Transposable elements have rewired the core regulatory network of human embryonic stem cells

By Galih Kunarso, N. Chia, Justin Jeyakani, Catalina Hwang, Xinyi Lu, Yun-Shen Chan, Huck-Hui Ng, Guillaume Bourque. Nature Genetics, 2010

771 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/60f510d82a805d3aee314ae020abd0f2cfe5bdf0

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Citations in the corpus

A computational pipeline for comparative ChIP-seq analyses (2011, background): “The common reference species is typically the one with the most complete genome assembly and annotation , which is Drosophila melanogaster when comparing Drosophila species 9,11 and humans when comparing mammals or vertebrates 10,12,13 .”
KRAB zinc finger proteins (2017, background): “…the tightly orchestrated transcription of TEcontaining loci during this period (Corsinotti et al., 2013; Theunissen et al., 2016; Macfarlan et al., 2012; Fort et al., 2014; Gifford et al., 2013; Goke et al., 2015; Grow et al., 2015; Kunarso et al., 2010; Xue et al., 2013; Yan et al., 2013).”
Enhancer Evolution across 20 Mammalian Species (2015, background): “, 2012), Oct4/Nanog (Kunarso et al., 2010), and NRSF (Mortazavi et al.”
Endogenous viruses: insights into viral evolution and impact on host biology (2012, result): “No less astounding are the results reported by two studie”
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, background): “GSE17611 GSM439776 primary keratinocyte p63 (13) GSM439777 primary keratinocyte p63 (13) GSM538930 primary keratinocyte p63 (13) GSE19235 GSM476650 K562 ZNF263 (14) GSM476651 K562 ZNF263 (14) GSE19013 GSM470418 MCF-7 cells ER (15) GSE12783 GSM320736 HeLa S3 STAT1 (16) GSE21200 GSM518373 embryonic st”
Induced pluripotency: history, mechanisms, and applications. (2010, background): “…extensive information is available on transcription factor binding in established human and mouse ESCs (Chen et al. 2008; J Kim et al. 2008; Kunarso et al. 2010) and iPSCs (Mikkelsen et al. 2008; Sridharan et al. 2009) that should be informative to build models on how they may act during…”
Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, neutral): “However, the rapid changes found in functional pol III binding to tRNA genes is similar to site-specific transcriptional regulators like Oct4 and CEBPA, where mouse to human comparisons show that only a minority of binding events are conserved in orthologous locations 6,7 .”
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells (2010, result): “Similar to what has been described for protein-coding gene”
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications (2010, background): “Approximately 45% of the human genome is derived from transposable elements, a major driving force in the evolution of mammalian gene regulatio”
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints (2012, background): “Such elements have been implicated in rewiring the core regulatory network of human and mouse ES cells [32].”
Insights into hominid evolution from the gorilla genome sequence (2012, result): “Consistent with previous results reporting strong CTCF binding conservatio”
The PR/SET Domain Zinc Finger Protein Prdm4 Regulates Gene Expression in Embryonic Stem Cells but Plays a Nonessential Role in the Developing Mouse Embryo (2013, background): “In some cases, mouse-specific families of transposable elements have been implicated in remodeling of the transcriptional circuitry in mouse ESCs, but the specific role of these ERV1:RLTR23 repeat regions has yet to be elucidated (55).”
Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells (2013, positive): “A gene ontology analysis of coding genes near H1-specific HERV-H/LTR7 sites revealed an enrichment of POU5F1-targeted genes (p value = 4 3 10 (15)), which is consistent with a previous study showing that NANOG and POU5F1 preferentially bind to repetitive elements (Kunarso et al., 2010).”