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Measuring quantitative effects of methylation on transcription factor–DNA binding affinity
Methylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even when known, such knowledge is often only qualitative. In reality, methylation...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Association for the Advancement of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694663/ https://www.ncbi.nlm.nih.gov/pubmed/29159284 http://dx.doi.org/10.1126/sciadv.aao1799 |
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author | Zuo, Zheng Roy, Basab Chang, Yiming Kenny Granas, David Stormo, Gary D. |
author_facet | Zuo, Zheng Roy, Basab Chang, Yiming Kenny Granas, David Stormo, Gary D. |
author_sort | Zuo, Zheng |
collection | PubMed |
description | Methylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even when known, such knowledge is often only qualitative. In reality, methylation sensitivity is a quantitative effect, just as changes to the DNA sequence have quantitative effects on TF binding affinity. We describe Methyl-Spec-seq, an easy-to-use method that measures the effects of CpG methylation (mCPG) on binding affinity for hundreds to thousands of variants in parallel, allowing one to quantitatively assess the effects at every position in a binding site. We demonstrate its use on several important DNA binding proteins. We calibrate the accuracy of Methyl-Spec-seq using a novel two-color competitive fluorescence anisotropy method that can accurately determine the relative affinities of two sequences in solution. We also present software that extends standard methods for representing, visualizing, and searching for matches to binding site motifs to include the effects of methylation. These tools facilitate the study of the consequences for gene regulation of epigenetic marks on DNA. |
format | Online Article Text |
id | pubmed-5694663 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-56946632017-11-20 Measuring quantitative effects of methylation on transcription factor–DNA binding affinity Zuo, Zheng Roy, Basab Chang, Yiming Kenny Granas, David Stormo, Gary D. Sci Adv Research Articles Methylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even when known, such knowledge is often only qualitative. In reality, methylation sensitivity is a quantitative effect, just as changes to the DNA sequence have quantitative effects on TF binding affinity. We describe Methyl-Spec-seq, an easy-to-use method that measures the effects of CpG methylation (mCPG) on binding affinity for hundreds to thousands of variants in parallel, allowing one to quantitatively assess the effects at every position in a binding site. We demonstrate its use on several important DNA binding proteins. We calibrate the accuracy of Methyl-Spec-seq using a novel two-color competitive fluorescence anisotropy method that can accurately determine the relative affinities of two sequences in solution. We also present software that extends standard methods for representing, visualizing, and searching for matches to binding site motifs to include the effects of methylation. These tools facilitate the study of the consequences for gene regulation of epigenetic marks on DNA. American Association for the Advancement of Science 2017-11-17 /pmc/articles/PMC5694663/ /pubmed/29159284 http://dx.doi.org/10.1126/sciadv.aao1799 Text en Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (http://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited. |
spellingShingle | Research Articles Zuo, Zheng Roy, Basab Chang, Yiming Kenny Granas, David Stormo, Gary D. Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title | Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title_full | Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title_fullStr | Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title_full_unstemmed | Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title_short | Measuring quantitative effects of methylation on transcription factor–DNA binding affinity |
title_sort | measuring quantitative effects of methylation on transcription factor–dna binding affinity |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694663/ https://www.ncbi.nlm.nih.gov/pubmed/29159284 http://dx.doi.org/10.1126/sciadv.aao1799 |
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