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Updated: May 18, 2026
12:12
Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on (TRO) Approach
Published on: March 12, 2017
Cell type-specific termination of transcription by transposable element sequences
Andrew B Conley1, I King Jordan
1School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA. king.jordan@biology.gatech.edu.
Mobile DNA
|October 2, 2012
Summary
Transposable elements (TEs) provide numerous transcription termination sites (TTS) for human genes, with TE-derived TTS being highly cell type-specific. This mechanism diversifies gene expression across different cell types and evolutionary lineages.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Transposable elements (TEs) contain sequences that regulate their own transposition, including transcription termination signals.
- Human genes often contain TEs in introns, with a bias towards antisense orientation, potentially to prevent transcription termination of host genes.
Purpose of the Study:
- To investigate the genome-wide role of TE sequences in providing transcription termination sites (TTS) for human genes.
- To characterize the orientation, cell type specificity, and chromatin environment of TE-derived TTS.
Main Methods:
- Utilized high-throughput sequencing data to identify TE-derived sequences functioning as TTS.
- Analyzed over 9,000 distinct TE-derived TTS across eight human cell types.
- Performed rarefaction curve analysis to estimate the total number of TE-derived TTS.
Main Results:
- Identified over 9,000 TE-derived TTS for 5,747 human genes, with potential for twice as many genome-wide.
- TE-derived TTS exhibit a distinct chromatin environment compared to other intragenic TEs but are more cell type-specific than canonical TTS.
- Sense-oriented TE-TTS are more efficient terminators and more common than previously thought, with Alu and LTR elements contributing distinct types of TTS.
Conclusions:
- TE sequences are a significant source of transcription termination sites for human genes.
- TE-derived TTS contribute to cell type-specific transcriptional profiles and evolutionary diversification due to their dynamic nature.
- The observed efficiency and orientation preference of TE-TTS support the model explaining the antisense bias of TEs in human gene introns.
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