Gene transcription is a fundamental process in biology, which is not only regulated by the linear DNA sequences, but also by the enhancers or repressors (or other regulatory elements) far in linear DNA sequences while spatially near in the 3D space. Chromatin Interaction Analysis by Paired-End-Tag sequencing (ChIA-PET) [1] is a method dedicated to the long-range chromatin interaction discovery with specific protein factors, which has been applied to discover chromatin interactions associated with ERalpha, CTCF, RNAPII and H3K4me2 [1-4].

ChIA-PET Tool [5] was developed as a package to processChIA-PET data, manage the interaction clusters, and visualize the interactions. In the original ChIA-PET package, paired-end reads were assumed at that time, since the next-generation sequencing machines just generated the reads of 36-50bp long in high quality at that time. Now with the advance of the sequencing technology, a single read can cover the whole DNA fragment constructs in ChIA-PET, which is about 78bp long. One way to apply the ChIA-PET Tool to the single reads is to divide the reads into paired-end reads after sequencing. A question in this way is how to divide the single reads into paired-end reads. A simple extraction of the first 36bp and last 36bp will ignore the boundary information s and introduce bias in the data – the full sequences in the single reads are not utilized.

A better way is to perform the linker filtering with the single reads directly. To facilitate the ChIA-PET data process, I provide a Java script for linker filtering in single reads. Please download the attachment and read the “readme” file for the command arguments.

References:

1.     Fullwood, M. J. et al. An oestrogen-receptor-alpha-boundhuman chromatin interactome. Nature 462, 58-64 (2009)

2.    Handoko,L., Xu, H., Guoliang Li, Ngan, C.Y., Chew, E., Schnapp, M., Lee, C.W., Ye, C.,Ping, J.L., Mulawadi, F., Wong, E., Sheng, J., Zhang, Y., Poh, T., Chan, C.S.,Kunarso, G., Shahab, A., Bourque, G., Cacheux-Rataboul, V., Sung, W.K., Ruan,Y. and Wei, C.L. CTCF-mediatedfunctional chromatin interactome in pluripotent cells. Nature Genetics, 43 (7). 630-638.

3.    GuoliangLi, Xiaoan Ruan, Raymond K. Auerbach, Michael Snyder, Yijun Ruan, et al. ExtensivePromoter-Centered Chromatin Interactions Provide a Topological Basis forTranscription Regulation. Cell 148, Issue 1, pp. 84-98

4.    Chepelev, et al, Characterization of genome-wide enhancer-promoter interactionsreveals co-expression of interacting genes and modes of higher order chromatinorganization, Cell Research (2012) 22:490–503

5.    Li Guoliang,Fullwood MJ, Xu H et al. ChIA-PETtool for comprehensive chromatin interaction analysis with paired-end tagsequencing. Genome Biology 2010, 11(2):R22

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