Genome-wide Analysis Of Cis-trans Interplay In Gene Transcriptional Regulation At Chromatin Accessibility And Chromatin 3D Architecture Levels Using Hybrid Mice

Interplay between cis-elements and trans-factors is an important mechanism of gene transcription regulation in mice,especially during cell differentiation.The establishment of cis-trans interplays largely depends on chromatin structure,including chromatin accessibility and three-dimensional(3D)chromatin architecture.Comparing chromatin structure between different cell types is a common method of studying cis-trans interplays.However,this method cannot distinguish cis-regulatory effects from trans-regulatory effects.To tackle this problem,F1 hybrid mouse systems are developed.In this dissertation,a genome-wide profiling of allele-specific gene expression levels,open chromatin regions,and chromatin interaction maps was performed in a C57BL×SPRET F1 hybrid mouse system.For this purpose,various methods based on high-throughput sequencing were employed such as RNA-seq,ATAC-seq,and BL-Hi-C.Computational approaches were also applied for differential analysis,peak calling,motif enrichment,etc.As a result,chromatin accessibility showed allelic divergence at promoter and enhancer regions.Both allele-specific promoters and enhancers were correlated with allele-specific gene expression,suggesting their regulatory effects.Furthermore,motif enrichment analysis on allele-specific fibroblast enhancers revealed that AP-1,a family of transcription factors,plays an important role in mediating enhancer selection during cell differentiation.At chromatin architecture level,chromatin loops were detected between AP-1 selected enhancers and differential expressed gene promoters.The intensity of loops was used to validate the physical interactions between enhancers and promoters.On larger scales,topologically associated domains called from BL-Hi-C sequencing data were used to reveal divergent chromatin organization patterns.Analysis showed higher correlation between chromatin accessibility and gene expression in topologically associated domains,suggesting their capability of creating independent regulatory environments.Taken together,chromatin accessibility and 3D chromatin architecture regulate gene expression by facilitating transcription factor binding and cis-trans interplay,respectively.This result has deepened our understanding on the function of chromatin structures and revealed new insights into gene regulation.