The human NTT gene: Identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4⁺ T cells

We describe the cloning and characterization of the NTT gene (noncoding transcript in T cells), identified by differential display RT-PCR based on the differential presence of its transcript in a subset of activated, human CD4⁺ T-cell clones. The full-length cDNA and genomic sequences were cloned and found to produce a 17-kb transcript that is polyadenylated, but is not spliced. Consistent with the transcript's nuclear predominance, NTT has no open reading frame larger than 270 bp. It is transcribed in a select subset of CD4⁺ T-cell clones propagated in vitro. Its transcription can also be induced in freshly isolated T cells by in vitro activation with PHA or with PMA and ionomycin. In vivo, NTT transcripts are found only in activated, but not resting, T cells. Transcripts were absent in a variety of lymphoid cell lines and transformed lines from other tissues. NTT is a new member of the small group of genes including XIST (X₁-specific transcript), H19, and IPW (imprinted gene in the Prader-Willi syndrome region), which are transcribed but not translated, and may have a role in the regulation of neighboring genes. XIST, H19, and IPW exhibit monoallelic expression, but both NTT alleles are expressed in CD4⁺ T-cell clones. Southern blot and fluorescence in situ hybridization analyses show that NTT is a single-copy gene residing in chromosome 6q23-q24, near the interferon-γ receptor gene (IFN-γR). Their proximity and shared expression pattern suggest a possible functional relationship.