# Transcriptional regulation of domesticated transposable elements-derived promoters in human genome

> **NIH NIH R35** · WASHINGTON UNIVERSITY · 2021 · $378,000

## Abstract

Project Summary
 Transposable elements (TEs) comprise roughly half of the human genomes, and some TE subfamilies
can even contain hundreds of thousands of copies, such as LINE and SINE elements. Highly enriched
transcriptional factor binding sites in the TEs sequence enable TEs the huge regulatory potential to the host
genome. Mounting evidence suggests some of TEs escaped from epigenetic silencing and actively involved in
multiple biological processes of host genome. TEs are significant contributors to the origin of vertebrate long
non-coding RNAs, and some TEs are also found to play roles as promoters in early development and some
terminally differentiated tissues. Our recent study found that domesticated rodent-specific TEs can play roles
as promoters to initiate the tissue-specific transcription of more than 300 genes during mouse tissue
differentiation. However, how the domesticated TEs-derived promoters in the human genome to regulate the
gene transcription in distinct tissues and cell types, is not clearly characterized. For example, we do not know
how many genes can be transcribed by TEs-derived promoters in particular human tissues; we have no idea
about the usage of TEs-derived promoters in the different cell types from the same tissue; finally, how
domesticated TEs in the human genome created novel tissue-specific expression pattern of conserved protein-
coding genes, is still mystified. Thus, in this proposed project, we will focus on investigating the tissue- and
cell type-specific gene transcription controlled by the domesticated TEs-derived promoters in the
human genome. Leveraging the big data generated by large consortiums, e.g., ENCODE, Roadmap
Epigenomics, GTEx, and Human Cell Atlas, we will perform a systematic survey of the usage of domesticated
TEs-derived promoters in the human genome. Firstly, we will identify the TEs that were domesticated as
promoters of protein-coding genes and non-coding genes in the human genome, and further characterize the
tissue-level expression pattern of domesticated TEs-derived transcripts, by using our established transcripts
assemble pipeline to analyze the tissue bulk RNA-seq data generated by ENCODE and GTEx. Secondly, we
will investigate the cell-type-specific expression pattern of domesticated TEs-derived transcripts, by
reconstructing the single-cell RNA-seq data analysis with novel bioinformatics analysis tool. Finally, we will
apply comparative-genomics approaches to create the expression matrix of orthologous TEs-derived protein-
coding genes across multi-species, and construct the phylogenetic trees to explore the expression pattern
changes of TEs-derived protein-coding genes during evolution.

## Key facts

- **NIH application ID:** 10276089
- **Project number:** 1R35GM142917-01
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Bo Aber Zhang
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $378,000
- **Award type:** 1
- **Project period:** 2021-08-01 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10276089

## Citation

> US National Institutes of Health, RePORTER application 10276089, Transcriptional regulation of domesticated transposable elements-derived promoters in human genome (1R35GM142917-01). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10276089. Licensed CC0.

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