Transposable elements drive species-specific and tissue-specific transcriptomes in human development
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Abstract
Background: Transposable elements (TEs) are an abundant and crucial regulatory resource in the human genome. Serving as alternative promoters, TEs can be reactivated and produce TE-initiated transcripts, which play importance roles in early development and differentiated tissues. However, the prevalence and function of TE-initiated transcription in human development are poorly characterized. Results: We identified 12,918 TE-initiated transcripts across 40 human body sites and embryonic stem cells. Among TE-initiated transcripts, 80% were activated in a tissue-specific manner. TEs with tissue-specific transcription factor binding motifs were enriched in particular tissues. Additionally, approximately half of TE-derived TSSs were primates-specific. Notably, 375 primates-specific TE-derived TSSs were found to create novel tissue-specific gene expression patterns during evolution. Conclusions: Our results characterize the global profile of TE-initiated transcription and enhance our understanding of TE contribution to the primate-specific gene regulatory networks in human development.
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Abstract
Background Transposable elements (TEs) are an abundant and crucial regulatory resource in the human genome. Serving as alternative promoters, TEs can be reactivated and produce TE-initiated transcripts, which play importance roles in early development and differentiated tissues. However, the prevalence and function of TE-initiated transcription in human development are poorly characterized.
Results
We identified 12,918 TE-initiated transcripts across 40 human body sites and embryonic stem cells. Among TE-initiated transcripts, 80% were activated in a tissue-specific manner. TEs with tissue-specific transcription factor binding motifs were enriched in particular tissues. Additionally, approximately half of TE-derived TSSs were primates-specific. Notably, 375 primates-specific TE-derived TSSs were found to create novel tissue-specific gene expression patterns during evolution.
Conclusions
Our results characterize the global profile of TE-initiated transcription and enhance our understanding of TE contribution to the primate-specific gene regulatory networks in human development.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- 5’ RACE
- 5’ rapid amplification of cDNA ends
- ADME
- Absorption, distribution, metabolism, and excretion
- BH
- Benjamini-Hochberg
- CAGE
- Cap analysis gene expression
- CDS
- Coding sequence
- ChIP
- chromatin immunoprecipitation
- ENTEx
- Epigenomes from four individuals
- FANTOM
- Functional annotation of the mammalian genome
- FDR
- False discovery rate
- GEO
- Gene expression omnibus
- GRCh38
- Genome reference consortium human build 38
- GTEx
- Genotype-Tissue Expression
- HERV
- Human endogenous retrovirus
- hSSCs
- Human adult spermatogonial stem cells
- LINE
- Long interspersed nuclear element
- lncRNA
- Long noncoding RNA
- LTR
- Long terminal repeat
- MGI
- Mouse Genome Informatics
- ONT
- Oxford Nanopore Technologies
- PacBio
- Pacific Biosciences
- RAMPAGE
- RNA annotation and mapping of promoters for the analysis of gene expression
- SINE
- Short interspersed nuclear element
- TE
- Transposable elements
- TFBS
- Transcription factor binding site
- TSS
- Transcription start site
- UMAP
- Uniform Manifold Approximation and Projection
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