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Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing

Transcription factor–DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown. In this report, we introduce Bind-n-Seq, a new high-throughput method for analyzing protein–DNA intera...

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Detalles Bibliográficos
Autores principales: Zykovich, Artem, Korf, Ian, Segal, David J.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794170/
https://www.ncbi.nlm.nih.gov/pubmed/19843614
http://dx.doi.org/10.1093/nar/gkp802
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author Zykovich, Artem
Korf, Ian
Segal, David J.
author_facet Zykovich, Artem
Korf, Ian
Segal, David J.
author_sort Zykovich, Artem
collection PubMed
description Transcription factor–DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown. In this report, we introduce Bind-n-Seq, a new high-throughput method for analyzing protein–DNA interactions in vitro, with several advantages over current methods. The procedure has three steps (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotide with massively parallel technology and (iii) finding motifs among the sequences. De novo binding motifs determined by this method for the DNA-binding domains of two well-characterized zinc-finger proteins were similar to those described previously. Furthermore, calculations of the relative affinity of the proteins for specific DNA sequences correlated significantly with previous studies (R(2 )= 0.9). These results present Bind-n-Seq as a highly rapid and parallel method for determining in vitro binding sites and relative affinities.
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spelling pubmed-27941702009-12-16 Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing Zykovich, Artem Korf, Ian Segal, David J. Nucleic Acids Res Methods Online Transcription factor–DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown. In this report, we introduce Bind-n-Seq, a new high-throughput method for analyzing protein–DNA interactions in vitro, with several advantages over current methods. The procedure has three steps (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotide with massively parallel technology and (iii) finding motifs among the sequences. De novo binding motifs determined by this method for the DNA-binding domains of two well-characterized zinc-finger proteins were similar to those described previously. Furthermore, calculations of the relative affinity of the proteins for specific DNA sequences correlated significantly with previous studies (R(2 )= 0.9). These results present Bind-n-Seq as a highly rapid and parallel method for determining in vitro binding sites and relative affinities. Oxford University Press 2009-12 2009-10-20 /pmc/articles/PMC2794170/ /pubmed/19843614 http://dx.doi.org/10.1093/nar/gkp802 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Zykovich, Artem
Korf, Ian
Segal, David J.
Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title_full Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title_fullStr Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title_full_unstemmed Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title_short Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
title_sort bind-n-seq: high-throughput analysis of in vitro protein–dna interactions using massively parallel sequencing
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794170/
https://www.ncbi.nlm.nih.gov/pubmed/19843614
http://dx.doi.org/10.1093/nar/gkp802
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