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… 
View on PubMed
jordan.biology.gatech.edu
7 Citations
Background Citations
3
Methods Citations
2

7 Citations

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.

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.

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 prostate cancer and prostatic cancer.

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

References

SHOWING 1-10 OF 48 REFERENCES

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

It is established that these repeat-associated binding sites (RABS) have been associated with significant regulatory expansions throughout the mammalian phylogeny and that transposable elements play an important role in expanding the repertoire of binding sites.

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication

It is proposed that transposon-mediated duplication and insertion of RE1s has led to the acquisition of novel target genes by REST during evolution.

Transposable element derived DNaseI-hypersensitive sites in the human genome

The results reported here support the notion that TEs provide a specific genome-wide mechanism for generating functionally relevant gene regulatory divergence between evolutionary lineages.

A c-Myc regulatory subnetwork from human transposable element sequences.

Data point to a substantial contribution of TEs to the regulation of human genes by c-Myc, and genes that are regulated by TE-derived c-myc binding sites appear to form a distinct c- myc regulatory subnetwork.

Transposable elements as a significant source of transcription regulating signals.

Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data

Using tag density as an indicator of DNA-binding affinity, it is shown that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites.

Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

It is found that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile element may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.