Abstract
BackgroundAlthough 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.ResultsWe 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.ConclusionsRepetitive 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.
Highlights
Nearly half of the human genome is comprised of repetitive sequences, the expression profile of these elements remains largely uncharacterized
Roughly half of the human genome is comprised of repetitive elements; these elements range from the 6Kb LINE1 to micro and minisatellites [1,2,3,4]
Repetitive Elements are expressed in the frontal cortex In order to determine the expression level of repetitive elements in cortical tissue, mRNA was extracted from 10 post mortem frontal cortex samples, converted to cDNA and paired end High throughput sequencing (HTS) libraries were constructed
Summary
Nearly half of the human genome is comprised of repetitive sequences, the expression profile of these elements remains largely uncharacterized. Half of the human genome is comprised of repetitive elements; these elements range from the 6Kb LINE1 to micro and minisatellites [1,2,3,4]. Some are remnants of ancient germline infections and transposition events [3,5]. These include the human endogenous retroviruses which at one time presumably existed as infectious exogenous agents [6]. Endogenous retroviruses and transposons are largely inactive either through DNA methylation or histone repeat elements need to be silenced and selected against because they have adverse effects Long and Short Interspersed Nuclear Elements (LINE/SINE) are active retrotransposons which continually insert themselves into the human genome, though the vast majority of the elements have mutated beyond function [3,7,8].
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