1. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion
- Author
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Marasca, F, Sinha, S, Vadalà, R, Polimeni, B, Ranzani, V, Paraboschi, E, Burattin, F, Ghilotti, M, Crosti, M, Negri, M, Campagnoli, S, Notarbartolo, S, Sartore-Bianchi, A, Siena, S, Prati, D, Montini, G, Viale, G, Torre, O, Harari, S, Grifantini, R, Soldà, G, Biffo, S, Abrignani, S, Bodega, B, Marasca, Federica, Sinha, Shruti, Vadalà, Rebecca, Polimeni, Benedetto, Ranzani, Valeria, Paraboschi, Elvezia Maria, Burattin, Filippo Vittorio, Ghilotti, Marco, Crosti, Mariacristina, Negri, Maria Luce, Campagnoli, Susanna, Notarbartolo, Samuele, Sartore-Bianchi, Andrea, Siena, Salvatore, Prati, Daniele, Montini, Giovanni, Viale, Giuseppe, Torre, Olga, Harari, Sergio, Grifantini, Renata, Soldà, Giulia, Biffo, Stefano, Abrignani, Sergio, Bodega, Beatrice, Marasca, F, Sinha, S, Vadalà, R, Polimeni, B, Ranzani, V, Paraboschi, E, Burattin, F, Ghilotti, M, Crosti, M, Negri, M, Campagnoli, S, Notarbartolo, S, Sartore-Bianchi, A, Siena, S, Prati, D, Montini, G, Viale, G, Torre, O, Harari, S, Grifantini, R, Soldà, G, Biffo, S, Abrignani, S, Bodega, B, Marasca, Federica, Sinha, Shruti, Vadalà, Rebecca, Polimeni, Benedetto, Ranzani, Valeria, Paraboschi, Elvezia Maria, Burattin, Filippo Vittorio, Ghilotti, Marco, Crosti, Mariacristina, Negri, Maria Luce, Campagnoli, Susanna, Notarbartolo, Samuele, Sartore-Bianchi, Andrea, Siena, Salvatore, Prati, Daniele, Montini, Giovanni, Viale, Giuseppe, Torre, Olga, Harari, Sergio, Grifantini, Renata, Soldà, Giulia, Biffo, Stefano, Abrignani, Sergio, and Bodega, Beatrice
- Abstract
How gene expression is controlled to preserve human T cell quiescence is poorly understood. Here we show that non-canonical splicing variants containing long interspersed nuclear element 1 (LINE1) enforce naive CD4+ T cell quiescence. LINE1-containing transcripts are derived from CD4+ T cell-specific genes upregulated during T cell activation. In naive CD4+ T cells, LINE1-containing transcripts are regulated by the transcription factor IRF4 and kept at chromatin by nucleolin; these transcripts act in cis, hampering levels of histone 3 (H3) lysine 36 trimethyl (H3K36me3) and stalling gene expression. T cell activation induces LINE1-containing transcript downregulation by the splicing suppressor PTBP1 and promotes expression of the corresponding protein-coding genes by the elongating factor GTF2F1 through mTORC1. Dysfunctional T cells, exhausted in vitro or tumor-infiltrating lymphocytes (TILs), accumulate LINE1-containing transcripts at chromatin. Remarkably, depletion of LINE1-containing transcripts restores TIL effector function. Our study identifies a role for LINE1 elements in maintaining T cell quiescence and suggests that an abundance of LINE1-containing transcripts is critical for T cell effector function and exhaustion.
- Published
- 2022