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APTE: identification of indirect read-out A-DNA promoter elements in genomes

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APTE: identification of indirect read-out A-DNA promoter elements in genomes. / Whitley, David C; Runfola, Valeria; Cary, Peter; Nazlamova, Liliya; Guille, Matt; Scarlett, Garry.

In: BMC Bioinformatics, Vol. 15, No. 288, 26.08.2014.

Research output: Contribution to journalArticlepeer-review

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Whitley, DC, Runfola, V, Cary, P, Nazlamova, L, Guille, M & Scarlett, G 2014, 'APTE: identification of indirect read-out A-DNA promoter elements in genomes', BMC Bioinformatics, vol. 15, no. 288. https://doi.org/10.1186/1471-2105-15-288

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Author

Whitley, David C ; Runfola, Valeria ; Cary, Peter ; Nazlamova, Liliya ; Guille, Matt ; Scarlett, Garry. / APTE: identification of indirect read-out A-DNA promoter elements in genomes. In: BMC Bioinformatics. 2014 ; Vol. 15, No. 288.

Bibtex

@article{6be9ff7df95744f2a4784e7541c038b2,
title = "APTE: identification of indirect read-out A-DNA promoter elements in genomes",
abstract = "BackgroundTranscriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure can also act as a recognition site for the transcription factor in a process known as indirect read-out, although this is much less understood. We have previously identified such a transcriptional control mechanism in early Xenopus development where the interaction of the transcription factor ilf3 and the gata2 promoter requires the presence of both an unusual A-form DNA structure and a CCAAT sequence. Rapid identification of such promoters elsewhere in the Xenopus and other genomes would provide insight into a less studied area of gene regulation, although currently there are few tools to analyse genomes in such ways.ResultsIn this paper we report the implementation of a novel bioinformatics approach that has identified 86 such putative promoters in the Xenopus genome. We have shown that five of these sites are A-form in solution, bind to transcription factors and fully validated one of these newly identified promoters as interacting with the ilf3 containing complex CBTF. This interaction regulates the transcription of a previously uncharacterised downstream gene that is active in early development.ConclusionsA Perl program (APTE) has located a number of potential A-form DNA promotor elements in the Xenopus genome, five of these putative targets have been experimentally validated as A-form and as targets for specific DNA binding proteins; one has also been shown to interact with the A-form binding transcription factor ilf3. ",
keywords = "APC-PAID",
author = "Whitley, {David C} and Valeria Runfola and Peter Cary and Liliya Nazlamova and Matt Guille and Garry Scarlett",
year = "2014",
month = aug,
day = "26",
doi = "10.1186/1471-2105-15-288",
language = "English",
volume = "15",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
number = "288",

}

RIS

TY - JOUR

T1 - APTE: identification of indirect read-out A-DNA promoter elements in genomes

AU - Whitley, David C

AU - Runfola, Valeria

AU - Cary, Peter

AU - Nazlamova, Liliya

AU - Guille, Matt

AU - Scarlett, Garry

PY - 2014/8/26

Y1 - 2014/8/26

N2 - BackgroundTranscriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure can also act as a recognition site for the transcription factor in a process known as indirect read-out, although this is much less understood. We have previously identified such a transcriptional control mechanism in early Xenopus development where the interaction of the transcription factor ilf3 and the gata2 promoter requires the presence of both an unusual A-form DNA structure and a CCAAT sequence. Rapid identification of such promoters elsewhere in the Xenopus and other genomes would provide insight into a less studied area of gene regulation, although currently there are few tools to analyse genomes in such ways.ResultsIn this paper we report the implementation of a novel bioinformatics approach that has identified 86 such putative promoters in the Xenopus genome. We have shown that five of these sites are A-form in solution, bind to transcription factors and fully validated one of these newly identified promoters as interacting with the ilf3 containing complex CBTF. This interaction regulates the transcription of a previously uncharacterised downstream gene that is active in early development.ConclusionsA Perl program (APTE) has located a number of potential A-form DNA promotor elements in the Xenopus genome, five of these putative targets have been experimentally validated as A-form and as targets for specific DNA binding proteins; one has also been shown to interact with the A-form binding transcription factor ilf3.

AB - BackgroundTranscriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure can also act as a recognition site for the transcription factor in a process known as indirect read-out, although this is much less understood. We have previously identified such a transcriptional control mechanism in early Xenopus development where the interaction of the transcription factor ilf3 and the gata2 promoter requires the presence of both an unusual A-form DNA structure and a CCAAT sequence. Rapid identification of such promoters elsewhere in the Xenopus and other genomes would provide insight into a less studied area of gene regulation, although currently there are few tools to analyse genomes in such ways.ResultsIn this paper we report the implementation of a novel bioinformatics approach that has identified 86 such putative promoters in the Xenopus genome. We have shown that five of these sites are A-form in solution, bind to transcription factors and fully validated one of these newly identified promoters as interacting with the ilf3 containing complex CBTF. This interaction regulates the transcription of a previously uncharacterised downstream gene that is active in early development.ConclusionsA Perl program (APTE) has located a number of potential A-form DNA promotor elements in the Xenopus genome, five of these putative targets have been experimentally validated as A-form and as targets for specific DNA binding proteins; one has also been shown to interact with the A-form binding transcription factor ilf3.

KW - APC-PAID

U2 - 10.1186/1471-2105-15-288

DO - 10.1186/1471-2105-15-288

M3 - Article

VL - 15

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - 288

ER -

ID: 1637940