ArticlePloS one2011
Prediction of transposable element derived enhancers using chromatin modification profiles.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.Genome biology · 2021Article
- Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- An atlas of transposable element-derived alternative splicing in cancer.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- SQuIRE reveals locus-specific regulation of interspersed repeat expression.Nucleic acids research · 2019Article
- Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions.Genome research · 2019Article
- Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines.Mobile DNA · 2019Article
- Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints.Molecular biology and evolution · 2017Article
- Transposable elements and G-quadruplexes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2015Review
- MIR retrotransposon sequences provide insulators to the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs.RNA (New York, N.Y.) · 2014Article
- Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.Mobile DNA · 2014Article
- Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.International journal of bioinformatics research and applications · 2014Article
- Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.Nucleic acids research · 2013Article
- Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription.Transcriptomics: open access · 2013Article
- Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?Molecular biology and evolution · 2013Review
- Transposable Elements: No More 'Junk DNA'.Genomics & informatics · 2012Article
- Article
- The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors.BMC genomics · 2012Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.