The chromatin accessibility landscape in the dental pulp of mouse molars and incisors

Pujan Joshi; Anushree Vijaykumar; Badam Enkhmandakh; Dong-Guk Shin; Mina Mina; Dashzeveg Bayarsaihan

doi:10.18388/abp.2020_5771

Pujan Joshi Computer Science and Engineering Department, University of Connecticut, Storrs, CT 06269, USA
Anushree Vijaykumar Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
Badam Enkhmandakh Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
Dong-Guk Shin Computer Science and Engineering Department, University of Connecticut, Storrs, CT 06269, USA
Mina Mina Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
Dashzeveg Bayarsaihan 3Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; 4Institute for System Genomics, University of Connecticut, Storrs, CT 06269, USA

DOI: https://doi.org/10.18388/abp.2020_5771

Abstract

The dental pulp is a promising source of progenitor cells for regenerative medicine. The natural function of dental pulp is to produce odontoblasts to generate reparative dentin. Stem cells within the pulp tissue originate from the migrating neural crest cells and possess mesenchymal stem cell properties with the ability to differentiate into multiple lineages. To elucidate the transcriptional control mechanisms underlying cell fate determination, we compared the transcriptome and chromatin accessibility in primary dental pulp tissue derived from 5-6-day-old mice. Using RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq), we correlated gene expression with chromatin accessibility. We found that the majority of ATAC-seq peaks were concentrated at genes associated with development and cell differentiation. Most of these genes were highly expressed in the mouse dental pulp. Surprisingly, we uncovered a group of genes encoding master transcription factors that were not expressed in the dental pulp but retained open chromatin states. Within this group, we identified key developmental genes important for specification of the neural crest, adipocyte, neural, myoblast, osteoblast and hepatocyte lineages. Collectively, our results uncover a complex relationship between gene expression and the chromatin accessibility landscape in the mouse dental pulp.