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3C-digital PCR for quantification of chromatin interactions

Overview of attention for article published in BMC Molecular and Cell Biology, December 2016
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Title
3C-digital PCR for quantification of chromatin interactions
Published in
BMC Molecular and Cell Biology, December 2016
DOI 10.1186/s12867-016-0076-6
Pubmed ID
Authors

Meijun Du, Liang Wang

Abstract

Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency. Recently, digital PCR (dPCR) technology has become available, which allows for highly sensitive nucleic acid quantification. Main advantage of dPCR is its high precision of absolute nucleic acid quantification without requirement of normalization controls. To demonstrate the utility of dPCR in quantifying chromatin interactions, we examined two prostate cancer risk loci at 8q24 and 2p11.2 for their interaction target genes MYC and CAPG in LNCaP cell line. We designed anchor and testing primers at known regulatory element fragments and target gene regions, respectively. dPCR results showed that interaction frequency between the regulatory element and MYC gene promoter was 0.7 (95% CI 0.40-1.10) copies per 1000 genome copies while other regions showed relatively low ligation frequencies. The dPCR results also showed that the ligation frequencies between the regulatory element and two EcoRI fragments containing CAPG gene promoter were 1.9 copies (95% CI 1.41-2.47) and 1.3 copies per 1000 genome copies (95% CI 0.76-1.92), respectively, while the interaction signals were reduced on either side of the promoter region of CAPG gene. Additionally, we observed comparable results from 3C-dPCR and 3C-qPCR at 2p11.2 in another cell line (DU145). Compared to traditional 3C-qPCR, our results show that 3C-dPCR is much simpler and more sensitive to detect weak chromatin interactions. It may eliminate multiple and complex normalization controls and provide accurate calculation of proximity-based fragment ligation frequency. Therefore, we recommend 3C-dPCR as a preferred method for sensitive detection of low frequency chromatin interactions.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 37 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 19%
Student > Ph. D. Student 4 11%
Student > Bachelor 4 11%
Student > Master 4 11%
Student > Postgraduate 2 5%
Other 7 19%
Unknown 9 24%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 8 22%
Agricultural and Biological Sciences 5 14%
Medicine and Dentistry 5 14%
Engineering 3 8%
Computer Science 2 5%
Other 5 14%
Unknown 9 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 May 2017.
All research outputs
#19,942,887
of 25,371,288 outputs
Outputs from BMC Molecular and Cell Biology
#896
of 1,233 outputs
Outputs of similar age
#301,661
of 420,258 outputs
Outputs of similar age from BMC Molecular and Cell Biology
#6
of 8 outputs
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