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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
Published on: May 19, 2019
Many LINE1 elements contribute to the transcriptome of human somatic cells
Sanjida H Rangwala1, Lili Zhang, Haig H Kazazian
1Department of Genetics, University of Pennsylvania School of Medicine, Hamilton Walk, Philadelphia, Pennsylvania 19104, USA. sanjida@mail.med.upenn.edu
Genome Biology
|September 24, 2009
Summary
Many Long Interspersed Nuclear Element 1 (L1) retroelements are transcribed in human cells, with expression levels varying significantly between individuals. This suggests widespread L1 transcript-level polymorphism in the human population.
Area of Science:
- Genomics
- Molecular Biology
- Human Genetics
Background:
- Long Interspersed Nuclear Element 1 (L1) retroelements constitute approximately 20% of the human genome.
- Most L1 elements are considered transcriptionally inactive due to mutations or epigenetic silencing.
- The extent of L1 element expression in human somatic cells remains largely uncharacterized.
Purpose of the Study:
- To identify and characterize actively transcribed L1 elements in human somatic cells.
- To investigate the inter-individual variability of L1 element expression.
Main Methods:
- Cloning of expressed sequence tags (ESTs) from the 5' and 3' flanks of L1 elements.
- Analysis of L1 element expression in human lymphoblastoid cell lines.
- Examination of differential expression of specific L1 elements in European-American individuals and families.
Main Results:
- Isolation of ESTs corresponding to 692 distinct L1 element sites, including 410 full-length elements.
- Identification of differential expression in four full-length human-specific L1Hs subfamily elements among family members.
- Observation that most expressed L1 elements are transcribed at low frequencies.
Conclusions:
- A substantial number of L1 element sites are expressed in human somatic tissues.
- L1 element expression exhibits significant inter-individual variation.
- A high degree of transcript-level polymorphism is predicted for L1 elements across individuals.
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