Published in Sci Bull (Beijing) on October 13, 2015
Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti. BMC Genomics (2017) 0.78
The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics Chromatin (2016) 0.77
Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. Biology (Basel) (2016) 0.76
Long non-coding RNA H19-mediated mouse cleft palate induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Exp Ther Med (2016) 0.75
Models of global gene expression define major domains of cell type and tissue identity. Nucleic Acids Res (2017) 0.75
Concise Review: Lessons from Naïve Human Pluripotent Cells. Stem Cells (2016) 0.75
New Frontiers in Our Understanding of Lymphatic Malformations of the Head and Neck: Natural History and Basic Research. Otolaryngol Clin North Am (2018) 0.75
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Stability and flexibility of epigenetic gene regulation in mammalian development. Nature (2007) 14.57
Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev (2005) 12.15
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol (2008) 10.97
Small RNAs as guardians of the genome. Cell (2009) 8.88
The impact of retrotransposons on human genome evolution. Nat Rev Genet (2009) 8.08
A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell (2010) 7.94
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet (1998) 7.49
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell (2009) 5.49
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature (2011) 5.42
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet (2010) 5.37
Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet (2010) 5.26
Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science (2013) 4.94
LINE-1 retrotransposition activity in human genomes. Cell (2010) 4.60
Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell (2008) 4.19
KAP1 controls endogenous retroviruses in embryonic stem cells. Nature (2010) 4.02
Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature (2012) 3.96
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell (2004) 3.85
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature (2010) 3.55
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol (2005) 3.50
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 3.08
Effects of retroviruses on host genome function. Annu Rev Genet (2008) 2.96
Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev (2001) 2.96
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol (2006) 2.93
RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev Biol (2004) 2.82
Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature (2009) 2.80
Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell (2013) 2.77
L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev (2009) 2.68
Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev (2010) 2.63
Identification of endogenous retroviral reading frames in the human genome. Retrovirology (2004) 2.58
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J (2011) 2.51
H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet (2012) 2.47
Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol (2003) 2.31
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
RYBP, a new repressor protein that interacts with components of the mammalian Polycomb complex, and with the transcription factor YY1. EMBO J (1999) 2.11
Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development. Development (2000) 2.09
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Virus particles in early mouse embryos. J Natl Cancer Inst (1973) 2.02
Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell (2014) 1.94
Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev (2011) 1.86
Trim28 is required for epigenetic stability during mouse oocyte to embryo transition. Science (2012) 1.84
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology (2011) 1.80
LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. Nat Cell Biol (2011) 1.76
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res (2006) 1.62
Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res (2005) 1.59
Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells. Cell (2015) 1.58
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol (2014) 1.55
Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability. Mol Cell Biol (2010) 1.51
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. PLoS Genet (2015) 1.49
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature (2014) 1.47
Coevolution of retroelements and tandem zinc finger genes. Genome Res (2011) 1.46
MuERV-L is one of the earliest transcribed genes in mouse one-cell embryos. Biol Reprod (2003) 1.43
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet (2014) 1.42
CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells. PLoS Genet (2006) 1.41
Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol (2010) 1.38
C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol (2015) 1.34
Spatial distribution of transcripts of the long repeated ETn sequence during early mouse embryogenesis. Proc Natl Acad Sci U S A (1985) 1.34
Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature (2015) 1.32
Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis. Genome Biol (2008) 1.31
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature (2014) 1.31
Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet (2011) 1.31
Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res (2014) 1.30
Amounts, synthesis, and some properties of intracisternal A particle-related RNA in early mouse embryos. Proc Natl Acad Sci U S A (1984) 1.30
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res (2012) 1.29
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature (2015) 1.29
Systems biology of the 2-cell mouse embryo. Cytogenet Genome Res (2004) 1.29
Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell (2014) 1.28
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology (2012) 1.27
De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development (2013) 1.23
A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS One (2008) 1.23
Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles. J Gen Virol (2008) 1.22
Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. Nat Struct Mol Biol (2015) 1.19
Rational optimization of reprogramming culture conditions for the generation of induced pluripotent stem cells with ultra-high efficiency and fast kinetics. Cell Res (2011) 1.19
Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem (2011) 1.18
Transposable elements as genetic regulatory substrates in early development. Trends Cell Biol (2013) 1.12
TIF1beta regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner. Proc Natl Acad Sci U S A (2010) 1.11
RYBP represses endogenous retroviruses and preimplantation- and germ line-specific genes in mouse embryonic stem cells. Mol Cell Biol (2012) 1.08
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin (2013) 1.08
Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell (2015) 1.06
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA (2014) 1.06
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res (2011) 1.05
Silencing of proviruses in embryonic cells: efficiency, stability and chromatin modifications. EMBO Rep (2012) 1.04
The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res (2014) 1.02
Proviral silencing in embryonic cells is regulated by Yin Yang 1. Cell Rep (2013) 1.02
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells (2012) 1.01
The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev (2015) 1.00
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biol (2014) 1.00
Alu: a parasite's parasite? Nat Genet (2003) 0.98
A repetitive elements perspective in Polycomb epigenetics. Front Genet (2012) 0.97
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell (2015) 0.97
Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells. Retrovirology (2013) 0.96
Role of Oct4 in the early embryo development. Cell Regen (Lond) (2014) 0.94
A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS One (2014) 0.94
Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res (2013) 0.94
Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42. Nucleic Acids Res (2012) 0.93
Chromatin plasticity in pluripotent cells. Essays Biochem (2010) 0.91