At least half of the human genome is derived from transposable elements (TEs). These highly repetitive elements often harbor transcription factor binding sites and epigenetic regulatory signals. TEs have shaped gene regulatory networks during evolution and are often dysregulated in diseases. However, the extent to which TEs contribute sequences to functional regulatory networks, and how TE sequences evolved from parasitic DNA to functional elements, remains unclear. Answering these questions will expand our understanding of regulatory networks by including the contributions of TEs to genome-wide patterns of gene regulation. In this proposal, we introduce a novel strategy that combines computational prediction of TE derived cell type-specific enhancers with massively parallel reporter gene assays to understand the impact of TEs to cell type-specific gene regulation.
In Specific Aim 1 we plan to develop an epigenomics-based approach to detect TE-derived enhancers and their target genes. We will then test their regulatory activities using CRE-seq, a massive parallel reporter gene assay. We will bring to bear computational models that allow us to predict TE-derived enhancers. If successful, not only will we produce the largest catalog of TE-derived cell type-specific enhancers, but also we will have created a robust framework for detecting the contributions of TEs to gene regulation in any cell type or tissue.
In Specific Aim 2 we will develop a phylogenetically informed functional association assay. We will reconstruct sequences representing the evolutionary intermediates of candidate TEs and test the regulatory activities of these sequences with CRE-seq. We will address questions including whether particular classes of TEs gained TF-binding sites and then spread quickly, or whether TEs first spread and later gained TF binding sites. If successful, we will develop an understanding of what sequence features drive the functional potential of TEs, and the modes of evolution followed by different families of TEs during regulatory network evolution. Such an understanding will dramatically improve our picture of gene regulatory network evolution by including the effects of TEs, a major class of fast evolving regulatory sequences that have been largely ignored in functional genomics studies. The methods developed in this proposal will have a high impact on the utility of data produced by consortia such as ENCODE, Roadmap Epigenomics, TCGA, and other large- scale genomics projects, which currently discard most TE derived sequences from their data. Such improvement will in turn accelerate research into understanding the impact of TEs'on normal gene regulation and in human diseases.

Public Health Relevance

Transposable elements (TEs) are a special class of DNA sequences which copy themselves and hop to many different locations in the genome. TEs are often referred to as junk DNA or parasitic DNA because they spread through the genome without apparent benefit to the host, and sometimes at the expense of the host. These elements comprise a huge fraction of the DNA in mammalian genomes, including 50% of the human genome. Because of their repetitive nature they are generally discarded in most genomics studies. We recently showed that these elements often carry regulatory sequences that are co-opted by host genomes to perform normal gene regulation. Here we propose to study the extent to which TEs contribute to normal gene regulation throughout the genome and how mis-regulation of TE derived sequences contributes to disease.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
1R01HG007175-01A1
Application #
8761201
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Feingold, Elise A
Project Start
Project End
Budget Start
Budget End
Support Year
1
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Washington University
Department
Genetics
Type
Schools of Medicine
DUNS #
City
Saint Louis
State
MO
Country
United States
Zip Code
63130
Li, Daofeng; Zhang, Bo; Xing, Xiaoyun et al. (2015) Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods 72:29-40
Zhang, Bo; Xing, XiaoYun; Li, Jing et al. (2014) Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. BMC Genomics 15:868
Sundaram, Vasavi; Cheng, Yong; Ma, Zhihai et al. (2014) Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res 24:1963-76