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Estimating enrichment of repetitive elements from high-throughput sequence data

Daniel S Day12, Lovelace J Luquette2, Peter J Park123 and Peter V Kharchenko23*

Author Affiliations

1 Harvard-MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA

2 Center for Biomedical Informatics, Harvard Medical School, 275 Longwood Avenue, Boston, MA 02115, USA

3 Informatics Program at Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA

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Genome Biology 2010, 11:R69  doi:10.1186/gb-2010-11-6-r69

Published: 28 June 2010


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.