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Genome-wide Analysis of Sp6/Epiprofin DNA Binding Sites in the Developing Mouse Molar Using ChIP-seq Analysis

ABSTRACT: In this study, whole-genome ChIP-seq analysis was performed to identify Sp6 regulatory targets from postnatal mouse molars. Enriched sequence reads (peaks) from Sp6 immunoprecipitations were located predominately adjacent to transcriptional start sites. Notably enriched for Sp6 peaks were genes highly-expressed in the tooth. Bioinformatic analysis of two pools of 1400 Sp6 enriched sequences identified a consensus nine-nucleotide DNA pulldown sequence of CTg/aTAATTA from mesenchyme and the nearly identical sequence, CTa/gTAATTA, from epithelium. Sp6 AT-rich interaction sequences are nearly identical to the ChIP-seq enriched sequences reported for Sp7 and Sp9. ChIP-seq analysis indicates Sp6 regulates a significant number of genes expressed in the tooth. GSE145909 is the original submission. GSE151391 is also from the same study. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151391

ORGANISM(S): Mus musculus

PROVIDER: GSE145909 | GEO | 2021/11/23

REPOSITORIES: GEO

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Project description:The organ development is dictated by the genes preferentially expressed in tissue or cell types uniquely. The clarification of gene expression profile and identification of specific genes in organ provide detailed understanding of organogenesis. Toward this purpose, the genome-wide analysis is a growing powerful tool for understanding development processes in organogenesis. Tooth is composed from enamel, dentin and cementum and these tissues are identical from other organs. The tooth-forming cell types are therefore unique and have complexed organization. The mechanisms of signal induction during tooth development is complicated because of the function of each cell types are still unclear. Previously, we performed the CAGE (Cap Analysis of Gene Expression) using mouse tooth germ to identify the genes preferentially expressed in tooth. The CAGE has advantage in quantification because it counts short reads of 5’ end without the bias of transcript length. Single-cell RNA-sequence (scRNA-seq) is a suitable tool revealing gene expression of each cells. The fundamental question of this study is how we can identify the tooth-specific and cell-type specific genes. In this study, we approach this using combination of scRNA-seq and CAGE (Cap Analysis of Gene Expression) as bioinformatics analyses. We obtained the scRNA-seq datasets of 12,212 cells from postnatal-day (P) 1 mouse molars, and the CAGE-seq datasets from P1 molars. scRNA-seq analysis revealed the spatio-temporal expression of tooth-related genes and CAGE determined whether these genes are truly tooth-specific or are expressed in ubiquitously. Furthermore, we identified candidate genes as novel tissue- and cell type- specific markers. Our results show that the integration of scRNA-seq and CAGE-seq improves the highlight genes important for tooth development from numerous gene profiles. These findings contribute resolving the mechanism of tooth development and establish the basis of tooth regeneration in future.

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Genome-wide Analysis of Sp6/Epiprofin DNA Binding Sites in the Developing Mouse Molar Using ChIP-seq Analysis

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