Accession PRJCA002611
Title Epithelial Cells in 2D and 3D Culture Exhibit Large Differences in Higher-Order Genomic Interactions
Relevance Model organism
Data types Raw sequence reads
Organisms Mus musculus
Description Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higherorder genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changed expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
Sample scope Monoisolate
Release date 2020-04-29
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) 11374207
National Key 417 R&D Program of China 2018YFC1003500
China Postdoctoral Science Foundation 2018M640419
National Natural Science Foundation of China (NSFC) 31670722
National Natural Science Foundation of China (NSFC) 31971151
National Natural Science Foundation of China (NSFC) 81627801
National Natural Science Foundation of China (NSFC) 31900430
Submitter HUA    LI  (kaikaixinxin@sjtu.edu.cn)
Organization Shanghai Jiao Tong University
Submission date 2020-04-29

Project Data

Resource name Description
BioSample (8)  show -
GSA (1) -
CRA002599 Epithelial Cells in 2D and 3D Culture Exhibit Large Differences in Higher-Order Genomic Interactions