title: Estimating enrichment of repetitive elements from high-throughput sequence data.
abstract: We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes.
authors.affiliation: Harvard-MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Day
authors.forename: Lovelace J
authors.initials: LJ
authors.lastname: Luquette
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
mesh_terms: D000818:Animals; D001483:Base Sequence; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism; D002460:Cell Line; D030561:Databases, Nucleic Acid; D004622:Embryo, Mammalian / Q000166:cytology; D005347:Fibroblasts / Q000378:metabolism; D057166:High-Throughput Screening Assays / Q000379:methods*; D006657:Histones / Q000378:metabolism; D006801:Humans; D051379:Mice; D010802:Phylogeny; D011499:Protein Processing, Post-Translational; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D006657:Histones