).
Hosoya-Ohmura, S. et al. An NK and T cell enhancer lies 280 kilobase pairs 3′ to the gata3 structural gene. Mol. Cell. Biol. 31, 1894–1904 (2011).
Yagi, R. et al. The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-γ. Immunity 32, 507–517 (2010).
Yamane, H., Zhu, J. & Paul, W.E. Independent roles for IL-2 and GATA-3 in stimulating naive CD4+ T cells to generate a Th2-inducing cytokine environment. J. Exp. Med. 202, 793–804 (2005).
Ichihara, M. et al. Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Res. 35, e123 (2007).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Zang, C.Z. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952–1958 (2009).
Wei, G. et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity 30, 155–167 (2009).
Deaton, A.M. et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 21, 1074–1086 (2011).
Nakayamada, S. et al. Early Th1 cell differentiation is marked by a Tfh cell-like transition. Immunity 35, 919–931 (2011).
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Huang. D., W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Eden, E., Navon, R., Steinfeld, I., Lipson, D. & Yakhini, Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48 (2009).
Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
Kelley, D. & Rinn, J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 13, R107 (2012).
Hollander, M. & Wolfe, D.A. Nonparametric Statistical Methods (Wiley, 1973).
Acknowledgements
We thank the DNA Sequencing Core facility of the National Heart, Lung and Blood Institute (NHLBI) for sequencing the ChIP-Seq and RNA-Seq libraries; J. Edwards for most cell-sorting experiments; the flow cytometry core of NHLBI for some cell-sorting experiments and analysis; H. Cao for comments on the knockdown of lincRNA by shRNA; D. Northrup for critical reading and editing of the manuscript; H. Zhang for sharing experience with chemokines and chemokine receptors; P. Burr for RNA-Seq; and X. Zheng for sharing code for binomial tests. This study used the Biowulf Linux cluster of the US National Institutes of Health. Supported by the Division of Intramural Research of the NHLBI and NIAID (US National Institutes of Health).
Author information
Authors and Affiliations
Contributions
G.H., J.Z. and K.Z. conceived of the study, designed experiments and data analysis, and wrote the manuscript; Q.T., S.S. and F.Y. did experiments and edited the manuscript; G.H. analyzed the data; and T.M.E. and S.A.M. contributed RNA-Seq data for STAT4-deficient TH1 cells, STAT6-deficient TH2 cells and the corresponding wild-type TH1 and TH2 cells.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–7 and Supplementary Tables 2–6 and 8–9 (DOC 1319 kb)
Supplementary Table 1
A compilation of lincRNAs during T cell development and differentiation. (XLSX 1558 kb)
Supplementary Table 7
Th2-preferred genes affected by LincR-Ccr2-5'AS knockdown in TH2 cells (XLSX 19 kb)
Rights and permissions
About this article
Cite this article
Hu, G., Tang, Q., Sharma, S. et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat Immunol 14, 1190–1198 (2013). https://doi.org/10.1038/ni.2712
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ni.2712
- Springer Nature America, Inc.
This article is cited by
-
Targeting non-coding RNAs to overcome cancer therapy resistance
Signal Transduction and Targeted Therapy (2022)
-
Long Intergenic Noncoding RNAs Affect Biological Pathways Underlying Autoimmune and Neurodegenerative Disorders
Molecular Neurobiology (2022)
-
LncRNA GATA3-AS1 promoted invasion and migration in human endometrial carcinoma by regulating the miR-361/ARRB2 axis
Journal of Molecular Medicine (2022)
-
Emerging Role of LncRNAs in Autoimmune Lupus
Inflammation (2022)
-
Genome-wide analysis of long noncoding RNA expression profile in nasal mucosa with allergic rhinitis
BMC Medical Genomics (2021)