Estimating enrichment of repetitive elements from high-throughput sequence data

被引：77

作者：

Day, Daniel S. ^{[1
,2
]}

Luquette, Lovelace J. ^{[1
]}

Park, Peter J. ^{[1
,2
,3
]}

Kharchenko, Peter V. ^{[1
,3
]}

机构：

[1] Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA

[2] Harvard MIT Hlth Sci & Technol, Cambridge, MA 02139 USA

[3] Childrens Hosp, Informat Program, Boston, MA 02115 USA

来源：

GENOME BIOLOGY | 2010年 / 11卷 / 06期

关键词：

H3; LYSINE-9; METHYLATION; EMBRYONIC STEM-CELLS; CHIP-SEQ EXPERIMENTS; ENDOGENOUS RETROVIRUSES; TRANSPOSABLE ELEMENTS; HUMAN GENOME; HISTONE H3; TRANSCRIPTIONAL NETWORK; SATELLITE REPEATS; DNA METHYLATION;

D O I：

10.1186/gb-2010-11-6-r69

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

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.

引用

页数：12

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