Preliminary Study On The Role Of Radiation-induced 3D Genome Structure Reorganization In Transcription Regulation

BackgroundRadiotherapy is one of the most indispensable techniques in the fight against cancer.After cancer cells receiving radiotherapy,some cancer cells are eliminated immediately while other part survive from the radiation where the alteration of radiation-related genes expression profile play an essential role.Far from linear structures determined by the simple DNA sequence,the cell genome harbors a delicate 3D structure,which can provide an extra spatial regulation of gene expression.The extra regulation is reported to related to cancer initiation and progression,cell differentiation,macrophage polarization,and mitotic senescence closely.Radiation can induce cellular 3D genome reorganization.However,the exact functional relevance of spatial rearrangements to gene transcription remains unknown.In this study,we assessed the role of radiation-induced genome reorganization in gene expression.ObjectivesTo explore the regulatory effects of genome spatial reorganization in the level of Compartments A/B,TAD,and Chromatin loops on gene expression in cancer cells irradiated by X-ray at a regular fraction dose.Materials and methodsHuman cancer cells HCC LM3 were irradiated by X-ray at a dose of 4Gy and subjected to cell crosslink,nuclei isolating.DNA was digested using the restriction endonuclease,DpnⅡ,and sticky ends were repaired and cyclized.DNA purification and capture were then conducted.3D genome interaction maps were obtained after DNA sequenced and gene transcription maps were also determined in RNA-seq data.After the integration of 3D genome conformation map and mRNA transcriptome map,the regulatory effects of radiation-induced genome spatial conformation alteration on gene expression profiles were analyzed and evaluation through biological information.ResultsAfter radiation,the contact frequency and interaction within the chromosomes in the 3D genome of human tumor cells remained basically unchanged while the contact frequency among chromosomes increased significantly.Only about 2%of the compartments were experienced A/B switches;245(4.49%)TAD borders disappeared,122(2.25%)borders were reconstructed,and the average size of TAD increased to 0.67Mbp from 0.65Mbp;119(4.61%)and 113(6.27%)un-cycling and ring-formation were identified in the dynamically changing Loop.The spatial structural changes such as A/B conversion,disappearance and reconstruction of TAD boundaries,have a significantly higher regulatory degree of gene transcription than Loop’s dynamic unlooping and looping(8.59-10.63%vs 3.49-5.48%).The disappearance of TAD borders can upregulate related genes most significantly,which can be maintained up to 24 hours after irradiation.The relevant genes with a dynamic expression level involved in the radiation-mediated 3D genome structural changes are mostly enriched in radiation-related signal pathways.ConclusionsOur study identified that,1).the 3D genome changes of tumor cells after irradiation at three levels and demonstrates the regulation of spatial genome rearrangement on gene transcription,2).high-level spatial structure changes,such as compartment A/B transformation and TAD boundaries dynamics,have a more significant regulatory effect on gene expression than that of small-scale DNA loop structures.This study provides a theoretical basis for further research on the regulatory effects of radiation-mediated 3D genome rearrangement on gene transcription in the radiation process.