Rapid genome-scale mapping of chromatin accessibility in tissue

Lars Grøntved, Russell Bandle, Sam John, Songjoon Baek, Hye-Jung Chung, Ying Liu, Greti Aguilera, Carl Oberholtzer, Gordon L Hager, David Levens

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples.

RESULTS: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh.

CONCLUSION: The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.

Original languageEnglish
JournalEpigenetics & Chromatin
Volume5
Issue number10
Number of pages12
ISSN1756-8935
DOIs
Publication statusPublished - 2012
Externally publishedYes

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Chromosome Mapping
Serratia marcescens nuclease
Deoxyribonuclease I
CpG Islands
Endonucleases
Liver

Cite this

Grøntved, Lars ; Bandle, Russell ; John, Sam ; Baek, Songjoon ; Chung, Hye-Jung ; Liu, Ying ; Aguilera, Greti ; Oberholtzer, Carl ; Hager, Gordon L ; Levens, David. / Rapid genome-scale mapping of chromatin accessibility in tissue. In: Epigenetics & Chromatin. 2012 ; Vol. 5, No. 10.
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abstract = "BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples.RESULTS: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh.CONCLUSION: The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.",
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Grøntved, L, Bandle, R, John, S, Baek, S, Chung, H-J, Liu, Y, Aguilera, G, Oberholtzer, C, Hager, GL & Levens, D 2012, 'Rapid genome-scale mapping of chromatin accessibility in tissue', Epigenetics & Chromatin, vol. 5, no. 10. https://doi.org/10.1186/1756-8935-5-10

Rapid genome-scale mapping of chromatin accessibility in tissue. / Grøntved, Lars; Bandle, Russell; John, Sam; Baek, Songjoon; Chung, Hye-Jung; Liu, Ying; Aguilera, Greti; Oberholtzer, Carl; Hager, Gordon L; Levens, David.

In: Epigenetics & Chromatin, Vol. 5, No. 10, 2012.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Rapid genome-scale mapping of chromatin accessibility in tissue

AU - Grøntved, Lars

AU - Bandle, Russell

AU - John, Sam

AU - Baek, Songjoon

AU - Chung, Hye-Jung

AU - Liu, Ying

AU - Aguilera, Greti

AU - Oberholtzer, Carl

AU - Hager, Gordon L

AU - Levens, David

PY - 2012

Y1 - 2012

N2 - BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples.RESULTS: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh.CONCLUSION: The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.

AB - BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples.RESULTS: Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh.CONCLUSION: The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.

U2 - 10.1186/1756-8935-5-10

DO - 10.1186/1756-8935-5-10

M3 - Journal article

C2 - 22734930

VL - 5

JO - Epigenetics & Chromatin

JF - Epigenetics & Chromatin

SN - 1756-8935

IS - 10

ER -