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

Tyekucheva, S., Yolken, R. H., McCombie, W. R., Parla, J., Kramer, M., Wheelan, S. J., Sabunciyan, S. (2011) Establishing the baseline level of repetitive element expression in the human cortex. BMC Genomics, 12. article number 495. ISSN 1471-2164

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21985647
DOI: 10.1186/1471-2164-12-495

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.

Item Type: Paper
Uncontrolled Keywords: endogenous retroviral promoter human genome gene retrotransposon transcriptome sequences schizophrenia methylation evolution disease
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organs, tissues, organelles, cell types and functions > tissues types and functions > cerebral cortex
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal
organs, tissues, organelles, cell types and functions
organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:
Communities: CSHL labs > McCombie lab
CSHL Post Doctoral Fellows
Depositing User: Matt Covey
Date Deposited: 06 Feb 2013 16:32
Last Modified: 03 May 2013 13:30
PMCID: PMC3207997
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27171

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