Genes & Genomics

, Volume 38, Issue 1, pp 69–79 | Cite as

Analysis of L1-chimeric transcripts derived from bidirectional promoter of human-specific L1

  • Songmi Kim
  • Yun-Ji Kim
  • Kyudong Han
Research Article


LINE-1s (L1s) have contributed to gene structure variation and they can affect the expression of nearby genes in the human genome. Here, we collected 35 human-specific L1s that may play a role as alternative promoters. In addition, we identified 54 L1-chimeric transcripts generated from these L1s using bioinformatics’ tools and carried out reverse transcription-PCR to analyze their expressional pattern in 20 human normal tissues and 9 human cancer tissues. Consequently, 30 L1-chimeric transcripts were experimentally confirmed. Most L1-chimeric transcripts were broadly expressed. Interestingly, we found that EST CD709363 derived from C14orf37 gene was expressed in trachea only among normal tissues, but it was expressed in several cancer tissues including brain, lung, skin, and esophagus. We also newly identified three alternative transcripts, which were not in the UCSC genome database. One alternative transcript was derived from RABGAP1L gene and the other two transcripts were from CAMK4 gene. In addition, we analyzed putative transcription binding sites within the four L1s located in the promoter region. These had several transcription factor binding sites related to promoters. Our results show that human-specific L1s could contribute to human transcriptome diversity and transcriptional gene expression in different types of human tissues.


Alternative splicing Human-specific LINE-1 (L1) L1-chimeric transcript Promoter 



The biospecimens and data used for this study were provided by the Seoul National University Hospital Human Biobank, Asan Bio-resource Center, Keimyung Human Bio-Resource Bank (KHBB), the Biobank of Chonnam National University Hwasun Hospital, and Pusan National University Hospital, members of the National Biobank of Korea (2014-9(78)), which is supported by the Ministry of Health and Welfare. All samples derived from the National Biobank of Korea were obtained with informed consent under institutional review board-approved protocols.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interests exists in this paper.

Ethical approval

Written informed consent was approved by the Institutional Review Board of the National Biobank of Korea. The experimental procedures followed the standard regulation of the Review Board.

Supplementary material

13258_2015_363_MOESM1_ESM.pptx (43 kb)
Structural scheme of human-specific L1s (A) L1 had inserted into the human genome after the divergence of human and chimpanzee lineages and generated human-specific alternative transcripts by providing new promoters. (B) A full-length L1 contains untranslated regions (UTRs) at both side of two open reading frames (ORFs) and is about 6.9 kb in length. The 5′UTR of L1 provides bidirectional promoters, which can result in L1-chimeric transcripts (PPTX 42 kb).
13258_2015_363_MOESM2_ESM.pptx (92 kb)
Sequencing analysis of L1-chimeric transcripts L1-chimeric transcripts (A) BE567753 and (B) DA456960 from sense L1s and (C) AV691164 and (D) CD709363 from antisense L1s were validated by sequencing analysis. We aligned and compared annotated sequences (upper) with analyzed sequences in this study (bottom). Gray box indicates L1 sequences (PPTX 92 kb).
13258_2015_363_MOESM3_ESM.xlsx (14 kb)
Supplementary material 3 (XLSX 13 kb)
13258_2015_363_MOESM4_ESM.xlsx (15 kb)
Supplementary material 4 (XLSX 14 kb)


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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2015

Authors and Affiliations

  1. 1.Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea

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