Abstract
Repetitive elements (RE) constitute the majority of the human genome and have a range of functions both structural and regulatory on genomic function and gene expression. RE overexpression has been observed in several neurodegenerative diseases, consistent with the observation of aberrant expression of RE posing a mutagenic threat. Despite reports that associate RE expression with PD no study has comprehensively analysed the role of these elements in the disease. This study presents the first genome-wide analysis of RE expression in PD to date. Analysis of RNA-sequencing data of 12 PD patients and 12 healthy controls identified tissue-specific expression differences and more significantly, differential expression of four satellite elements; two simple satellite III (repName = CATTC_n and _GAATG_n) a high-copy satellite II (HSATII) and a centromeric satellite (ALR_Alpha) in the blood of PD patients. In support of the growing body of recent evidence associating REs with neurodegenerative disease, this study highlights the potential importance of characterization of RE expression in such diseases.
Highlights
Parkinson’s disease (PD) is the second most common progressive neurodegenerative condition[1], with late-onset forms of PD affecting around 3–4% of individuals over the age of 802,3
In the blood we identified that satellite elements are upregulated in PD patients and most significantly that a group of satellite elements, which are a group of elements that have been collectively associated with genome instability[26,28], are significantly differentially expressed
Our data is in agreement with that reported by Faulkner et al who performed a comprehensive Repetitive element (RE) analysis using cap analysis gene expression (CAGE) sequencing data and determined that in human tissue, on average around 20% of all CAGE tags detected were mapped to REs and overall RE expression varied significantly between tissue[25]
Summary
Parkinson’s disease (PD) is the second most common progressive neurodegenerative condition[1], with late-onset forms of PD affecting around 3–4% of individuals over the age of 802,3. It is characterized pathologically by the degeneration and loss of the dopaminergic neurons in the substantia nigra and the presence of a-synuclein aggregates called Lewy bodies in the central nervous system (CNS)[3,4]. TEs constitute ~45% of the human genome and can be subdivided based on their method of replication, i.e via an RNA (retrotransposable elements (RTEs)) or DNA (DNA transposons) intermediate. For a detailed review of the impact of RTE in the human genome and their role in disease see[15] and an overview the classification of RE is shown in (Fig. 1)
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