Functional analysis of transposable elements

Almost all the cells of the human body contain the same DNA, and thus the same set of genes. Nevertheless, they are able to develop different structures and functions. This is because not all genes are turned on or expressed in a given cell. The subset of genes that are expressed in each cell is controlled by a process known as gene regulation. Instructions determining when, where, and how strongly a gene will be expressed are encoded by DNA sequences called cis-regulatory elements. These sequences are recognized and bound by transcription factor proteins. Transcription factor proteins act as master switches, turning genes on and off. Cis-regulatory elements and genes are hidden within a high-order structure, the chromatin, consisting of the DNA wrapped around histone proteins. The chromatin packs the DNA into a volume small enough to fit into the cell nucleus. For the cells machinery to express the genes, the chromatin must first be unfolded. Chromatin folding and unfolding is associated with the addition of chemical tags or epigenetic marks to specific positions of the DNA or the histones. Combinations of epigenetic marks are assumed to determine the role of cis-regulatory elements in turning genes on and off. Epigenetic marks have been the study focus of several international research projects. Thus, the Encyclopedia of DNA Elements (ENCODE) has catalogued the epigenetic marks observed in different cell types using methods such as chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Even if the approach has proven fruitful, the analysis of the data generated by ChIP-seq is challenging for repetitive DNA sequences. And unfortunately, approximately two thirds of the DNA in a human cell comprises sequences that are present in multiple copies. Many of such sequences are transposable elements or jumping genes, i.e., DNA sequences that can move (jump) or introduce copies of themselves into a different location of the DNA. Although transposable elements were once written off as junk, they are now appreciated for their functional roles in a variety of biological phenomena. Unfortunately, the repetitive nature of transposable elements makes them not amenable to standard bioinformatics tools. For this reason, and despite considerable research in the last few years, our knowledge of transposable elements remains limited. By developing a new bioinformatics approach that aims at characterizing groups of similar transposable elements rather than individual transposable elements this project is set to identify transposable elements with cis-regulatory function.

Transposable elements, or "jumping genes", are mobile pieces of DNA comprising roughly half of the human genome. Because they can cut and paste or copy and paste themselves throughout the genome, their sequences are repetitive, meaning a particular instance of a transposable element in the genome is very similar to another instance. Consequently, sequencing data arising from transposable elements cannot be definitely attributed to a specific location in the genome. Transposable elements were once considered genomic "parasites" or "junk". This view was popularized by a 1972 paper by Japanese-American geneticist and evolutionary biologist Susumu Ohno that suggested that transposable elements might be non-functional. Today, we recognize that transposable elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. RNA-seq and ChIP-seq have become essential tools for characterizing the genome. RNA-seq ("RNA sequencing") is a large-scale technique used to peek inside a cell and see what genes are turned on or off. Similarly, ChIP-seq ("Chromatin Immunoprecipitation Sequencing") has emerged as a powerful large-scale technique to identify where specific proteins bind to DNA. DNA-binding proteins perform a variety of important functions that are essential for the cell. Particularly interesting are the interactions between the DNA and histone proteins, which are fundamental in DNA organization and compaction. Histones can be chemically modified and these modifications -called epigenetic modifications- act like tags that tell the cell whether a gene should be turned on or off. Therefore, knowing where histones bind in DNA and how they are modified allows us to decode the instructions written alongside our genes. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. Our research shows that systematically excluding data arising from repetitive genomic sequences -as it is typically done- has consequences. For example, it leads to the underrepresentation of recently active transposable elements and the underestimation of the activity of certain gene families with hihgly similar genes, like many involved in our immune system. To address this issue, we developed a computational tool called "Transposable Element Enrichment Estimator" (T3E). Rather than rather focusing on individual instances of transposable elements in the genome, T3E groups different genomic instances according to their sequences to account for the ambiguity in the origin of the data. We are currently applying this tool to obtain a more complete picture of our genomes. By enabling a more comprehensive analysis of transposable elements, T3E opens doors to a deeper understanding of their role in gene regulation, evolution, and human health.