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Functional analysis of TMEM53, the disease gene for a novel type of sclerosing bone disorder

ABSTRACT: Purpose: The goal of this study is to explore the molecular mechanism of the phenotypes found in the TMEM53 mutant human and mouse. Methods: Calvarial mRNA profiles of 3-day-old Tmem53+/- and Tmem53-/- mice were generated by sequencing, in triplicate, using NovaSeq 6000 sequencer. The reads from the RNA-seq were aligned to the mouse genome (NCBI build37.2) using Tophat. Aligned reads were quantified using Cufflinks. Differential gene expression analysis was performed with Cuffdiff. Gene ontology (GO) term enrichment analysis was performed by DAVID 6.8. Results:The gene expression profiling displayed a total of 14,836 genes, including 1,278 differentially expressed genes (DEGs). These DEGs were enriched in some GO terms, and the most enriched term is “ossification”, which is considered to be closely associated with the thickened calvaria in the Tmem53-/- mice. The known marker genes of osteogenic precursors, osteoblasts and osteocytes (Runx2, Sp7, Alpl, Bglap and Ibsp) were up-regulated in Tmem53-/- mice according to the RNA-seq dataset. The DEGs were also enriched in the reported target gene set of Bmp-Smad pathway. The representative downstream transcriptional targets of Bmp signaling, Id1, Dlx3 and Dlx5, were up-regulated in the calvaria of the Tmem53-/- mice. Conclusions: Our results shows enhanced osteoblastogenesis in the calvaria of the Tmem53-/- mice, which would be attributed to the over-activated Bmp-Smad pathway caused by the Tmem53 deficiency.

ORGANISM(S): Mus musculus

PROVIDER: GSE161193 | GEO | 2021/01/25

REPOSITORIES: GEO

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Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

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Functional analysis of TMEM53, the disease gene for a novel type of sclerosing bone disorder

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