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Open Access Research article

Establishing the baseline level of repetitive element expression in the human cortex

Svitlana Tyekucheva12, Robert H Yolken3, W Richard McCombie4, Jennifer Parla4, Melissa Kramer4, Sarah J Wheelan567* and Sarven Sabunciyan3*

Author Affiliations

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, 02115, USA

2 Department of Biostatistics, Harvard School of Public Health, 677 Huntington Ave, Boston, 02115, USA

3 Department of Pediatrics, Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, 21287, USA

4 Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, USA

5 Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 550 N. Broadway, Baltimore, 21205, USA

6 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, 21205, USA

7 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, 21205, USA

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BMC Genomics 2011, 12:495  doi:10.1186/1471-2164-12-495

Published: 10 October 2011

Abstract

Background

Although nearly half of the human genome is comprised of repetitive sequences, the expression profile of these elements remains largely uncharacterized. Recently developed high throughput sequencing technologies provide us with a powerful new set of tools to study repeat elements. Hence, we performed whole transcriptome sequencing to investigate the expression of repetitive elements in human frontal cortex using postmortem tissue obtained from the Stanley Medical Research Institute.

Results

We found a significant amount of reads from the human frontal cortex originate from repeat elements. We also noticed that Alu elements were expressed at levels higher than expected by random or background transcription. In contrast, L1 elements were expressed at lower than expected amounts.

Conclusions

Repetitive elements are expressed abundantly in the human brain. This expression pattern appears to be element specific and can not be explained by random or background transcription. These results demonstrate that our knowledge about repetitive elements is far from complete. Further characterization is required to determine the mechanism, the control, and the effects of repeat element expression.