Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Bioinformatics. 2023 Nov 1;39(11). doi: 10.1093/bioinformatics/btad638.
Reconstruction of 3D structure models is of great importance for the study of chromosome function. Software tools for this task are highly needed.
We present a novel reconstruction algorithm, called EVRC, which utilizes co-clustering coefficients and error-vector resultant for chromosome 3D structure reconstruction. As an update of our previous EVR algorithm, EVRC now can deal with both single and multiple chromosomes in structure modeling. To evaluate the effectiveness and accuracy of the EVRC algorithm, we applied it to simulation datasets and real Hi-C datasets. The results show that the reconstructed structures have high similarity to the original/real structures, indicating the effectiveness and robustness of the EVRC algorithm. Furthermore, we applied the algorithm to the 3D conformation reconstruction of the wild-type and mutant Arabidopsis thaliana chromosomes and demonstrated the differences in structural characteristics between different chromosomes. We also accurately showed the conformational change in the centromere region of the mutant compared with the wild-type of Arabidopsis chromosome 1. Our EVRC algorithm is a valuable software tool for the field of chromatin structure reconstruction, and holds great promise for advancing our understanding on the chromosome functions.
The software is available at https://github.com/mbglab/EVRC.
三维结构模型的重建对于研究染色体功能非常重要。非常需要用于此任务的软件工具。
我们提出了一种称为 EVRC 的新型重建算法，该算法利用共聚类系数和误差向量结果来进行染色体三维结构重建。作为我们之前的 EVR 算法的更新，EVRC 现在可以处理结构建模中的单个和多个染色体。为了评估 EVRC 算法的有效性和准确性，我们将其应用于模拟数据集和真实的 Hi-C 数据集。结果表明，重建的结构与原始/真实结构具有高度相似性，表明 EVRC 算法的有效性和鲁棒性。此外，我们将该算法应用于野生型和突变拟南芥染色体的三维构象重建，并证明了不同染色体之间结构特征的差异。我们还准确地显示了与野生型拟南芥染色体 1 相比，突变体中心粒区域的构象变化。我们的 EVRC 算法是一个用于染色质结构重建的有价值的软件工具，有望增进我们对染色体功能的理解。
该软件可在 https://github.com/mbglab/EVRC 上获得。
