title: The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
abstract: 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.
authors: National Key Laboratory of Crop Genetic Improvement, Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
authors: Cheng
authors: C
authors: Peng
authors: Liang-Yu
authors: LY
authors: Fu
authors: Peng-Fei
authors: PF
authors: Dong
authors: Zhi-Luo
authors: ZL
authors: Deng
authors: Jian-Xin
authors: JX
authors: Li
authors: Xiao-Tao
authors: XT
authors: Wang
authors: Hong-Yu
authors: HY
authors: Zhang
mesh_terms: D002460:Cell Line; D002843:Chromatin / Q000737:chemistry*; D003627:Data Interpretation, Statistical; D006801:Humans; D020014:K562 Cells; D008958:Models, Molecular; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D002843:Chromatin
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