Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.

@article{Conley2010IdentificationOT,
  title={Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.},
  author={Andrew B. Conley and I. King Jordan},
  journal={Methods in molecular biology},
  year={2010},
  volume={674},
  pages={
          225-40
        }
}
Transposable elements (TEs) form a substantial fraction of the non-coding DNA of many eukaryotic genomes. There are numerous examples of TEs being exapted for regulatory function by the host, many of which were identified through their high conservation. However, given that TEs are often the youngest part of a genome and typically exhibit a high turnover, conservation-based methods will fail to identify lineage- or species-specific exaptations. ChIP-seq has become a very popular and effective… 
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7 Citations
Background Citations
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Methods Citations
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7 Citations

An atlas of transposable element-derived alternative splicing in cancer

A number of cancer-associated genes, including MYH11, WHSC1 and CANT1, were shown to have overexpressed TE-derived isoforms across a range of cancer types, suggesting a novel mechanism for the generation of transcriptome diversity via trans-splicing mediated by dispersed TE repeats.

RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes.

Tissue-specific usage of transposable element-derived promoters in mouse development

The results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.

Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements

In-silico evidences of regulatory roles of WT1 transcription factor binding sites on the intervening sequences of the human Bcl-2 gene

This data provides supporting evidences for the existence of regulatory regions in the intronic sequences of the hBcl2 gene especially in the In-2, and also represents new targets for WT1-TF which might contribute to hB Cl2 regulation and apoptosis process.

Retraction Note to: ChIP-seq analysis of androgen receptor in LNCaP cell line

The analysis of AR target genes and gene functions help to elucidate the mechanism of the prostate cancer on a molecular level and pave the way to effective therapies for prostatic cancer.

RETRACTED ARTICLE: ChIP-seq analysis of androgen receptor in LNCaP cell line

The analysis of AR target genes and gene functions help to elucidate the mechanism of the prostate cancer on a molecular level and pave the way to effective therapies for prostatic cancer.

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