Tissue-specific usage of transposable element-derived promoters in mouse development
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RESEARCH
Open Access
Tissue-specific usage of transposable element-derived promoters in mouse development Benpeng Miao1,2, Shuhua Fu1, Cheng Lyu1, Paul Gontarz1, Ting Wang2* and Bo Zhang1* * Correspondence: twang@wustl. edu; [email protected] 2 Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA 1 Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
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. Keywords: Accessible transposable element, Mouse, Embryo development, Tissues
Background In the mammalian genome, only about 2% of DNA can be translated into protein products; the remaining ~ 98% of non-coding genome is considered to be “genomic dark matter” with unknown function [1–3]. Within these non-coding sequences, approximately 37% of the mouse genome and 45% of the human genome are derived from different kinds of transposable elements (TEs), including LINE, SINE, ERV, and DNA transposons [1–6]. TEs are highly repetitive DNA units and can reproduce themselves in the host genome. TEs generally belong to two main categories: DNA transposons, which mobilize themselves in the genome through a “cut and paste” mechanism; © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in
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