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Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

BACKGROUND: DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identifi...

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Detalles Bibliográficos
Autores principales: Koohy, Hashem, Down, Thomas A., Hubbard, Tim J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724795/
https://www.ncbi.nlm.nih.gov/pubmed/23922824
http://dx.doi.org/10.1371/journal.pone.0069853
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author Koohy, Hashem
Down, Thomas A.
Hubbard, Tim J.
author_facet Koohy, Hashem
Down, Thomas A.
Hubbard, Tim J.
author_sort Koohy, Hashem
collection PubMed
description BACKGROUND: DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data. RESULTS: We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. The patterns are substantially different from biases seen in other types of HTS data sets, and in some cases the most constrained position lies outside the sequenced fragment, implying that this constraint must relate to the digestion process rather than events occurring during library preparation or sequencing. CONCLUSIONS: DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. This sequence specificity is not taken into account by existing pipelines for identifying open chromatin regions. Care must be taken when interpreting DNase I results, especially when looking at the precise locations of the reads. Future studies may be able to improve the sensitivity and precision of chromatin state measurement by compensating for sequence bias.
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spelling pubmed-37247952013-08-06 Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme Koohy, Hashem Down, Thomas A. Hubbard, Tim J. PLoS One Research Article BACKGROUND: DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data. RESULTS: We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. The patterns are substantially different from biases seen in other types of HTS data sets, and in some cases the most constrained position lies outside the sequenced fragment, implying that this constraint must relate to the digestion process rather than events occurring during library preparation or sequencing. CONCLUSIONS: DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. This sequence specificity is not taken into account by existing pipelines for identifying open chromatin regions. Care must be taken when interpreting DNase I results, especially when looking at the precise locations of the reads. Future studies may be able to improve the sensitivity and precision of chromatin state measurement by compensating for sequence bias. Public Library of Science 2013-07-26 /pmc/articles/PMC3724795/ /pubmed/23922824 http://dx.doi.org/10.1371/journal.pone.0069853 Text en © 2013 Koohy et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Koohy, Hashem
Down, Thomas A.
Hubbard, Tim J.
Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title_full Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title_fullStr Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title_full_unstemmed Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title_short Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
title_sort chromatin accessibility data sets show bias due to sequence specificity of the dnase i enzyme
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724795/
https://www.ncbi.nlm.nih.gov/pubmed/23922824
http://dx.doi.org/10.1371/journal.pone.0069853
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