TE composition of human long noncoding RNAs and their expression patterns in human tissues
High-throughput sequencing analyses have revealed that transposable elements (TEs) comprise approximately half of the human genome and frequently involved in genomic rearrangements and instability by various mechanisms. Interestingly, many noncoding RNAs (ncRNAs) contain TEs and the TE-containing ncRNAs that have been implicated in cellular processes and various diseases in mammals. In this study, we retrieved 94 human long noncoding RNAs (lncRNAs; >200 nucleotides in length) from lncRNAdb and analyzed TEs which are embedded within the lncRNAs, focusing on their chromosomal distribution. The result showed that TEs occupy ~27 % of the lncRNA transcripts in mass and lncRNA containing TEs are enriched in human chromosome 11. We further analyzed subfamily of the TEs and found that most of the TEs belong to AluSx and L1 which are the most successful TE subfamilies in the human genome. Numerous lncRNAs have been reported to be expressed in a cell-type specific manner. Thus, using reverse transcription PCR with specific primers for the lncRNAs, we examined their expression pattern in human normal tissues and cancer cells. Most of the lncRNAs were universally amplified from 20 different types of normal human tissues but some of them displayed tissue-specific expression. Especially, 11 lncRNAs were expressed only in human cancer cells, implying the possibility of their involvement in carcinogenesis.
KeywordsExpression pattern Gene composition Human genome Long noncoding RNAs Transposable elements
The present work was conducted with funding from the Research Fund of Dankook University in 2013.
Conflict of interest
The authors declare that there is no conflict of interests exists in this paper.
- Alfano G, Vitiello C, Caccioppoli C, Caramico T, Carola A, Szego MJ, McInnes RR, Auricchio A, Banfi S (2005) Natural antisense transcripts associated with genes involved in eye development. Hum Mol Genet 14:913-923Google Scholar
- Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19:454–492Google Scholar
- Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR et al (2011) SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17:878–891Google Scholar
- Cartault F, Munier P, Benko E, Desguerre I, Hanein S, Boddaert N, Bandiera S, Vellayoudom J, Krejbich-Trotot P, Bintner M et al (2012) Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy. Proc Natl Acad Sci USA 109:4980–4985PubMedCentralCrossRefPubMedGoogle Scholar
- Delgado André N, De Lucca FL (2008) Non-coding transcript in T cells (NTT): antisense transcript activates PKR and NF-kappaB in human lymphocytes. Blood Cells Mol Dis 40:227–232Google Scholar
- Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
- Hernandez A, Garcia B, Obregon MJ (2007) Gene expression from the imprinted Dio3 locus is associated with cell proliferation of cultured brown adipocytes. Endocrinology 148:3968–3976Google Scholar
- Liu AY, Torchia BS, Migeon BR, Siliciano RF (1997) The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics 39:171–184Google Scholar
- Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S et al (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 42:1113–1117Google Scholar
- Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:45–58Google Scholar
- Vandeweyer G, Reyniers E, Wuyts W, Rooms L, Kooy RF (2011) CNV-WebStore: online CNV analysis, storage and interpretation. BMC Bioinformatics 12:4Google Scholar
- Wevrick R, Francke U (1997) An imprinted mouse transcript homologous to the human imprinted in Prader-Willi syndrome (IPW) gene. Hum Mol Genet 6:325–332Google Scholar
- Yan MD, Hong CC, Lai GM, Cheng AL, Lin YW, Chuang SE (2005) Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 14:1465–1474Google Scholar