StripeDiff: Model-based algorithm for differential analysis of chromatin stripe

Krishan Gupta; Guangyu Wang; Shuo Zhang; Xinlei Gao; Rongbin Zheng; Yanchun Zhang; Qingshu Meng; Lili Zhang; Qi Cao; Kaifu Chen

doi:10.1126/sciadv.abk2246

StripeDiff: Model-based algorithm for differential analysis of chromatin stripe

Krishan Gupta, Guangyu Wang, Shuo Zhang, Xinlei Gao, Rongbin Zheng, Yanchun Zhang, Qingshu Meng, Lili Zhang, Qi Cao, Kaifu Chen^*

^*Corresponding author for this work

Urology

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Multiple recent studies revealed stripes as an architectural feature of three-dimensional chromatin and found stripes connected to epigenetic regulation of transcription. Whereas a couple of tools are available to define stripes in a single sample, there is yet no reported method to quantitatively measure the dynamic change of each stripe between samples. Here,we developed StripeDiff, a bioinformatics tool that delivers a set of statistical methods to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to 12 sets of Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation. StripeDiff will be a robust tool for the community to facilitate understanding of stripes and their function in numerous biological models.

Original language	English (US)
Article number	abk2246
Journal	Science Advances
Volume	8
Issue number	49
DOIs	https://doi.org/10.1126/sciadv.abk2246
State	Published - 2022

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title = "StripeDiff: Model-based algorithm for differential analysis of chromatin stripe",

abstract = "Multiple recent studies revealed stripes as an architectural feature of three-dimensional chromatin and found stripes connected to epigenetic regulation of transcription. Whereas a couple of tools are available to define stripes in a single sample, there is yet no reported method to quantitatively measure the dynamic change of each stripe between samples. Here,we developed StripeDiff, a bioinformatics tool that delivers a set of statistical methods to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to 12 sets of Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation. StripeDiff will be a robust tool for the community to facilitate understanding of stripes and their function in numerous biological models.",

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AU - Gupta, Krishan

AU - Wang, Guangyu

AU - Zhang, Shuo

AU - Gao, Xinlei

AU - Zheng, Rongbin

AU - Zhang, Yanchun

AU - Meng, Qingshu

AU - Zhang, Lili

AU - Cao, Qi

AU - Chen, Kaifu

PY - 2022

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AB - Multiple recent studies revealed stripes as an architectural feature of three-dimensional chromatin and found stripes connected to epigenetic regulation of transcription. Whereas a couple of tools are available to define stripes in a single sample, there is yet no reported method to quantitatively measure the dynamic change of each stripe between samples. Here,we developed StripeDiff, a bioinformatics tool that delivers a set of statistical methods to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to 12 sets of Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation. StripeDiff will be a robust tool for the community to facilitate understanding of stripes and their function in numerous biological models.

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StripeDiff: Model-based algorithm for differential analysis of chromatin stripe

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