Estimating enrichment of repetitive elements from high-throughput sequence data

被引：0
作者：
Daniel S Day
Lovelace J Luquette
Peter J Park
Peter V Kharchenko
机构：
[1] Harvard-MIT Health Sciences and Technology,
[2] Center for Biomedical Informatics,undefined
[3] Harvard Medical School,undefined
[4] Informatics Program at Children's Hospital,undefined
来源：
Genome Biology | / 11卷
关键词：
Repetitive Element; Neural Progenitor Cell; Repeat Type; Mouse Embryonic Fibroblast Cell; Canonical Sequence;
D O I：
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学科分类号：
摘要：
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.
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