德国马克斯普朗克研究所Juan M. Vaquerizas小组开发出染色质接触数据定量比较和自动特征提取的新方法。这一研究成果于2020年10月19日在线发表在国际顶尖学术期刊《自然—遗传学》上。

Title: CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

Author: Silvia Galan, Nick Machnik, Kai Kruse, Noelia Daz, Marc A. Marti-Renom, Juan M. Vaquerizas

Issue&Volume: 2020-10-19

Abstract: Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data. CHESS is an algorithm that compares chromatin contact maps and identifies differential features. It can analyze interspecies syntenic regions and three-dimensional changes caused by genetic perturbation.

DOI: 10.1038/s41588-020-00712-y

Source: https://www.nature.com/articles/s41588-020-00712-y