title: Massive contribution of transposable elements to mammalian regulatory sequences.
abstract: Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes.
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, 60 Biopolis Street, 138672, Singapore.
authors.forename: Nirmala Arul
authors.initials: NA
authors.lastname: Rayan
authors.affiliation: Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA.
authors.forename: Ricardo C H
authors.initials: RCH
authors.lastname: Del Rosario
authors.affiliation: Computational and Systems Biology, Genome Institute of Singapore, #02-01 Genome, 60 Biopolis Street, 138672, Singapore. Electronic address: prabhakars@gis.a-star.edu.sg.
authors.forename: Shyam
authors.initials: S
authors.lastname: Prabhakar
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics*; D016678:Genome; D006801:Humans; D008322:Mammals / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements
keywords: Primate-specific; Regulatory elements; Transposable element functionalization; Transposons