The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling
The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments.Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth.We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions.Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter.This method is validated by intra and inter cell-line comparisons among various chromatin regions for four human cell-lines (K562, GM12878, IMR90 and H1hESC), which shows that the openness of chromatin region is well correlated with chromatin function.This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used.
Cheng Peng Liang-Yu Fu Peng-Fei Dong Zhi-Luo Deng Jian-Xin Li Xiao-TaoWang Hong-Yu Zhang
National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
国内会议
苏州
英文
485-495
2014-10-26（万方平台首次上网日期，不代表论文的发表时间）