Dataset Information

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.

ABSTRACT:

Background

DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions.

Results

Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome.

Conclusion

Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separators" between protein-recognition sites in the promoter region.

SUBMITTER: Goni JR

PROVIDER: S-EPMC1435886 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature

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Publications

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.

Goñi Josep Ramon JR Vaquerizas Juan Manuel JM Dopazo Joaquin J Orozco Modesto M

BMC genomics 20060327

<h4>Background</h4>DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions.<h4>Results</h4>Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome.<h4>Conclusion</h4>Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separat ...[more]

PMID: 16566817

Similar Datasets

Project description:BackgroundDNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and micro-RNA (miRNA) precursors. Specific genome localizations of triplex target DNA sites (TTSs) may cause abnormalities in a double-helix DNA structure and can be directly involved in some human diseases. However, genome localization of specific TTSs, their interconnection with regulatory DNA elements and physiological roles in a cell are poor defined. Therefore, it is important to identify comprehensive and reliable catalogue of specific potential TTSs (pTTSs) and their co-localization patterns with other regulatory DNA elements in the human genome.Results"TTS mapping" database is a web-based search engine developed here, which is aimed to find and annotate pTTSs within a region of interest of the human genome. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G4 motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based onto a sequence location provided by UCSC genome browser, G4 database http://www.quadruplex.org and several other datasets. The results pages provide links to UCSC genome browser annotation tracks and relative DBs. BLASTN program was included to check the uniqueness of a given pTTS in the human genome. Recombination- and mutation-prone genes (e.g. EVI-1, MYC) were found to be significantly enriched by TTSs and multiple co-occurring with our regulatory DNA elements. TTS mapping reveals that a high-complementary and evolutionarily conserved polypurine and polypyrimidine DNA sequence pair linked by a non-conserved short DNA sequence can form miR-483 transcribed from intron 2 of IGF2 gene and bound double-strand nucleic acid TTSs forming natural triplex structures.ConclusionTTS mapping provides comprehensive visual and analytical tools to help users to find pTTSs, G-quadruplets and other regulatory DNA elements in various genome regions. TTS Mapping not only provides sequence visualization and statistical information, but also integrates knowledge about co-localization TTS with various DNA elements and facilitates that data analysis. In particular, TTS Mapping reveals complex structural-functional regulatory module of gene IGF2 including TF MZF1 binding site and ncRNA precursor mir-483 formed by the high-complementary and evolutionarily conserved polypurine- and polypyrimidine-rich DNA pair. Such ncRNAs capable of forming helical triplex structures with a polypurine strand of a nucleic acid duplexes (DNA or RNA) via Hoogsteen or reverse Hoogsteen hydrogen bonds. Our web tool could be used to discover biologically meaningful genome modules and to optimize experimental design of anti-gene treatment.

Dataset Information

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.

Background

Results

Conclusion

Publications

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.

Similar Datasets

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