Lainscsek, X. | Search bioRxiv

bioRxiv2024

ENT3C: an entropy-based similarity measure for contact matrices

Hi-C and micro-C sequencing have shed light on the profound importance of 3D genome organization in cellular function by probing 3D contact frequencies across the linear genome. The resulting contact matrices are extremely sparse and susceptible to technical- and sequence-based biases, making their comparison challenging. The development of reliable, robust and efficient methods for quantifying similarity between contact matrix is crucial for investigating variations in the 3D genome organization between different cell types or under different conditions, as well as evaluating experimental reproducibility. We present a novel method, ENT3C, which measures the change in pattern complexity in the vicinity of contact matrix diagonals to quantify their similarity. ENT3C provides a robust, user-friendly Hi-C or micro-C contact matrix similarity metric and a characteristic entropy signal that can be used to gain detailed biological insights into 3D genome organization. Availabilityhttps://github.com/xX3N1A/ENT3C

bioinformatics↗

bioRxiv2022

Predicting 3D genome architecture directly from the nucleotide sequence with DNA-DDA

3D genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly, and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-DDA, a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby. Availabilityhttps://github.com/xX3N1A/DNA-DDA Contactleila.taher@tugraz.at Supplementary informationSupplementary data are available at ... online.

bioinformatics↗