Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells.

PLoS Computational Biology
Judith ReichmannIan R Adams

Abstract

Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and ...Continue Reading

References

Jan 1, 1990·Annual Review of Cell Biology·N Kleckner
Jan 1, 1996·Methods in Enzymology·D G HigginsT J Gibson
Nov 29, 1996·Cell·J V MoranH H Kazazian
Jul 17, 1998·Current Opinion in Structural Biology·J Jurka
Nov 30, 2000·American Journal of Physiology. Gastrointestinal and Liver Physiology·Z DongB M Evers
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Apr 5, 2002·Genome Research·W James Kent
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
May 5, 2004·Genome Research·Ewan BirneyRichard Durbin
Aug 20, 2004·Nature·Déborah Bourc'his, Timothy H Bestor
May 14, 2005·Journal of Molecular Biology·Marie Dewannieux, Thierry Heidmann
Jul 8, 2005·Applied and Environmental Microbiology·Zhili HeJizhong Zhou
Jan 28, 2006·PLoS Genetics·Irina A MaksakovaDixie L Mager
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Jul 11, 2006·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Akiko TsumuraMasaki Okano
Aug 29, 2006·Nature Structural & Molecular Biology·Nuo Yang, Haig H Kazazian
Aug 31, 2006·Molecular and Cellular Biology·Gordin ZupkovitzChristian Seiser
Feb 17, 2007·Trends in Biochemical Sciences·Rebecca K HolmesKate N Bishop
Mar 21, 2007·Genes & Development·Elizabeth P MurchisonGregory J Hannon
May 10, 2007·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Jan 16, 2008·Molecular and Cellular Biology·Lakshmi N ChangolkarJohn R Pehrson
Feb 23, 2008·Nature Reviews. Molecular Cell Biology·Xiang-Jiao Yang, Edward Seto
Mar 18, 2008·Molecular Phylogenetics and Evolution·Wei Zhang, Zhirong Sun
May 10, 2008·Bioinformatics·Pan DuSimon M Lin
Aug 30, 2008·Cell·Daniel B StetsonRuslan Medzhitov
Oct 16, 2008·Cell·John L Goodier, Haig H Kazazian
Apr 21, 2009·Nature Genetics·Geoffrey J FaulknerPiero Carninci
Sep 10, 2009·Nature Reviews. Molecular Cell Biology·Jeffrey A Simon, Robert E Kingston

❮ Previous
Next ❯

Citations

Dec 26, 2013·Genome Biology·Donncha S DunicanRichard R Meehan
Sep 21, 2013·Cellular and Molecular Life Sciences : CMLS·James H CrichtonIan R Adams
Apr 22, 2014·Carcinogenesis·Bin Xue, Lin He
Jan 9, 2014·Cellular and Molecular Life Sciences : CMLS·Ryoiti Kiyama, Yun Zhu
Jul 19, 2014·Annual Review of Genetics·Sandra R RichardsonGeoffrey J Faulkner
Dec 12, 2013·BMC Genomics·Veena P GnanakkanKathleen H Burns
Jun 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Patrick L CollinsEugene M Oltz
Mar 25, 2014·Journal of Genetics and Genomics = Yi Chuan Xue Bao·James H CrichtonIan R Adams
May 24, 2013·Biochemical Society Transactions·Catherine M RoseAmanda J Drake
May 30, 2015·Retrovirology·Luisa Robbez-Masson, Helen M Rowe
Aug 5, 2015·PloS One·Mrigaya MehraRavi Shankar
Oct 25, 2012·PLoS Genetics·John L GoodierHaig H Kazazian
Jun 8, 2017·Stem Cell Reports·Jamie A HackettM Azim Surani
Dec 17, 2014·Nature Communications·William A PastorSteven E Jacobsen
Apr 19, 2017·Journal of Experimental Botany·James W CooperChristine H Foyer
Jul 15, 2017·PLoS Genetics·James H CrichtonIan R Adams
Nov 23, 2016·Development·Jose L Garcia-PerezIan R Adams
Dec 12, 2012·Journal of Virology·Natalia ShalginskikhRichard A Katz
Oct 21, 2016·Stem Cells·Denise Catherine MilesMaarten van Lohuizen
Jun 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mathieu BoulardTimothy H Bestor
Sep 9, 2020·Nature Structural & Molecular Biology·Akihiko SakashitaSatoshi H Namekawa
Jun 25, 2020·Nature Reviews. Genetics·Sophie Lanciano, Gael Cristofari
Jan 24, 2019·Frontiers in Immunology·Olivier TaboneJulien Textoris
May 23, 2015·PLoS Genetics·John L GoodierHaig H Kazazian
May 27, 2021·Molecular Genetics & Genomic Medicine·Faisal A AlzahraniLamjed Mansour
Dec 19, 2012·Molecular Cell·Michelle C WardDuncan T Odom

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE30461
GSE27844

Methods Mentioned

BETA
RNA-seq
ChIP-seq
immunoprecipitation
PCR
RNAseq

Software Mentioned

MEGA4
ClustalW
Bioconductor
UCSC genome browser
affy Bioconductor
limma
R Bioconductor package
Perl script
Genewise
Repeatmasker

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.