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Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

Nature volume 429, pages 268–274 (2004)Cite this article

Abstract

LINE-1 (L1) elements are the most abundant autonomous retrotransposons in the human genome, accounting for about 17% of human DNA. The L1 retrotransposon encodes two proteins, open reading frame (ORF)1 and the ORF2 endonuclease/reverse transcriptase. L1 RNA and ORF2 protein are difficult to detect in mammalian cells, even in the context of overexpression systems. Here we show that inserting L1 sequences on a transcript significantly decreases RNA expression and therefore protein expression. This decreased RNA concentration does not result from major effects on the transcription initiation rate or RNA stability. Rather, the poor L1 expression is primarily due to inadequate transcriptional elongation. Because L1 is an abundant and broadly distributed mobile element, the inhibition of transcriptional elongation by L1 might profoundly affect expression of endogenous human genes. We propose a model in which L1 affects gene expression genome-wide by acting as a ‘molecular rheostat’ of target genes. Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome.

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Figure 1: ORF2 sequence decreases expression.
Figure 2: Decreased RNA amounts are not due to ORF2 protein.
Figure 3: Decrease in L1 expression is dependent on length.
Figure 4: Analysis of ORF2 stability and transcription.
Figure 5: Bioinformatic analysis of L1 content in genes.
Figure 6: Models for L1-mediated modulation of gene expression/structure.

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Acknowledgements

We thank Y. Aizawa, J. Corden, J. Moran, J. Nathans, S.-L. Ooi and D. Valle for helpful discussions and critical reading of the manuscript, S. Wheelan for unpublished bioinformatics data, S. Murphy for providing a detailed nuclear run-on protocol, J. Moran for pY104, H. Kazazian for pTN201, and R. Bandaru for help with statistical analysis. This work was supported by the NIH (J.D.B.) and the Medical Scientist Training Program (J.S.H.).

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  1. Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA

    Jeffrey S. Han & Jef D. Boeke

  2. Biogen, Inc., Cambridge, Massachusetts, 02142, USA

    Suzanne T. Szak

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Correspondence to Jef D. Boeke.

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Supplementary information

Supplementary Methods (DOC 27 kb)

Supplementary Figure Legends (DOC 23 kb)

Supplementary Table S1

The sequence of oligonucleotides used. (PDF 93 kb)

Supplementary Figures S1 to S4

Supplementary Figure S1: The structure of the test expression reporter used is depicted for each lane of each figure in this manuscript; Supplementary Figure S2: Northern blot analysis of total RNA in different cells; Supplementary Figure S3: Protein levels in ORF2 deletion constructs; Supplementary Figure S4: Comparison of GFPlacZ and GFPORF2 RNA half-life by real time RT-PCT. (PDF 2444 kb)

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Han, J., Szak, S. & Boeke, J. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429, 268–274 (2004). https://doi.org/10.1038/nature02536

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