Abstract
BackgroundLong-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.ResultsThis article introduces the experimental protocol and data analysis process of ChIA-PET, as well as discusses some applications using this technology. It also unveils the direction of future studies based on this technology.ConclusionsOverall we show that ChIA-PET is the cornerstone to explore the three-dimensional (3D) chromatin structure, and certainly will lead the forthcoming wave of 3D genomics studies.
Highlights
Long-range chromatin interactions play an important role in transcription regulation
Many technologies have been developed to study the binding of transcription factors (TF) for transcription regulation, such as chromatin immunoprecipitation (ChIP) microarray (ChIP-chip) [1], ChIP-paired-end tags (PETs) [2] and ChIP-Seq [3], but they are unable to determine the target genes of the distal TF binding sites
* Correspondence: guoliang.li@mail.hzau.edu.cn 1National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, 1, Shizishan Street, Wuhan, 430070, China Full list of author information is available at the end of the article conformation capture (3C) [4] and its derivatives, 4C [5,6] and 5C [7] can reveal long-range chromatin interactions involved in transcription regulation, but these techniques are limited either because they are low-throughout, such as 3C, or they can’t map interacting regions with high resolution in the whole genome [8] (Figure 1)
Summary
Long-range chromatin interactions play an important role in transcription regulation. Identification of genome-wide distal chromatin interactions that lead the regulatory elements to their target genes may provide novel insights into the study of transcription regulation. * Correspondence: guoliang.li@mail.hzau.edu.cn 1National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, 1, Shizishan Street, Wuhan, 430070, China Full list of author information is available at the end of the article conformation capture (3C) [4] and its derivatives, 4C [5,6] and 5C [7] can reveal long-range chromatin interactions involved in transcription regulation, but these techniques are limited either because they are low-throughout, such as 3C, or they can’t map interacting regions with high resolution in the whole genome [8] (Figure 1).
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