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
收藏
页数：12
相关论文
共 50 条
  • [21] Management and analysis of high-throughput sequence data for infectious animal diseases
    Ellis, R. J.
    Jenkins, T. L.
    REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES, 2023, 42
  • [22] Methods for the detection and assembly of novel sequence in high-throughput sequencing data
    Holtgrewe, Manuel
    Kuchenbecker, Leon
    Reinert, Knut
    BIOINFORMATICS, 2015, 31 (12) : 1904 - 1912
  • [23] Estimating the ratio of CD4+to CD8+T cells using high-throughput sequence data
    Emerson, Ryan
    Sherwood, Anna
    Desmarais, Cindy
    Malhotra, Sachin
    Phippard, Deborah
    Robins, Harlan
    JOURNAL OF IMMUNOLOGICAL METHODS, 2013, 391 (1-2) : 14 - 21
  • [24] Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats
    Cardoso, Sara D.
    Goncalves, David
    Robalo, Joana I.
    Almada, Vitor C.
    Canario, Adelino V. M.
    Oliveira, Rui F.
    MARINE GENOMICS, 2013, 11 : 11 - 16
  • [25] InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining
    Zhongjia Wu
    Yufeng Wu
    Jingyang Gao
    BMC Genomics, 21
  • [26] InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining
    Wu, Zhongjia
    Wu, Yufeng
    Gao, Jingyang
    BMC GENOMICS, 2020, 21 (Suppl 1)
  • [27] Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data
    Allentoft, Morten E.
    Schuster, Stephan C.
    Holdaway, Richard N.
    Hale, Marie L.
    McLay, Emma
    Oskam, Charlotte
    Gilbert, M. Thomas P.
    Spencer, Peter
    Willerslev, Eske
    Bunce, Michael
    BIOTECHNIQUES, 2009, 46 (03) : 195 - +
  • [28] SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data
    Epping, Lennard
    van Tonder, Andries J.
    Gladstone, Rebecca A.
    Bentley, Stephen D.
    Page, Andrew J.
    Keane, Jacqueline A.
    MICROBIAL GENOMICS, 2018, 4 (07):
  • [29] Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification
    Hagen, Charles
    Frizzi, Alessandra
    Gabriels, Suzan
    Huang, Mingya
    Salati, Raquel
    Gabor, Brad
    Huang, Shihshieh
    ARCHIVES OF VIROLOGY, 2012, 157 (05) : 907 - 915
  • [30] Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification
    Charles Hagen
    Alessandra Frizzi
    Suzan Gabriels
    Mingya Huang
    Raquel Salati
    Brad Gabor
    Shihshieh Huang
    Archives of Virology, 2012, 157 : 907 - 915
12345