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bioRxiv · 10.1101/562280

Amplification-free Library Preparation Improves Quality of Hi-C Analysis

Niu, L.·Shen, W.·Huang, Y.·He, N.·Zhang, Y.·Sun, J.·Wan, J.·Jiang, D.·Yang, M.·Tse, Y. C.·Li, L.·Hou, C.
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Abstract

PCR amplification of Hi-C libraries introduces unusable duplicates and results in a biased representation of chromatin interactions. We present a simplified, fast, and economically efficient Hi-C library preparation procedure that generates sufficient non-amplified ligation products for deep sequencing from 30 million Drosophila cells. Comprehensive analysis of the resulting data indicates that amplification-free Hi-C preserves higher complexity of chromatin interaction and lowers sequencing depth dramatically for the same number of unique paired reads. For human cells which has a large genome, this method recovers an amount of ligated fragments enough for direct high-throughput sequencing without amplification on as low as 250 thousand of cells. Comparison with published in situ Hi-C on millions of human cells reveals that amplification introduces distance-dependent amplification bias, which results in increasing background noise level against genomic distance. With amplification bias avoided, our method may produce a chromatin interaction network more faithfully reflecting the real three-dimensional genomic architecture.

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Niu, L., Shen, W., Huang, Y., He, N., Zhang, Y., Sun, J., Wan, J., Jiang, D., Yang, M., Tse, Y. C., Li, L., Hou, C.. 2019-02-27. Amplification-free Library Preparation Improves Quality of Hi-C Analysis. https://doi.org/10.1101/562280

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