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Tissue-specific usage of transposable element-derived promoters in mouse development
- Source :
- Genome Biology, Genome Biology, Vol 21, Iss 1, Pp 1-25 (2020)
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
Abstract
- Background Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology. Results We examine the epigenetic dynamics of mouse TEs during the development of five tissues: intestine, liver, lung, stomach, and kidney. We found that TEs are associated with over 20% of open chromatin regions during development. Close to half of these accessible TEs are only activated in a single tissue and a specific developmental stage. Most accessible TEs are rodent-specific. Across these five tissues, 453 accessible TEs are found to create the transcription start sites of downstream genes in mouse, including 117 protein-coding genes and 144 lincRNA genes, 93.7% of which are mouse-specific. Species-specific TE-derived transcription start sites are found to drive the expression of tissue-specific genes and change their tissue-specific expression patterns during evolution. Conclusion Our results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.
- Subjects :
- Transposable element
Genome evolution
lcsh:QH426-470
Mouse
Embryonic Development
Biology
Embryo development
Genome
Mice
Species Specificity
Accessible transposable element
Animals
Epigenetics
Promoter Regions, Genetic
lcsh:QH301-705.5
Gene
Research
Gene Expression Regulation, Developmental
food and beverages
Promoter
Human genetics
Cell biology
Chromatin
lcsh:Genetics
Tissues
lcsh:Biology (General)
DNA Transposable Elements
Transcription Factors
Subjects
Details
- ISSN :
- 1474760X
- Volume :
- 21
- Database :
- OpenAIRE
- Journal :
- Genome Biology
- Accession number :
- edsair.doi.dedup.....fe770c8c923aa380534bc42fadcd51fb